Article(id=1226554097206210577, tenantId=1146029695717560320, journalId=1192105938417971205, issueId=1226554095926952065, articleNumber=null, orderNo=null, doi=10.13343/j.cnki.wsxb.20250019, pmid=null, cstr=null, oa=null, hot=null, price=null, onlineType=0, articleFormat=0, articleType=null, articleTypeStr=research-article, receivedDate=1736265600000, receivedDateStr=2025-01-08, revisedDate=null, revisedDateStr=null, acceptedDate=1739203200000, acceptedDateStr=2025-02-11, onlineDate=1770362885046, onlineDateStr=2026-02-06, pubDate=1751558400000, pubDateStr=2025-07-04, doiRegisterDate=null, doiRegisterDateStr=null, onlineIssueDate=1770362885046, onlineIssueDateStr=2026-02-06, onlineJustAcceptDate=null, onlineJustAcceptDateStr=null, onlineFirstDate=null, onlineFirstDateStr=null, sourceXml=null, magXml=null, createTime=1770362885046, creator=13701087609, updateTime=1770362885046, updator=13701087609, issue=Issue{id=1226554095926952065, tenantId=1146029695717560320, journalId=1192105938417971205, year='2025', volume='65', issue='7', pageStart='2771', pageEnd='3233', issueExtLink='null', onlineDate='null', pubDate='null', beforeIssueId=null, nextIssueId=null, price=null, status=1, issueComplete=1, articleOrder=1, issueType=-1, specialIssue=null, createTime=1770362884741, creator=13701087609, updateTime=1770363575040, updator=13701087609, preIssue=null, nextIssue=null, ext={EN=IssueExt(id=1226556991309529548, tenantId=1146029695717560320, journalId=1192105938417971205, issueId=1226554095926952065, language=EN, specialIssueTitle=, coverIllustrator=null, specialIssueEditor=, specialIssueAbout=), CN=IssueExt(id=1226556991309529549, tenantId=1146029695717560320, journalId=1192105938417971205, issueId=1226554095926952065, language=CN, specialIssueTitle=, coverIllustrator=null, specialIssueEditor=, specialIssueAbout=)}, issueFiles=null}, startPage=2864, endPage=2873, ext={EN=ArticleExt(id=1226554098762297365, articleId=1226554097206210577, tenantId=1146029695717560320, journalId=1192105938417971205, language=EN, title=Research strategies for the regulatory functions of bacterial transcription factors, columnId=1192149543727808575, journalTitle=Acta Microbiologica Sinica, columnName=Review, runingTitle=null, highlight=null, articleAbstract=

Transcription factors are essential for the survival of bacteria, and revealing their functions is conducive to the development of antimicrobials, industrial applications, and environmental protection. At present, there are many methods and strategies for the research on transcription factors, which have been developed rapidly in the fields of bioinformatics and molecular biology. This paper summarizes the methods for identifying unknown transcription factors, unveiling the regulatory functions of transcription factors, constructing regulatory networks of transcription factors, and validating the regulatory genes of transcription factors. This review aims to provide new strategies and new ideas for the analysis and verification of the regulatory functions of bacterial transcription factors.

, correspAuthors=null, authorNote=null, correspAuthorsNote=
*Tel: +86-514-87971136, E-mail:
, copyrightStatement=null, copyrightOwner=null, extLink=null, articleAbsUrl=null, sourceXml=null, magXml=null, pdfUrl=null, pdf=null, pdfFileSize=null, pdfExtLink=null, richHtmlUrl=null, mobilePdfUrl=null, reviewReport=null, pdfFirstPage=null, abstractGraph=null, abstractGraphContent=null, abstractVideo=null, citation=null, cebUrl=null, magXmlContent=null, mapNumber=null, authorCompany=null, fund=null, authors=null, authorsList=Lingli CHEN, Xiaofei LI, Ying LIU, Fangzhe REN, Xin’an JIAO, Jinlin HUANG), CN=ArticleExt(id=1226554100318384171, articleId=1226554097206210577, tenantId=1146029695717560320, journalId=1192105938417971205, language=CN, title=细菌转录因子调控功能的研究策略, columnId=1192149543882997826, journalTitle=微生物学报, columnName=综述, runingTitle=null, highlight=null, articleAbstract=

转录因子对细菌的生存至关重要,其功能解析有助于推动抗菌药物研发、工业应用以及环境保护等多个领域的发展。目前,转录因子的研究方法与策略种类繁多,在生物信息学和分子生物学等领域均取得了迅速发展。本文从未知转录因子的鉴定方法、转录因子调控功能的鉴定方法、转录因子调控网络的构建方法以及转录因子调控基因的验证方法等4个方面进行综述,为细菌转录因子调控功能的分析与验证提供了新策略与新思路。

, correspAuthors=null, authorNote=null, correspAuthorsNote=null, copyrightStatement=null, copyrightOwner=null, extLink=null, articleAbsUrl=null, sourceXml=YWCwN16eUzqat5MOZOi/pA==, magXml=sJVje50GY07qKjkfZHYQ7g==, pdfUrl=null, pdf=0UTQ0yz6lqDp6KZsSXmfBg==, pdfFileSize=1329928, pdfExtLink=null, richHtmlUrl=null, mobilePdfUrl=null, reviewReport=null, pdfFirstPage=null, abstractGraph=yY/2NS0hDLysSsG8ShsRqg==, abstractGraphContent=null, abstractVideo=null, citation=null, cebUrl=null, magXmlContent=lFtlRj/+cN5qqmZEa2vV8Q==, mapNumber=null, authorCompany=null, fund=null, authors=

作者贡献声明

陈玲莉:负责论文设计与构思,论文撰写与修改;李晓飞:参与论文讨论,论文修改与校对;刘莹:参与论文讨论,论文修改与校对;任方哲:参与论文讨论,论文修改与校对;焦新安:提供资源;黄金林:获取基金,提供资源,指导论文修改与审阅。

, authorsList=陈玲莉, 李晓飞, 刘莹, 任方哲, 焦新安, 黄金林)}, authors=[Author(id=1227681718526735009, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226554097206210577, orderNo=0, firstName=null, middleName=null, lastName=null, nameCn=null, orcid=null, stid=null, country=null, authorPic=null, dead=0, email=null, emailSecond=null, emailThird=null, correspondingAuthor=0, authorType=1, ext={EN=AuthorExt(id=1227681718736450221, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226554097206210577, authorId=1227681718526735009, language=EN, stringName=Lingli CHEN, firstName=Lingli, middleName=null, lastName=CHEN, prefix=null, suffix=null, authorComment=null, nameInitials=null, affiliation=null, department=null, xref=1, address=1.Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, Jiangsu, China, bio=null, bioImg=null, bioContent=null, aboutCorrespAuthor=null), CN=AuthorExt(id=1227681718837113529, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226554097206210577, authorId=1227681718526735009, language=CN, stringName=陈玲莉, firstName=null, middleName=null, lastName=null, prefix=null, suffix=null, authorComment=null, nameInitials=null, affiliation=null, department=null, xref=1, address=1.扬州大学,江苏省人兽共患病学重点实验室,江苏 扬州, bio=null, bioImg=null, bioContent=null, aboutCorrespAuthor=null)}, companyList=[AuthorCompany(id=1227681717754983008, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226554097206210577, xref=1., ext=[AuthorCompanyExt(id=1227681717771760227, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226554097206210577, companyId=1227681717754983008, language=EN, country=null, province=null, city=null, postcode=null, companyName=null, departmentName=null, remark=1.Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, Jiangsu, China), AuthorCompanyExt(id=1227681717780148837, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226554097206210577, companyId=1227681717754983008, language=CN, country=null, province=null, city=null, postcode=null, companyName=null, departmentName=null, remark=1.扬州大学,江苏省人兽共患病学重点实验室,江苏 扬州)])]), Author(id=1227681718962942656, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226554097206210577, orderNo=1, firstName=null, middleName=null, lastName=null, nameCn=null, orcid=null, stid=null, country=null, authorPic=null, dead=0, email=null, emailSecond=null, emailThird=null, correspondingAuthor=0, authorType=1, ext={EN=AuthorExt(id=1227681719084577485, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226554097206210577, authorId=1227681718962942656, language=EN, stringName=Xiaofei LI, firstName=Xiaofei, middleName=null, lastName=LI, prefix=null, suffix=null, authorComment=null, nameInitials=null, affiliation=null, department=null, xref=2, address=2.Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, Jiangsu, China, bio=null, bioImg=null, bioContent=null, aboutCorrespAuthor=null), CN=AuthorExt(id=1227681719206212315, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226554097206210577, authorId=1227681718962942656, language=CN, stringName=李晓飞, firstName=null, middleName=null, lastName=null, prefix=null, suffix=null, authorComment=null, nameInitials=null, affiliation=null, department=null, xref=2, address=2.江苏高校动物重要疫病与人兽共患病防控协同创新中心,江苏 扬州, bio=null, bioImg=null, bioContent=null, aboutCorrespAuthor=null)}, companyList=[AuthorCompany(id=1227681717876617836, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226554097206210577, xref=2., ext=[AuthorCompanyExt(id=1227681717885006446, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226554097206210577, companyId=1227681717876617836, language=EN, country=null, province=null, city=null, postcode=null, companyName=null, departmentName=null, remark=2.Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, Jiangsu, China), AuthorCompanyExt(id=1227681717893395056, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226554097206210577, companyId=1227681717876617836, language=CN, country=null, province=null, city=null, postcode=null, companyName=null, departmentName=null, remark=2.江苏高校动物重要疫病与人兽共患病防控协同创新中心,江苏 扬州)])]), Author(id=1227681719290098406, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226554097206210577, orderNo=2, firstName=null, middleName=null, lastName=null, nameCn=null, orcid=null, stid=null, country=null, authorPic=null, dead=0, email=null, emailSecond=null, emailThird=null, correspondingAuthor=0, authorType=1, ext={EN=AuthorExt(id=1227681719390761708, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226554097206210577, authorId=1227681719290098406, language=EN, stringName=Ying LIU, firstName=Ying, middleName=null, lastName=LIU, prefix=null, suffix=null, authorComment=null, nameInitials=null, affiliation=null, department=null, xref=1, address=1.Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, Jiangsu, China, bio=null, bioImg=null, bioContent=null, aboutCorrespAuthor=null), CN=AuthorExt(id=1227681720368034561, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226554097206210577, authorId=1227681719290098406, language=CN, stringName=刘莹, firstName=null, middleName=null, lastName=null, prefix=null, suffix=null, authorComment=null, nameInitials=null, affiliation=null, department=null, xref=1, address=1.扬州大学,江苏省人兽共患病学重点实验室,江苏 扬州, bio=null, bioImg=null, bioContent=null, aboutCorrespAuthor=null)}, companyList=[AuthorCompany(id=1227681717754983008, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226554097206210577, xref=1., ext=[AuthorCompanyExt(id=1227681717771760227, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226554097206210577, companyId=1227681717754983008, language=EN, country=null, province=null, city=null, postcode=null, companyName=null, departmentName=null, remark=1.Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, Jiangsu, China), AuthorCompanyExt(id=1227681717780148837, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226554097206210577, companyId=1227681717754983008, language=CN, country=null, province=null, city=null, postcode=null, companyName=null, departmentName=null, remark=1.扬州大学,江苏省人兽共患病学重点实验室,江苏 扬州)])]), Author(id=1227681720862962441, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226554097206210577, orderNo=3, firstName=null, middleName=null, lastName=null, nameCn=null, orcid=null, stid=null, country=null, authorPic=null, dead=0, email=null, emailSecond=null, emailThird=null, correspondingAuthor=0, authorType=1, ext={EN=AuthorExt(id=1227681721013957394, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226554097206210577, authorId=1227681720862962441, language=EN, stringName=Fangzhe REN, firstName=Fangzhe, middleName=null, lastName=REN, prefix=null, suffix=null, authorComment=null, nameInitials=null, affiliation=null, department=null, xref=2, address=2.Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, Jiangsu, China, bio=null, bioImg=null, bioContent=null, aboutCorrespAuthor=null), CN=AuthorExt(id=1227681721152369443, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226554097206210577, authorId=1227681720862962441, language=CN, stringName=任方哲, firstName=null, middleName=null, lastName=null, prefix=null, suffix=null, authorComment=null, nameInitials=null, affiliation=null, department=null, xref=2, address=2.江苏高校动物重要疫病与人兽共患病防控协同创新中心,江苏 扬州, bio=null, bioImg=null, bioContent=null, aboutCorrespAuthor=null)}, companyList=[AuthorCompany(id=1227681717876617836, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226554097206210577, xref=2., ext=[AuthorCompanyExt(id=1227681717885006446, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226554097206210577, companyId=1227681717876617836, language=EN, country=null, province=null, city=null, postcode=null, companyName=null, departmentName=null, remark=2.Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, Jiangsu, China), AuthorCompanyExt(id=1227681717893395056, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226554097206210577, companyId=1227681717876617836, language=CN, country=null, province=null, city=null, postcode=null, companyName=null, departmentName=null, remark=2.江苏高校动物重要疫病与人兽共患病防控协同创新中心,江苏 扬州)])]), Author(id=1227681721257227060, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226554097206210577, orderNo=4, firstName=null, middleName=null, lastName=null, nameCn=null, orcid=null, stid=null, country=null, authorPic=null, dead=0, email=null, emailSecond=null, emailThird=null, correspondingAuthor=0, authorType=1, ext={EN=AuthorExt(id=1227681721408222017, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226554097206210577, authorId=1227681721257227060, language=EN, stringName=Xin’an JIAO, firstName=Xin’an, middleName=null, lastName=JIAO, prefix=null, suffix=null, authorComment=null, nameInitials=null, affiliation=null, department=null, xref=3, address=3.Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture and Rural Affairs, Yangzhou, Jiangsu, China, bio=null, bioImg=null, bioContent=null, aboutCorrespAuthor=null), CN=AuthorExt(id=1227681721529856842, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226554097206210577, authorId=1227681721257227060, language=CN, stringName=焦新安, firstName=null, middleName=null, lastName=null, prefix=null, suffix=null, authorComment=null, nameInitials=null, affiliation=null, department=null, xref=3, address=3.农业农村部农产品质量安全生物性危害因子(动物源)控制重点实验室,江苏 扬州, bio=null, bioImg=null, bioContent=null, aboutCorrespAuthor=null)}, companyList=[AuthorCompany(id=1227681717998252663, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226554097206210577, xref=3., ext=[AuthorCompanyExt(id=1227681718006641272, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226554097206210577, companyId=1227681717998252663, language=EN, country=null, province=null, city=null, postcode=null, companyName=null, departmentName=null, remark=3.Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture and Rural Affairs, Yangzhou, Jiangsu, China), AuthorCompanyExt(id=1227681718015029882, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226554097206210577, companyId=1227681717998252663, language=CN, country=null, province=null, city=null, postcode=null, companyName=null, departmentName=null, remark=3.农业农村部农产品质量安全生物性危害因子(动物源)控制重点实验室,江苏 扬州)])]), Author(id=1227681721676657497, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226554097206210577, orderNo=5, firstName=null, middleName=null, lastName=null, nameCn=null, orcid=null, stid=null, country=null, authorPic=null, dead=0, email=jinlin@yzu.edu.cn, emailSecond=null, emailThird=null, correspondingAuthor=0, authorType=1, ext={EN=AuthorExt(id=1227681721840235369, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226554097206210577, authorId=1227681721676657497, language=EN, stringName=Jinlin HUANG, firstName=Jinlin, middleName=null, lastName=HUANG, prefix=null, suffix=null, authorComment=null, nameInitials=null, affiliation=null, department=null, xref=1, 2, 3, 4, address=1.Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, Jiangsu, China
2.Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, Jiangsu, China
3.Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture and Rural Affairs, Yangzhou, Jiangsu, China
4.Joint International Research Laboratory of Agriculture and Agri-product Safety, Ministry of Education, Yangzhou, Jiangsu, China, bio=null, bioImg=null, bioContent=null, aboutCorrespAuthor=null), CN=AuthorExt(id=1227681721940898675, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226554097206210577, authorId=1227681721676657497, language=CN, stringName=黄金林, firstName=null, middleName=null, lastName=null, prefix=null, suffix=null, authorComment=null, nameInitials=null, affiliation=null, department=null, xref=1, 2, 3, 4, address=1.扬州大学,江苏省人兽共患病学重点实验室,江苏 扬州
2.江苏高校动物重要疫病与人兽共患病防控协同创新中心,江苏 扬州
3.农业农村部农产品质量安全生物性危害因子(动物源)控制重点实验室,江苏 扬州
4.教育部农业与农产品安全国际合作联合实验室,江苏 扬州, bio=null, bioImg=null, bioContent=null, aboutCorrespAuthor=null)}, companyList=[AuthorCompany(id=1227681717754983008, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226554097206210577, xref=1., ext=[AuthorCompanyExt(id=1227681717771760227, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226554097206210577, companyId=1227681717754983008, language=EN, country=null, province=null, city=null, postcode=null, companyName=null, departmentName=null, remark=1.Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, Jiangsu, China), AuthorCompanyExt(id=1227681717780148837, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226554097206210577, companyId=1227681717754983008, language=CN, country=null, province=null, city=null, postcode=null, companyName=null, departmentName=null, remark=1.扬州大学,江苏省人兽共患病学重点实验室,江苏 扬州)]), AuthorCompany(id=1227681717876617836, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226554097206210577, xref=2., ext=[AuthorCompanyExt(id=1227681717885006446, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226554097206210577, companyId=1227681717876617836, language=EN, country=null, province=null, city=null, postcode=null, companyName=null, departmentName=null, remark=2.Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, Jiangsu, China), AuthorCompanyExt(id=1227681717893395056, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226554097206210577, companyId=1227681717876617836, language=CN, country=null, province=null, city=null, postcode=null, companyName=null, departmentName=null, remark=2.江苏高校动物重要疫病与人兽共患病防控协同创新中心,江苏 扬州)]), AuthorCompany(id=1227681717998252663, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226554097206210577, xref=3., ext=[AuthorCompanyExt(id=1227681718006641272, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226554097206210577, companyId=1227681717998252663, language=EN, country=null, province=null, city=null, postcode=null, companyName=null, departmentName=null, remark=3.Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture and Rural Affairs, Yangzhou, Jiangsu, China), AuthorCompanyExt(id=1227681718015029882, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226554097206210577, companyId=1227681717998252663, language=CN, country=null, province=null, city=null, postcode=null, companyName=null, departmentName=null, remark=3.农业农村部农产品质量安全生物性危害因子(动物源)控制重点实验室,江苏 扬州)]), AuthorCompany(id=1227681718186996362, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226554097206210577, xref=4., ext=[AuthorCompanyExt(id=1227681718199579275, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226554097206210577, companyId=1227681718186996362, language=EN, country=null, province=null, city=null, postcode=null, companyName=null, departmentName=null, remark=4.Joint International Research Laboratory of Agriculture and Agri-product Safety, Ministry of Education, Yangzhou, Jiangsu, China), AuthorCompanyExt(id=1227681718245716621, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226554097206210577, companyId=1227681718186996362, language=CN, country=null, province=null, city=null, postcode=null, companyName=null, departmentName=null, remark=4.教育部农业与农产品安全国际合作联合实验室,江苏 扬州)])])], keywords=[Keyword(id=1227681722205139857, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226554097206210577, language=EN, orderNo=1, keyword=bacteria), Keyword(id=1227681722322580379, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226554097206210577, language=EN, orderNo=2, keyword=transcription factors), Keyword(id=1227681722448409514, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226554097206210577, language=EN, orderNo=3, keyword=regulation), Keyword(id=1227681722603598776, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226554097206210577, language=EN, orderNo=4, keyword=bioinformatics), Keyword(id=1227681722716844992, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226554097206210577, language=CN, orderNo=1, keyword=细菌), Keyword(id=1227681722842674123, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226554097206210577, language=CN, orderNo=2, keyword=转录因子), Keyword(id=1227681722934948822, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226554097206210577, language=CN, orderNo=3, keyword=调控), Keyword(id=1227681723027223521, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226554097206210577, language=CN, orderNo=4, keyword=生物信息学)], refs=[Reference(id=1227681727536099434, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226554097206210577, doi=null, pmid=null, pmcid=null, year=2019, volume=7, issue=10, pageStart=454, pageEnd=null, url=null, language=null, rfNumber=[1], rfOrder=0, authorNames=DIESER M, SMITH HJ, RAMARAJ T, FOREMAN CM, journalName=Microorganisms, refType=null, unstructuredReference=DIESER M, SMITH HJ, RAMARAJ T, FOREMAN CM. Janthinobacterium CG23_2: comparative genome analysis reveals enhanced environmental sensing and transcriptional regulation for adaptation to life in an Antarctic supraglacial stream[J]. Microorganisms, 2019, 7(10): 454., articleTitle=Janthinobacterium CG23_2: comparative genome analysis reveals enhanced environmental sensing and transcriptional regulation for adaptation to life in an Antarctic supraglacial stream, refAbstract=null), Reference(id=1227681727640957043, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226554097206210577, doi=null, pmid=null, pmcid=null, year=2012, volume=13, issue=null, pageStart=628, pageEnd=null, url=null, language=null, rfNumber=[2], rfOrder=1, authorNames=ORTET P, de LUCA G, WHITWORTH DE, BARAKAT M, journalName=BMC Genomics, refType=null, unstructuredReference=ORTET P, de LUCA G, WHITWORTH DE, BARAKAT M. P2TF: a comprehensive resource for analysis of prokaryotic transcription factors[J]. BMC Genomics, 2012, 13: 628., articleTitle=P2TF: a comprehensive resource for analysis of prokaryotic transcription factors, refAbstract=null), Reference(id=1227681727745814653, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226554097206210577, doi=null, pmid=null, pmcid=null, year=2020, volume=21, issue=11, pageStart=699, pageEnd=714, url=null, language=null, rfNumber=[3], rfOrder=2, authorNames=MEJÍA-ALMONTE C, BUSBY SJW, WADE JT, van HELDEN J, ARKIN AP, STORMO GD, EILBECK K, PALSSON BO, GALAGAN JE, COLLADO-VIDES J, journalName=Nature Reviews Genetics, refType=null, unstructuredReference=MEJÍA-ALMONTE C, BUSBY SJW, WADE JT, van HELDEN J, ARKIN AP, STORMO GD, EILBECK K, PALSSON BO, GALAGAN JE, COLLADO-VIDES J. Redefining fundamental concepts of transcription initiation in bacteria[J]. Nature Reviews Genetics, 2020, 21(11): 699-714., articleTitle=Redefining fundamental concepts of transcription initiation in bacteria, refAbstract=null), Reference(id=1227681727859060873, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226554097206210577, doi=null, pmid=null, pmcid=null, year=2024, volume=626, issue=7999, pageStart=661, pageEnd=669, url=null, language=null, rfNumber=[4], rfOrder=3, authorNames=POUNTAIN AW, JIANG PE, YAO TY, HOMAEE E, GUAN YC, McDONALD KJC, PODKOWIK M, SHOPSIN B, TORRES VJ, GOLDING I, YANAI I, journalName=Nature, refType=null, unstructuredReference=POUNTAIN AW, JIANG PE, YAO TY, HOMAEE E, GUAN YC, McDONALD KJC, PODKOWIK M, SHOPSIN B, TORRES VJ, GOLDING I, YANAI I. Transcription-replication interactions reveal bacterial genome regulation[J]. Nature, 2024, 626(7999): 661-669., articleTitle=Transcription-replication interactions reveal bacterial genome regulation, refAbstract=null), Reference(id=1227681727989084306, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226554097206210577, doi=null, pmid=null, pmcid=null, year=2022, volume=17, issue=11, pageStart=3086, pageEnd=3099, url=null, language=null, rfNumber=[5], rfOrder=4, authorNames=FORSTER ER, YANG XL, TAI AK, HANG HC, SHEN A, journalName=ACS Chemical Biology, refType=null, unstructuredReference=FORSTER ER, YANG XL, TAI AK, HANG HC, SHEN A. Identification of a bile acid-binding transcription factor in Clostridioides difficile using chemical proteomics[J]. ACS Chemical Biology, 2022, 17(11): 3086-3099., articleTitle=Identification of a bile acid-binding transcription factor in Clostridioides difficile using chemical proteomics, refAbstract=null), Reference(id=1227681728135884965, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226554097206210577, doi=null, pmid=null, pmcid=null, year=2022, volume=null, issue=null, pageStart=103, pageEnd=112, url=null, language=null, rfNumber=[6], rfOrder=5, authorNames=LEDESMA L, HERNANDEZ-GUERRERO R, PEREZ-RUEDA E, journalName=Prokaryotic Gene Regulation, refType=null, unstructuredReference=LEDESMA L, HERNANDEZ-GUERRERO R, PEREZ-RUEDA E. Prediction of DNA-binding transcription factors in bacteria and Archaea genomes[M]//Prokaryotic Gene Regulation. New York, NY: Springer US, 2022: 103-112., articleTitle=Prediction of DNA-binding transcription factors in bacteria and Archaea genomes, refAbstract=null), Reference(id=1227681728274297003, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226554097206210577, doi=null, pmid=null, pmcid=null, year=2021, volume=49, issue=D1, pageStart=D412, pageEnd=D419, url=null, language=null, rfNumber=[7], rfOrder=6, authorNames=MISTRY J, CHUGURANSKY S, WILLIAMS L, QURESHI M, SALAZAR GA, SONNHAMMER ELL, TOSATTO SCE, PALADIN L, RAJ S, RICHARDSON LJ, FINN RD, BATEMAN A, journalName=Nucleic Acids Research, refType=null, unstructuredReference=MISTRY J, CHUGURANSKY S, WILLIAMS L, QURESHI M, SALAZAR GA, SONNHAMMER ELL, TOSATTO SCE, PALADIN L, RAJ S, RICHARDSON LJ, FINN RD, BATEMAN A. Pfam: the protein families database in 2021[J]. Nucleic Acids Research, 2021, 49(D1): D412-D419., articleTitle=Pfam: the protein families database in 2021, refAbstract=null), Reference(id=1227681728387543218, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226554097206210577, doi=null, pmid=null, pmcid=null, year=2006, volume=34, issue=Database issue, pageStart=D74, pageEnd=D81, url=null, language=null, rfNumber=[8], rfOrder=7, authorNames=KUMMERFELD SK, TEICHMANN SA, journalName=Nucleic Acids Research, refType=null, unstructuredReference=KUMMERFELD SK, TEICHMANN SA. DBD: a transcription factor prediction database[J]. Nucleic Acids Research, 2006, 34(Database issue): D74-D81., articleTitle=DBD: a transcription factor prediction database, refAbstract=null), Reference(id=1227681729813606588, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226554097206210577, doi=null, pmid=null, pmcid=null, year=2008, volume=36, issue=Database issue, pageStart=D93, pageEnd=D96, url=null, language=null, rfNumber=[9], rfOrder=8, authorNames=SIERRO N, MAKITA Y, de HOON M, NAKAI KT, journalName=Nucleic Acids Research, refType=null, unstructuredReference=SIERRO N, MAKITA Y, de HOON M, NAKAI KT. DBTBS: a database of transcriptional regulation in Bacillus subtilis containing upstream intergenic conservation information[J]. Nucleic Acids Research, 2008, 36(Database issue): D93-D96., articleTitle=DBTBS: a database of transcriptional regulation in Bacillus subtilis containing upstream intergenic conservation information, refAbstract=null), Reference(id=1227681730065264844, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226554097206210577, doi=null, pmid=null, pmcid=null, year=2016, volume=44, issue=D1, pageStart=D133, pageEnd=D143, url=null, language=null, rfNumber=[10], rfOrder=9, authorNames=GAMA-CASTRO S, SALGADO H, SANTOS-ZAVALETA A, LEDEZMA-TEJEIDA D, MUÑIZ-RASCADO L, GARCÍA-SOTELO JS, ALQUICIRA-HERNÁNDEZ K, MARTÍNEZ-FLORES I, PANNIER L, CASTRO-MONDRAGÓN JA, MEDINA-RIVERA A, SOLANO-LIRA H, BONAVIDES-MARTÍNEZ C, PÉREZ-RUEDA E, ALQUICIRA-HERNÁNDEZ S, PORRÓN-SOTELO L, LÓPEZ-FUENTES A, HERNÁNDEZ-KOUTOUCHEVA A, del MORAL-CHÁVEZ V, RINALDI F, journalName=Nucleic Acids Research, refType=null, unstructuredReference=GAMA-CASTRO S, SALGADO H, SANTOS-ZAVALETA A, LEDEZMA-TEJEIDA D, MUÑIZ-RASCADO L, GARCÍA-SOTELO JS, ALQUICIRA-HERNÁNDEZ K, MARTÍNEZ-FLORES I, PANNIER L, CASTRO-MONDRAGÓN JA, MEDINA-RIVERA A, SOLANO-LIRA H, BONAVIDES-MARTÍNEZ C, PÉREZ-RUEDA E, ALQUICIRA-HERNÁNDEZ S, PORRÓN-SOTELO L, LÓPEZ-FUENTES A, HERNÁNDEZ-KOUTOUCHEVA A, del MORAL-CHÁVEZ V, RINALDI F, et al. RegulonDB version 9.0: high-level integration of gene regulation, coexpression, motif clustering and beyond[J]. Nucleic Acids Research, 2016, 44(D1): D133-D143., articleTitle=RegulonDB version 9.0: high-level integration of gene regulation, coexpression, motif clustering and beyond, refAbstract=null), Reference(id=1227681730182705366, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226554097206210577, doi=null, pmid=null, pmcid=null, year=2011, volume=12, issue=null, pageStart=124, pageEnd=null, url=null, language=null, rfNumber=[11], rfOrder=10, authorNames=LECHNER M, FINDEISS S, STEINER L, MARZ M, STADLER PF, PROHASKA SJ, journalName=BMC Bioinformatics, refType=null, unstructuredReference=LECHNER M, FINDEISS S, STEINER L, MARZ M, STADLER PF, PROHASKA SJ. Proteinortho: detection of (co-)orthologs in large-scale analysis[J]. BMC Bioinformatics, 2011, 12: 124., articleTitle=Proteinortho: detection of (co-)orthologs in large-scale analysis, refAbstract=null), Reference(id=1227681730291757280, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226554097206210577, doi=null, pmid=null, pmcid=null, year=2020, volume=15, issue=8, pageStart=null, pageEnd=null, url=null, language=null, rfNumber=[12], rfOrder=11, authorNames=FLORES-BAUTISTA E, HERNANDEZ-GUERRERO R, HUERTA-SAQUERO A, TENORIO-SALGADO S, RIVERA-GOMEZ N, ROMERO A, IBARRA JA, PEREZ-RUEDA E, journalName=PLoS One, refType=null, unstructuredReference=FLORES-BAUTISTA E, HERNANDEZ-GUERRERO R, HUERTA-SAQUERO A, TENORIO-SALGADO S, RIVERA-GOMEZ N, ROMERO A, IBARRA JA, PEREZ-RUEDA E. Deciphering the functional diversity of DNA-binding transcription factors in bacteria and archaea organisms[J]. PLoS One, 2020, 15(8): e0237135., articleTitle=Deciphering the functional diversity of DNA-binding transcription factors in bacteria and archaea organisms, refAbstract=null), Reference(id=1227681732279857381, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226554097206210577, doi=null, pmid=null, pmcid=null, year=1990, volume=18, issue=17, pageStart=5019, pageEnd=5026, url=null, language=null, rfNumber=[13], rfOrder=12, authorNames=DODD IB, EGAN JB, journalName=Nucleic Acids Research, refType=null, unstructuredReference=DODD IB, EGAN JB. Improved detection of helix-turn-helix DNA-binding motifs in protein sequences[J]. Nucleic Acids Research, 1990, 18(17): 5019-5026., articleTitle=Improved detection of helix-turn-helix DNA-binding motifs in protein sequences, refAbstract=null), Reference(id=1227681732422463727, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226554097206210577, doi=null, pmid=null, pmcid=null, year=2015, volume=6, issue=null, pageStart=770, pageEnd=null, url=null, language=null, rfNumber=[14], rfOrder=13, authorNames=REUTER M, PERIAGO PM, MULHOLLAND F, BROWN HL, van VLIET AHM, journalName=Frontiers in Microbiology, refType=null, unstructuredReference=REUTER M, PERIAGO PM, MULHOLLAND F, BROWN HL, van VLIET AHM. A PAS domain-containing regulator controls flagella-flagella interactions in Campylobacter jejuni [J]. Frontiers in Microbiology, 2015, 6: 770., articleTitle=A PAS domain-containing regulator controls flagella-flagella interactions in Campylobacter jejuni, refAbstract=null), Reference(id=1227681732569264378, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226554097206210577, doi=null, pmid=null, pmcid=null, year=2022, volume=167, issue=null, pageStart=105546, pageEnd=null, url=null, language=null, rfNumber=[15], rfOrder=14, authorNames=LI YY, SUN WD, WANG Q, YU Y, WAN Y, ZHOU K, GUO R, HAN XG, CHEN ZG, FANG WH, JIANG W, journalName=Microbial Pathogenesis, refType=null, unstructuredReference=LI YY, SUN WD, WANG Q, YU Y, WAN Y, ZHOU K, GUO R, HAN XG, CHEN ZG, FANG WH, JIANG W. The GntR-like transcriptional regulator HutC involved in motility, biofilm-forming ability, and virulence in Vibrio parahaemolyticus [J]. Microbial Pathogenesis, 2022, 167: 105546., articleTitle=The GntR-like transcriptional regulator HutC involved in motility, biofilm-forming ability, and virulence in Vibrio parahaemolyticus, refAbstract=null), Reference(id=1227681732686704897, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226554097206210577, doi=null, pmid=null, pmcid=null, year=2024, volume=22, issue=1, pageStart=100349, pageEnd=null, url=null, language=null, rfNumber=[16], rfOrder=15, authorNames=ABD-EL-HALEEM D, journalName=Journal of Genetic Engineering and Biotechnology, refType=null, unstructuredReference=ABD-EL-HALEEM D. AraC transcriptional regulator, aspartate semialdehyde dehydrogenase and acyltransferase: three putative genes in phenol catabolic pathway of Acinetobacter sp. strain DF4[J]. Journal of Genetic Engineering and Biotechnology, 2024, 22(1): 100349., articleTitle=AraC transcriptional regulator, aspartate semialdehyde dehydrogenase and acyltransferase: three putative genes in phenol catabolic pathway of Acinetobacter sp. strain DF4, refAbstract=null), Reference(id=1227681732778979596, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226554097206210577, doi=null, pmid=null, pmcid=null, year=2021, volume=118, issue=2, pageStart=null, pageEnd=null, url=null, language=null, rfNumber=[17], rfOrder=16, authorNames=KIM GB, GAO Y, PALSSON BO, LEE SY, journalName=Proceedings of the National Academy of Sciences of the United States of America, refType=null, unstructuredReference=KIM GB, GAO Y, PALSSON BO, LEE SY. DeepTFactor: a deep learning-based tool for the prediction of transcription factors[J]. Proceedings of the National Academy of Sciences of the United States of America, 2021, 118(2): e2021171118., articleTitle=DeepTFactor: a deep learning-based tool for the prediction of transcription factors, refAbstract=null), Reference(id=1227681732867059986, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226554097206210577, doi=null, pmid=null, pmcid=null, year=2023, volume=11, issue=null, pageStart=null, pageEnd=null, url=null, language=null, rfNumber=[18], rfOrder=17, authorNames=TONG CY, LIANG YM, ZHANG ZL, WANG S, ZHENG XH, LIU Q, SONG BC, journalName=PeerJ, refType=null, unstructuredReference=TONG CY, LIANG YM, ZHANG ZL, WANG S, ZHENG XH, LIU Q, SONG BC. Review of knockout technology approaches in bacterial drug resistance research[J]. PeerJ, 2023, 11: e15790., articleTitle=Review of knockout technology approaches in bacterial drug resistance research, refAbstract=null), Reference(id=1227681734284734749, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226554097206210577, doi=null, pmid=null, pmcid=null, year=2022, volume=23, issue=20, pageStart=12306, pageEnd=null, url=null, language=null, rfNumber=[19], rfOrder=18, authorNames=ZHAO F, ZHI TH, HU RJ, FAN R, LONG YH, TIAN FH, ZHAO ZB, journalName=International Journal of Molecular Sciences, refType=null, unstructuredReference=ZHAO F, ZHI TH, HU RJ, FAN R, LONG YH, TIAN FH, ZHAO ZB. The OmpR-like transcription factor as a negative regulator of hrpR/S in Pseudomonas syringae pv. actinidiae [J]. International Journal of Molecular Sciences, 2022, 23(20): 12306., articleTitle=The OmpR-like transcription factor as a negative regulator of hrpR/S in Pseudomonas syringae pv. actinidiae, refAbstract=null), Reference(id=1227681734439924004, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226554097206210577, doi=null, pmid=null, pmcid=null, year=2016, volume=17, issue=1, pageStart=686, pageEnd=null, url=null, language=null, rfNumber=[20], rfOrder=19, authorNames=OLIVER P, PERALTA-GIL M, TABCHE ML, MERINO E, journalName=BMC Genomics, refType=null, unstructuredReference=OLIVER P, PERALTA-GIL M, TABCHE ML, MERINO E. Molecular and structural considerations of TF-DNA binding for the generation of biologically meaningful and accurate phylogenetic footprinting analysis: the LysR-type transcriptional regulator family as a study model[J]. BMC Genomics, 2016, 17(1): 686., articleTitle=Molecular and structural considerations of TF-DNA binding for the generation of biologically meaningful and accurate phylogenetic footprinting analysis: the LysR-type transcriptional regulator family as a study model, refAbstract=null), Reference(id=1227681734553170219, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226554097206210577, doi=null, pmid=null, pmcid=null, year=2015, volume=14, issue=2, pageStart=130, pageEnd=142, url=null, language=null, rfNumber=[21], rfOrder=20, authorNames=FINOTELLO F, di CAMILLO B, journalName=Briefings in Functional Genomics, refType=null, unstructuredReference=FINOTELLO F, di CAMILLO B. Measuring differential gene expression with RNA-seq: challenges and strategies for data analysis[J]. Briefings in Functional Genomics, 2015, 14(2): 130-142., articleTitle=Measuring differential gene expression with RNA-seq: challenges and strategies for data analysis, refAbstract=null), Reference(id=1227681734687387955, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226554097206210577, doi=null, pmid=null, pmcid=null, year=2020, volume=215, issue=4, pageStart=1171, pageEnd=1189, url=null, language=null, rfNumber=[22], rfOrder=21, authorNames=DO E, CHO YJ, KIM D, KRONSTAD JW, JUNG WH, journalName=Genetics, refType=null, unstructuredReference=DO E, CHO YJ, KIM D, KRONSTAD JW, JUNG WH. A transcriptional regulatory map of iron homeostasis reveals a new control circuit for capsule formation in Cryptococcus neoformans [J]. Genetics, 2020, 215(4): 1171-1189., articleTitle=A transcriptional regulatory map of iron homeostasis reveals a new control circuit for capsule formation in Cryptococcus neoformans, refAbstract=null), Reference(id=1227681734905491775, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226554097206210577, doi=null, pmid=null, pmcid=null, year=2018, volume=19, issue=1, pageStart=245, pageEnd=null, url=null, language=null, rfNumber=[23], rfOrder=22, authorNames=SUDHAGAR A, KUMAR G, EL-MATBOULI M, journalName=International Journal of Molecular Sciences, refType=null, unstructuredReference=SUDHAGAR A, KUMAR G, EL-MATBOULI M. Transcriptome analysis based on RNA-seq in understanding pathogenic mechanisms of diseases and the immune system of fish: a comprehensive review[J]. International Journal of Molecular Sciences, 2018, 19(1): 245., articleTitle=Transcriptome analysis based on RNA-seq in understanding pathogenic mechanisms of diseases and the immune system of fish: a comprehensive review, refAbstract=null), Reference(id=1227681735035515207, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226554097206210577, doi=null, pmid=null, pmcid=null, year=2020, volume=114, issue=5, pageStart=857, pageEnd=869, url=null, language=null, rfNumber=[24], rfOrder=23, authorNames=WANG TT, QI YH, WANG ZH, ZHAO JR, JI LX, LI J, CAI Z, YANG L, WU M, LIANG HH, journalName=Molecular Microbiology, refType=null, unstructuredReference=WANG TT, QI YH, WANG ZH, ZHAO JR, JI LX, LI J, CAI Z, YANG L, WU M, LIANG HH. Coordinated regulation of anthranilate metabolism and bacterial virulence by the GntR family regulator MpaR in Pseudomonas aeruginosa [J]. Molecular Microbiology, 2020, 114(5): 857-869., articleTitle=Coordinated regulation of anthranilate metabolism and bacterial virulence by the GntR family regulator MpaR in Pseudomonas aeruginosa, refAbstract=null), Reference(id=1227681735253619022, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226554097206210577, doi=null, pmid=null, pmcid=null, year=2023, volume=13, issue=null, pageStart=1063287, pageEnd=null, url=null, language=null, rfNumber=[25], rfOrder=24, authorNames=SUN ZX, HEACOCK-KANG Y, McMILLAN IA, CABANAS D, ZARZYCKI-SIEK J, HOANG TT, journalName=Frontiers in Microbiology, refType=null, unstructuredReference=SUN ZX, HEACOCK-KANG Y, McMILLAN IA, CABANAS D, ZARZYCKI-SIEK J, HOANG TT. A virulence activator of a surface attachment protein in Burkholderia pseudomallei acts as a global regulator of other membrane-associated virulence factors[J]. Frontiers in Microbiology, 2023, 13: 1063287., articleTitle=A virulence activator of a surface attachment protein in Burkholderia pseudomallei acts as a global regulator of other membrane-associated virulence factors, refAbstract=null), Reference(id=1227681735387836759, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226554097206210577, doi=null, pmid=null, pmcid=null, year=2017, volume=18, issue=2, pageStart=279, pageEnd=290, url=null, language=null, rfNumber=[26], rfOrder=25, authorNames=NAKATO R, SHIRAHIGE K, journalName=Briefings in Bioinformatics, refType=null, unstructuredReference=NAKATO R, SHIRAHIGE K. Recent advances in ChIP-seq analysis: from quality management to whole-genome annotation[J]. Briefings in Bioinformatics, 2017, 18(2): 279-290., articleTitle=Recent advances in ChIP-seq analysis: from quality management to whole-genome annotation, refAbstract=null), Reference(id=1227681735509471579, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226554097206210577, doi=null, pmid=null, pmcid=null, year=2020, volume=45, issue=null, pageStart=53, pageEnd=59, url=null, language=null, rfNumber=[27], rfOrder=26, authorNames=BAI Y, LI WL, XU GY, CUI GH, journalName=Electronic Journal of Biotechnology, refType=null, unstructuredReference=BAI Y, LI WL, XU GY, CUI GH. A bioinformatics approach revealed the transcription factors of Helicobacter pylori pathogenic genes and their regulatory network nodes[J]. Electronic Journal of Biotechnology, 2020, 45: 53-59., articleTitle=A bioinformatics approach revealed the transcription factors of Helicobacter pylori pathogenic genes and their regulatory network nodes, refAbstract=null), Reference(id=1227681735635300707, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226554097206210577, doi=null, pmid=null, pmcid=null, year=2022, volume=12, issue=null, pageStart=1081614, pageEnd=null, url=null, language=null, rfNumber=[28], rfOrder=27, authorNames=LIANG QA, YAN JQ, ZHANG SW, YANG N, LI MF, JIN YX, BAI F, WU WH, CHENG ZH, journalName=Frontiers in Cellular and Infection Microbiology, refType=null, unstructuredReference=LIANG QA, YAN JQ, ZHANG SW, YANG N, LI MF, JIN YX, BAI F, WU WH, CHENG ZH. CtrA activates the expression of glutathione S-transferase conferring oxidative stress resistance to Ehrlichia chaffeensis [J]. Frontiers in Cellular and Infection Microbiology, 2022, 12: 1081614., articleTitle=CtrA activates the expression of glutathione S-transferase conferring oxidative stress resistance to Ehrlichia chaffeensis, refAbstract=null), Reference(id=1227681735756935534, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226554097206210577, doi=null, pmid=null, pmcid=null, year=2022, volume=17, issue=9, pageStart=null, pageEnd=null, url=null, language=null, rfNumber=[29], rfOrder=28, authorNames=RIVAS-SOLANO O, van der HENST M, CASTILLO-ZELEDÓN A, SUÁREZ-ESQUIVEL M, MUÑOZ-VARGAS L, CAPITAN-BARRIOS Z, THOMSON NR, CHAVES-OLARTE E, MORENO E, de BOLLE X, GUZMÁN-VERRI C, journalName=PLoS One, refType=null, unstructuredReference=RIVAS-SOLANO O, van der HENST M, CASTILLO-ZELEDÓN A, SUÁREZ-ESQUIVEL M, MUÑOZ-VARGAS L, CAPITAN-BARRIOS Z, THOMSON NR, CHAVES-OLARTE E, MORENO E, de BOLLE X, GUZMÁN-VERRI C. The regulon of Brucella abortus two-component system BvrR/BvrS reveals the coordination of metabolic pathways required for intracellular life[J]. PLoS One, 2022, 17(9): e0274397., articleTitle=The regulon of Brucella abortus two-component system BvrR/BvrS reveals the coordination of metabolic pathways required for intracellular life, refAbstract=null), Reference(id=1227681735886958962, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226554097206210577, doi=null, pmid=null, pmcid=null, year=2009, volume=10, issue=10, pageStart=669, pageEnd=680, url=null, language=null, rfNumber=[30], rfOrder=29, authorNames=PARK PJ, journalName=Nature Reviews Genetics, refType=null, unstructuredReference=PARK PJ. ChIP-seq: advantages and challenges of a maturing technology[J]. Nature Reviews Genetics, 2009, 10(10): 669-680., articleTitle=ChIP-seq: advantages and challenges of a maturing technology, refAbstract=null), Reference(id=1227681736021176698, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226554097206210577, doi=null, pmid=null, pmcid=null, year=2023, volume=24, issue=null, pageStart=739, pageEnd=754, url=null, language=null, rfNumber=[31], rfOrder=30, authorNames=BADIA-I-MOMPEL P, WESSELS L, MÜLLER-DOTT S, TRIMBOUR R, RAMIREZ FLORES RO, ARGELAGUET R, SAEZ-RODRIGUEZ J, journalName=Nature Reviews Genetics, refType=null, unstructuredReference=BADIA-I-MOMPEL P, WESSELS L, MÜLLER-DOTT S, TRIMBOUR R, RAMIREZ FLORES RO, ARGELAGUET R, SAEZ-RODRIGUEZ J. Gene regulatory network inference in the era of single-cell multi-omics[J]. Nature Reviews Genetics, 2023, 24: 739-754., articleTitle=Gene regulatory network inference in the era of single-cell multi-omics, refAbstract=null), Reference(id=1227681736155394429, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226554097206210577, doi=null, pmid=null, pmcid=null, year=2018, volume=38, issue=1, pageStart=49, pageEnd=52, url=null, language=null, rfNumber=[32], rfOrder=31, authorNames=王娟红, 臧明, 郑毛亮, 常卫华, journalName=中国草食动物科学, refType=null, unstructuredReference=王娟红, 臧明, 郑毛亮, 常卫华. 绵羊繁殖调控的转录组学和蛋白组学研究进展[J]. 中国草食动物科学, 2018, 38(1): 49-52., articleTitle=绵羊繁殖调控的转录组学和蛋白组学研究进展, refAbstract=null), Reference(id=1227681736293806471, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226554097206210577, doi=null, pmid=null, pmcid=null, year=2018, volume=38, issue=1, pageStart=49, pageEnd=52, url=null, language=null, rfNumber=[32], rfOrder=32, authorNames=WANG JH, ZANG M, ZHENG ML, CHANG WH, journalName=China Herbivore Science, refType=null, unstructuredReference=WANG JH, ZANG M, ZHENG ML, CHANG WH. Progress and prospects in the research on sheep transcriptomics and proteomics[J]. China Herbivore Science, 2018, 38(1): 49-52 (in Chinese)., articleTitle=null, refAbstract=null), Reference(id=1227681736428024205, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226554097206210577, doi=null, pmid=null, pmcid=null, year=2015, volume=31, issue=17, pageStart=2912, pageEnd=2914, url=null, language=null, rfNumber=[33], rfOrder=33, authorNames=WALTER W, SÁNCHEZ-CABO F, RICOTE M, journalName=Bioinformatics, refType=null, unstructuredReference=WALTER W, SÁNCHEZ-CABO F, RICOTE M. GOplot: an R package for visually combining expression data with functional analysis[J]. Bioinformatics, 2015, 31(17): 2912-2914., articleTitle=GOplot: an R package for visually combining expression data with functional analysis, refAbstract=null), Reference(id=1227681736545464726, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226554097206210577, doi=null, pmid=null, pmcid=null, year=2021, volume=244, issue=null, pageStart=104275, pageEnd=null, url=null, language=null, rfNumber=[34], rfOrder=34, authorNames=LI Z, ZHANG LS, SUN LN, WANG YQ, CHEN JZ, TANG HM, LIN L, LIN XM, journalName=Journal of Proteomics, refType=null, unstructuredReference=LI Z, ZHANG LS, SUN LN, WANG YQ, CHEN JZ, TANG HM, LIN L, LIN XM. Proteomics analysis reveals the importance of transcriptional regulator slyA in regulation of several physiological functions in Aeromonas hydrophila [J]. Journal of Proteomics, 2021, 244: 104275., articleTitle=Proteomics analysis reveals the importance of transcriptional regulator slyA in regulation of several physiological functions in Aeromonas hydrophila, refAbstract=null), Reference(id=1227681736667099548, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226554097206210577, doi=null, pmid=null, pmcid=null, year=2015, volume=null, issue=null, pageStart=119, pageEnd=134, url=null, language=null, rfNumber=[35], rfOrder=35, authorNames=WADE JT, journalName=Prokaryotic Systems Biology, refType=null, unstructuredReference=WADE JT. Mapping transcription regulatory networks with ChIP-seq and RNA-seq[M]//Prokaryotic Systems Biology. Cham: Springer International Publishing, 2015: 119-134., articleTitle=Mapping transcription regulatory networks with ChIP-seq and RNA-seq, refAbstract=null), Reference(id=1227681736776151458, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226554097206210577, doi=null, pmid=null, pmcid=null, year=2016, volume=12, issue=2, pageStart=null, pageEnd=null, url=null, language=null, rfNumber=[36], rfOrder=36, authorNames=LOBEL L, HERSKOVITS AA, journalName=PLoS Genetics, refType=null, unstructuredReference=LOBEL L, HERSKOVITS AA. Systems level analyses reveal multiple regulatory activities of CodY controlling metabolism, motility and virulence in Listeria monocytogenes [J]. PLoS Genetics, 2016, 12(2): e1005870., articleTitle=Systems level analyses reveal multiple regulatory activities of CodY controlling metabolism, motility and virulence in Listeria monocytogenes, refAbstract=null), Reference(id=1227681736897786284, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226554097206210577, doi=null, pmid=null, pmcid=null, year=2024, volume=12, issue=3, pageStart=null, pageEnd=null, url=null, language=null, rfNumber=[37], rfOrder=37, authorNames=GERGES E, RODRÍGUEZ-ORDOÑEZ MD, DURAND N, HERRMANN JL, CRÉMAZY F, journalName=Microbiology Spectrum, refType=null, unstructuredReference=GERGES E, RODRÍGUEZ-ORDOÑEZ MD, DURAND N, HERRMANN JL, CRÉMAZY F. Lsr2, a pleiotropic regulator at the core of the infectious strategy of Mycobacterium abscessus [J]. Microbiology Spectrum, 2024, 12(3): e0352823., articleTitle=Lsr2, a pleiotropic regulator at the core of the infectious strategy of Mycobacterium abscessus, refAbstract=null), Reference(id=1227681737015226803, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226554097206210577, doi=null, pmid=null, pmcid=null, year=2021, volume=113, issue=null, pageStart=12, pageEnd=25, url=null, language=null, rfNumber=[38], rfOrder=38, authorNames=BASSEY AP, YE KP, LI CB, ZHOU GH, journalName=Trends in Food Science & Technology, refType=null, unstructuredReference=BASSEY AP, YE KP, LI CB, ZHOU GH. Transcriptomic-proteomic integration: a powerful synergy to elucidate the mechanisms of meat spoilage in the cold chain[J]. Trends in Food Science & Technology, 2021, 113: 12-25., articleTitle=Transcriptomic-proteomic integration: a powerful synergy to elucidate the mechanisms of meat spoilage in the cold chain, refAbstract=null), Reference(id=1227681737141055928, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226554097206210577, doi=null, pmid=null, pmcid=null, year=2019, volume=10, issue=null, pageStart=94, pageEnd=null, url=null, language=null, rfNumber=[39], rfOrder=39, authorNames=LIU XX, XU J, ZHU JL, DU P, SUN AH, journalName=Frontiers in Microbiology, refType=null, unstructuredReference=LIU XX, XU J, ZHU JL, DU P, SUN AH. Combined transcriptome and proteome analysis of RpoS regulon reveals its role in spoilage potential of Pseudomonas fluorescens [J]. Frontiers in Microbiology, 2019, 10: 94., articleTitle=Combined transcriptome and proteome analysis of RpoS regulon reveals its role in spoilage potential of Pseudomonas fluorescens, refAbstract=null), Reference(id=1227681737237524929, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226554097206210577, doi=null, pmid=null, pmcid=null, year=2007, volume=2, issue=8, pageStart=1849, pageEnd=1861, url=null, language=null, rfNumber=[40], rfOrder=40, authorNames=HELLMAN LM, FRIED MG, journalName=Nature Protocols, refType=null, unstructuredReference=HELLMAN LM, FRIED MG. Electrophoretic mobility shift assay (EMSA) for detecting protein-nucleic acid interactions[J]. Nature Protocols, 2007, 2(8): 1849-1861., articleTitle=Electrophoretic mobility shift assay (EMSA) for detecting protein-nucleic acid interactions, refAbstract=null), Reference(id=1227681737346576837, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226554097206210577, doi=null, pmid=null, pmcid=null, year=2018, volume=30, issue=5, pageStart=585, pageEnd=592, url=null, language=null, rfNumber=[41], rfOrder=41, authorNames=孙宇航, 王宇祥, journalName=生命科学, refType=null, unstructuredReference=孙宇航, 王宇祥. DNA与蛋白质的相互作用及其生物学研究方法[J]. 生命科学, 2018, 30(5): 585-592., articleTitle=DNA与蛋白质的相互作用及其生物学研究方法, refAbstract=null), Reference(id=1227681737493377486, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226554097206210577, doi=null, pmid=null, pmcid=null, year=2018, volume=30, issue=5, pageStart=585, pageEnd=592, url=null, language=null, rfNumber=[41], rfOrder=42, authorNames=SUN YH, WANG YX, journalName=Chinese Bulletin of Life Sciences, refType=null, unstructuredReference=SUN YH, WANG YX. Interaction and biological research methods of DNA-protein[J]. Chinese Bulletin of Life Sciences, 2018, 30(5): 585-592 (in Chinese)., articleTitle=null, refAbstract=null), Reference(id=1227681738739085778, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226554097206210577, doi=null, pmid=null, pmcid=null, year=2020, volume=11, issue=null, pageStart=460, pageEnd=null, url=null, language=null, rfNumber=[42], rfOrder=43, authorNames=LI XF, REN FZ, CAI GQ, HUANG PY, CHAI QW, GUNDOGDU O, JIAO XN, HUANG JL, journalName=Frontiers in Microbiology, refType=null, unstructuredReference=LI XF, REN FZ, CAI GQ, HUANG PY, CHAI QW, GUNDOGDU O, JIAO XN, HUANG JL. Investigating the role of FlhF identifies novel interactions with genes involved in flagellar synthesis in Campylobacter jejuni [J]. Frontiers in Microbiology, 2020, 11: 460., articleTitle=Investigating the role of FlhF identifies novel interactions with genes involved in flagellar synthesis in Campylobacter jejuni, refAbstract=null), Reference(id=1227681738919440859, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226554097206210577, doi=null, pmid=null, pmcid=null, year=2023, volume=182, issue=null, pageStart=106263, pageEnd=null, url=null, language=null, rfNumber=[43], rfOrder=44, authorNames=XIAO JM, ZHANG YP, ZHANG JH, LIU BC, WANG HY, YANG R, YIN YB, ZHANG XM, journalName=Microbial Pathogenesis, refType=null, unstructuredReference=XIAO JM, ZHANG YP, ZHANG JH, LIU BC, WANG HY, YANG R, YIN YB, ZHANG XM. Identification of Cis-acting elements upstream of regR gene in Streptococcus pneumoniae [J]. Microbial Pathogenesis, 2023, 182: 106263., articleTitle=Identification of Cis-acting elements upstream of regR gene in Streptococcus pneumoniae, refAbstract=null), Reference(id=1227681739070435813, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226554097206210577, doi=null, pmid=null, pmcid=null, year=2015, volume=15, issue=14, pageStart=2794, pageEnd=2800, url=null, language=null, rfNumber=[44], rfOrder=45, authorNames=王秋岩, 何淑雅, 马云, 李俐娟, 李斌元, journalName=现代生物医学进展, refType=null, unstructuredReference=王秋岩, 何淑雅, 马云, 李俐娟, 李斌元. 启动子分析方法的研究进展[J]. 现代生物医学进展, 2015, 15(14): 2794-2800., articleTitle=启动子分析方法的研究进展, refAbstract=null), Reference(id=1227681739213042155, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226554097206210577, doi=null, pmid=null, pmcid=null, year=2015, volume=15, issue=14, pageStart=2794, pageEnd=2800, url=null, language=null, rfNumber=[44], rfOrder=46, authorNames=WANG QY, HE SY, MA Y, LI LJ, LI BY, journalName=Progress in Modern Biomedicine, refType=null, unstructuredReference=WANG QY, HE SY, MA Y, LI LJ, LI BY. Advances in analytical methods of promoter[J]. Progress in Modern Biomedicine, 2015, 15(14): 2794-2800 (in Chinese)., articleTitle=null, refAbstract=null), Reference(id=1227681739359842800, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226554097206210577, doi=null, pmid=null, pmcid=null, year=2009, volume=null, issue=null, pageStart=153, pageEnd=172, url=null, language=null, rfNumber=[45], rfOrder=47, authorNames=CARDEW AS, FOX KR, journalName=Drug-DNA Interaction Protocols, refType=null, unstructuredReference=CARDEW AS, FOX KR. DNase I footprinting[M]//Drug-DNA Interaction Protocols. Totowa, NJ: Humana Press, 2009: 153-172., articleTitle=DNase I footprinting, refAbstract=null), Reference(id=1227681739481477622, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226554097206210577, doi=null, pmid=null, pmcid=null, year=2015, volume=null, issue=null, pageStart=17, pageEnd=27, url=null, language=null, rfNumber=[46], rfOrder=48, authorNames=LEBLANC BP, MOSS T, journalName=DNA-Protein Interactions, refType=null, unstructuredReference=LEBLANC BP, MOSS T. In vitro DNase I footprinting[M]//DNA-Protein Interactions. New York, NY: Springer New York, 2015: 17-27., articleTitle=In vitro DNase I footprinting, refAbstract=null), Reference(id=1227681739590529530, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226554097206210577, doi=null, pmid=null, pmcid=null, year=2020, volume=8, issue=8, pageStart=1161, pageEnd=null, url=null, language=null, rfNumber=[47], rfOrder=49, authorNames=PALOMBO M, SCARLATO V, RONCARATI D, journalName=Microorganisms, refType=null, unstructuredReference=PALOMBO M, SCARLATO V, RONCARATI D. Cooperative regulation of Campylobacter jejuni heat-shock genes by HspR and HrcA[J]. Microorganisms, 2020, 8(8): 1161., articleTitle=Cooperative regulation of Campylobacter jejuni heat-shock genes by HspR and HrcA, refAbstract=null), Reference(id=1227681739707970052, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226554097206210577, doi=null, pmid=null, pmcid=null, year=2021, volume=203, issue=15, pageStart=null, pageEnd=null, url=null, language=null, rfNumber=[48], rfOrder=50, authorNames=KELLEY BR, CALLAHAN SM, JOHNSON JG, journalName=Journal of Bacteriology, refType=null, unstructuredReference=KELLEY BR, CALLAHAN SM, JOHNSON JG. Transcription of cystathionine β-lyase (MetC) is repressed by HeuR in Campylobacter jejuni, and methionine biosynthesis facilitates colonocyte invasion[J]. Journal of Bacteriology, 2021, 203(15): e0016421., articleTitle=Transcription of cystathionine β-lyase (MetC) is repressed by HeuR in Campylobacter jejuni, and methionine biosynthesis facilitates colonocyte invasion, refAbstract=null), Reference(id=1227681739867353608, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226554097206210577, doi=null, pmid=null, pmcid=null, year=2021, volume=9, issue=6, pageStart=1281, pageEnd=null, url=null, language=null, rfNumber=[49], rfOrder=51, authorNames=PARK M, HWANG S, RYU S, JEON B, journalName=Microorganisms, refType=null, unstructuredReference=PARK M, HWANG S, RYU S, JEON B. CosR regulation of perR transcription for the control of oxidative stress defense in Campylobacter jejuni [J]. Microorganisms, 2021, 9(6): 1281., articleTitle=CosR regulation of perR transcription for the control of oxidative stress defense in Campylobacter jejuni, refAbstract=null), Reference(id=1227681739972211212, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226554097206210577, doi=null, pmid=null, pmcid=null, year=2007, volume=null, issue=null, pageStart=140, pageEnd=158, url=null, language=null, rfNumber=[50], rfOrder=52, authorNames=HUGHES KT, MALOY SR, journalName=Advanced Bacterial Genetics: Use of Transposons and Phage for Genomic Engineering, refType=null, unstructuredReference=HUGHES KT, MALOY SR. Use of operon and gene fusions to study gene regulation in Salmonella [M]//Advanced Bacterial Genetics: Use of Transposons and Phage for Genomic Engineering. Amsterdam: Elsevier, 2007: 140-158., articleTitle=Use of operon and gene fusions to study gene regulation in Salmonella, refAbstract=null), Reference(id=1227681740093846034, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226554097206210577, doi=null, pmid=null, pmcid=null, year=2022, volume=10, issue=6, pageStart=null, pageEnd=null, url=null, language=null, rfNumber=[51], rfOrder=53, authorNames=LONG X, WANG XL, MAO DQ, WU WH, LUO Y, journalName=Microbiology Spectrum, refType=null, unstructuredReference=LONG X, WANG XL, MAO DQ, WU WH, LUO Y. A novel XRE-type regulator mediates phage lytic development and multiple host metabolic processes in Pseudomonas aeruginosa [J]. Microbiology Spectrum, 2022, 10(6): e0351122., articleTitle=A novel XRE-type regulator mediates phage lytic development and multiple host metabolic processes in Pseudomonas aeruginosa, refAbstract=null), Reference(id=1227681740177732118, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226554097206210577, doi=null, pmid=null, pmcid=null, year=2024, volume=70, issue=4, pageStart=128, pageEnd=134, url=null, language=null, rfNumber=[52], rfOrder=54, authorNames=LI X, LIAN W, ZHANG MM, LUO X, ZHANG YQ, LU RF, journalName=Canadian Journal of Microbiology, refType=null, unstructuredReference=LI X, LIAN W, ZHANG MM, LUO X, ZHANG YQ, LU RF. QsvR and OpaR coordinately regulate the transcription of cpsS and cpsR in Vibrio parahaemolyticus [J]. Canadian Journal of Microbiology, 2024, 70(4): 128-134., articleTitle=QsvR and OpaR coordinately regulate the transcription of cpsS and cpsR in Vibrio parahaemolyticus, refAbstract=null), Reference(id=1227681740249035294, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226554097206210577, doi=null, pmid=null, pmcid=null, year=2018, volume=2018, issue=5, pageStart=10.1101/pdb.prot082628, pageEnd=null, url=null, language=null, rfNumber=[53], rfOrder=55, authorNames=KIM TH, DEKKER J, journalName=Cold Spring Harbor Protocols, refType=null, unstructuredReference=KIM TH, DEKKER J. ChIP-quantitative polymerase chain reaction (ChIP-qPCR)[J]. Cold Spring Harbor Protocols, 2018, 2018(5): 10.1101/pdb.prot082628., articleTitle=ChIP-quantitative polymerase chain reaction (ChIP-qPCR), refAbstract=null), Reference(id=1227681740324532772, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226554097206210577, doi=null, pmid=null, pmcid=null, year=2024, volume=null, issue=null, pageStart=55, pageEnd=75, url=null, language=null, rfNumber=[54], rfOrder=56, authorNames=GE PZ, RASHID FM, CRÉMAZY FGE, DAME RT, journalName=Bacterial Chromatin, refType=null, unstructuredReference=GE PZ, RASHID FM, CRÉMAZY FGE, DAME RT. ChIP-qPCR of FLAG-tagged proteins in bacteria[M]//Bacterial Chromatin. New York, NY: Springer US, 2024: 55-75., articleTitle=ChIP-qPCR of FLAG-tagged proteins in bacteria, refAbstract=null), Reference(id=1227681740425196069, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226554097206210577, doi=null, pmid=null, pmcid=null, year=2019, volume=47, issue=D1, pageStart=D46, pageEnd=D49, url=null, language=null, rfNumber=[55], rfOrder=57, authorNames=KURTENBACH S, REDDY R, WILLIAM HARBOUR J, journalName=Nucleic Acids Research, refType=null, unstructuredReference=KURTENBACH S, REDDY R, WILLIAM HARBOUR J. ChIPprimersDB: a public repository of verified qPCR primers for chromatin immunoprecipitation (ChIP)[J]. Nucleic Acids Research, 2019, 47(D1): D46-D49., articleTitle=ChIPprimersDB: a public repository of verified qPCR primers for chromatin immunoprecipitation (ChIP), refAbstract=null), Reference(id=1227681740551025196, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226554097206210577, doi=null, pmid=null, pmcid=null, year=2019, volume=85, issue=4, pageStart=null, pageEnd=null, url=null, language=null, rfNumber=[56], rfOrder=58, authorNames=LIU M, ZHANG PP, ZHU YP, LU T, WANG YM, CAO GX, SHI M, CHEN XL, TAO MF, PANG XH, journalName=Applied and Environmental Microbiology, refType=null, unstructuredReference=LIU M, ZHANG PP, ZHU YP, LU T, WANG YM, CAO GX, SHI M, CHEN XL, TAO MF, PANG XH. Novel two-component system MacRS is a pleiotropic regulator that controls multiple morphogenic membrane protein genes in Streptomyces coelicolor [J]. Applied and Environmental Microbiology, 2019, 85(4): e02178-18., articleTitle=Novel two-component system MacRS is a pleiotropic regulator that controls multiple morphogenic membrane protein genes in Streptomyces coelicolor, refAbstract=null), Reference(id=1227681740685242931, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226554097206210577, doi=null, pmid=null, pmcid=null, year=2023, volume=14, issue=null, pageStart=1191209, pageEnd=null, url=null, language=null, rfNumber=[57], rfOrder=59, authorNames=ZHANG LS, SUN LN, SRINIVASAN R, LIN MZ, GONG LQ, LIN XM, journalName=Frontiers in Immunology, refType=null, unstructuredReference=ZHANG LS, SUN LN, SRINIVASAN R, LIN MZ, GONG LQ, LIN XM. Unveiling a virulence-regulating mechanism in Aeromonas hydrophila: a quantitative exoproteomic analysis of an AraC-like protein[J]. Frontiers in Immunology, 2023, 14: 1191209., articleTitle=Unveiling a virulence-regulating mechanism in Aeromonas hydrophila: a quantitative exoproteomic analysis of an AraC-like protein, refAbstract=null)], funds=[Fund(id=1227681726730792990, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226554097206210577, awardId=32473117, language=EN, fundingSource=National Natural Science Foundation of China(32473117), fundOrder=null, country=null), Fund(id=1227681726902759466, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226554097206210577, awardId=32473117, language=CN, fundingSource=国家自然科学基金(32473117), fundOrder=null, country=null), Fund(id=1227681727066337338, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226554097206210577, awardId=32172939, language=CN, fundingSource=国家自然科学基金(32172939), fundOrder=null, country=null), Fund(id=1227681727179583557, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226554097206210577, awardId=2024YFC2310300, language=EN, fundingSource=National Key Research and Development Program of China(2024YFC2310300), fundOrder=null, country=null), Fund(id=1227681727313801296, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226554097206210577, awardId=2024YFC2310300, language=CN, fundingSource=国家重点研发计划(2024YFC2310300), fundOrder=null, country=null)], companyList=[AuthorCompany(id=1227681717754983008, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226554097206210577, xref=1., ext=[AuthorCompanyExt(id=1227681717771760227, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226554097206210577, companyId=1227681717754983008, language=EN, country=null, province=null, city=null, postcode=null, companyName=null, departmentName=null, remark=1.Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, Jiangsu, China), AuthorCompanyExt(id=1227681717780148837, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226554097206210577, companyId=1227681717754983008, language=CN, country=null, province=null, city=null, postcode=null, companyName=null, departmentName=null, remark=1.扬州大学,江苏省人兽共患病学重点实验室,江苏 扬州)]), AuthorCompany(id=1227681717876617836, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226554097206210577, xref=2., ext=[AuthorCompanyExt(id=1227681717885006446, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226554097206210577, companyId=1227681717876617836, language=EN, country=null, province=null, city=null, postcode=null, companyName=null, departmentName=null, remark=2.Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, Jiangsu, China), AuthorCompanyExt(id=1227681717893395056, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226554097206210577, companyId=1227681717876617836, language=CN, country=null, province=null, city=null, postcode=null, companyName=null, departmentName=null, remark=2.江苏高校动物重要疫病与人兽共患病防控协同创新中心,江苏 扬州)]), AuthorCompany(id=1227681717998252663, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226554097206210577, xref=3., ext=[AuthorCompanyExt(id=1227681718006641272, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226554097206210577, companyId=1227681717998252663, language=EN, country=null, province=null, city=null, postcode=null, companyName=null, departmentName=null, remark=3.Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture and Rural Affairs, Yangzhou, Jiangsu, China), AuthorCompanyExt(id=1227681718015029882, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226554097206210577, companyId=1227681717998252663, language=CN, country=null, province=null, city=null, postcode=null, companyName=null, departmentName=null, remark=3.农业农村部农产品质量安全生物性危害因子(动物源)控制重点实验室,江苏 扬州)]), AuthorCompany(id=1227681718186996362, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226554097206210577, xref=4., ext=[AuthorCompanyExt(id=1227681718199579275, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226554097206210577, companyId=1227681718186996362, language=EN, country=null, province=null, city=null, postcode=null, companyName=null, departmentName=null, remark=4.Joint International Research Laboratory of Agriculture and Agri-product Safety, Ministry of Education, Yangzhou, Jiangsu, China), AuthorCompanyExt(id=1227681718245716621, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226554097206210577, companyId=1227681718186996362, language=CN, country=null, province=null, city=null, postcode=null, companyName=null, departmentName=null, remark=4.教育部农业与农产品安全国际合作联合实验室,江苏 扬州)])], figs=[ArticleFig(id=1227681723245327351, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226554097206210577, language=EN, label=Figure 1, caption=Schematic flowchart of researching the regulatory functions of bacterial transcription factors., figureFileSmall=/LpMJP9GZh2kf7EzPUB6cA==, figureFileBig=7mObb23vDaLH9iTMDahAGA==, tableContent=null), ArticleFig(id=1227681723354378243, tenantId=1146029695717560320, journalId=1192105938417971205, articleId=1226554097206210577, language=CN, label=图1, caption=研究细菌转录因子调控功能流程图, figureFileSmall=/LpMJP9GZh2kf7EzPUB6cA==, figureFileBig=7mObb23vDaLH9iTMDahAGA==, tableContent=null)], attaches=null, journal=Journal(id=1192105720683257860, delFlag=0, nameCn=微生物学报, nameEn=Acta Microbiologica Sinica, nameHistory1=null, nameHistory2=null, issn=0001-6209, eissn=null, cn=11-1995/Q, coden=null, periodic=0, language=CN, oaType=null, ccby=null, superviseOffice=null, ownerOffice=null, pubOffice=null, editorOffice=null, officeType=null, aims=null, clcCode=null, officeProv=null, officeCity=null, officeAddr=null, officeZip=null, officeEmail=null, officePhone=null, editDirector=null, officeDirector=null, officeDirectorPhone=null, officeStaffNum=null, officeEmpNum=null, coverPicUrl=tNA7JigLZj/rxynSmzKgDQ==, journalPrice=null, startedYear=null, abbrevIsoEn=null, journalRemark=null, publicationField=null, createdTime=1762149752067, updatedTime=1762150746905, createdBy=18614031015, updatedBy=13701087609, firstLetterCn=A, firstLetterEn=A, subjectCode=Life Sciences, subjectName=Life Sciences, subjectCodeEn=Life Sciences, subjectNameEn=null, picCn=tNA7JigLZj/rxynSmzKgDQ==, picEn=R/d5eSUu8/o5mAGWCF3M5Q==, jcr=null, cjcr=null, exts=[JournalExt(id=1192109893441171829, language=CN, name=微生物学报, nameHistory1=null, nameHistory2=null, managedBy=, sponsoredBy=, publishedBy=, editorOffice=, officeProv=null, officeCity=null, officeAddr=, officeZip=, editDirector=, officeDirector=null, officePhone=null, coverPicUrl=null, journalRemark=, submitArticleUrl=null, websiteUrl=, createdTime=1762150746928, updatedTime=1762150746928, createdBy=13701087609, updatedBy=13701087609, submissionGuidelinesUrl=, submissionAuthorUrl=https://actamicro.ijournals.cn/actamicrocn/author/login, submissionEditorUrl=https://actamicro.ijournals.cn/actamicrocn/editor/login, submissionReviewUrl=https://actamicro.ijournals.cn/actamicrocn/reviewer/login, submissionCeEditorUrl=, submissionAeEditorUrl=, option={"copyright":""}), JournalExt(id=1192109893512474998, language=EN, name=Acta Microbiologica Sinica, nameHistory1=null, nameHistory2=null, managedBy=, sponsoredBy=, publishedBy=, editorOffice=, officeProv=null, officeCity=null, officeAddr=, officeZip=, editDirector=, officeDirector=null, officePhone=null, coverPicUrl=null, journalRemark=, submitArticleUrl=null, websiteUrl=, createdTime=1762150746944, updatedTime=1762150746944, createdBy=13701087609, updatedBy=13701087609, submissionGuidelinesUrl=, submissionAuthorUrl=https://actamicro.ijournals.cn/actamicrocn/author/login, submissionEditorUrl=https://actamicro.ijournals.cn/actamicrocn/editor/login, submissionReviewUrl=https://actamicro.ijournals.cn/actamicrocn/reviewer/login, submissionCeEditorUrl=, submissionAeEditorUrl=, option={"copyright":""})], databaseList=null, tenantJournalId=1192105938417971205, websiteList=[Website(id=1192106105867223981, webName=null, webTitle=null, webDomain=null, webCopyrigh=null, webIpcNo=null, seoTitle=null, seoKeywords=null, seoDescription=null, tenantJournalId=null, journalId=1192105938417971205, journalNameCn=null, journalNameEn=null, grayFlag=null, tenantId=1146029695717560320, platformId=null, journalGroupId=null, journalGroupNameCn=null, journalGroupNameEn=null, type=1, domain=https://castjournals.cast.org.cn/joweb/wswxb/CN, language=CN, createTime=1762149843899, createBy=18614031015, updateTime=1762149888800, updateBy=18614031015, name=微生物学报-中文, tplId=1146099689490845704, title=微生物学报, delFlag=0, indexPage=/home, props=[WebsiteProps(id=1192107120863626198, tenantId=1146029695717560320, journalId=null, journalGroupId=null, siteId=1192106105867223981, code=articleTextType, value=kx, createTime=1762150085893, updateTime=1762150085893, creator=18614031015, updator=18614031015), WebsiteProps(id=1192107120834266067, tenantId=1146029695717560320, journalId=null, journalGroupId=null, siteId=1192106105867223981, code=banner, value=null, createTime=1762150085886, updateTime=1762150085886, creator=18614031015, updator=18614031015), WebsiteProps(id=1192107120892986329, tenantId=1146029695717560320, journalId=null, journalGroupId=null, siteId=1192106105867223981, code=grayFlag, value=0, createTime=1762150085900, updateTime=1762150085900, creator=18614031015, updator=18614031015), WebsiteProps(id=1192107120825877458, tenantId=1146029695717560320, journalId=null, journalGroupId=null, siteId=1192106105867223981, code=logo, value=https://castjournals.cast.org.cn/joweb/wswxb/CN/file/pic?fileId=FOz4Ks7dC79FYnCEBIlMdw==, createTime=1762150085884, updateTime=1762150085884, creator=18614031015, updator=18614031015), WebsiteProps(id=1192107120905569243, tenantId=1146029695717560320, journalId=null, journalGroupId=null, siteId=1192106105867223981, code=minRunFlag, value=0, createTime=1762150085903, updateTime=1762150085903, creator=18614031015, updator=18614031015), WebsiteProps(id=1192107120846848981, tenantId=1146029695717560320, journalId=null, journalGroupId=null, siteId=1192106105867223981, code=picServerUrl, value=https://castjournals.cast.org.cn/joweb/wswxb/CN/file/pic, createTime=1762150085889, updateTime=1762150085889, creator=18614031015, updator=18614031015), WebsiteProps(id=1192107120897180634, tenantId=1146029695717560320, journalId=null, journalGroupId=null, siteId=1192106105867223981, code=silenceFlag, value=0, createTime=1762150085901, updateTime=1762150085901, creator=18614031015, updator=18614031015), WebsiteProps(id=1192107120842654676, tenantId=1146029695717560320, journalId=null, journalGroupId=null, siteId=1192106105867223981, code=staticResourcePath, value=https://castjournals.cast.org.cn/joweb/cast_kjdb_cn_619/, createTime=1762150085888, updateTime=1762150085888, creator=18614031015, updator=18614031015), WebsiteProps(id=1192107120872014807, tenantId=1146029695717560320, journalId=null, journalGroupId=null, siteId=1192106105867223981, code=themeColor, value=null, createTime=1762150085895, updateTime=1762150085895, creator=18614031015, updator=18614031015), WebsiteProps(id=1192107120880403416, tenantId=1146029695717560320, journalId=null, journalGroupId=null, siteId=1192106105867223981, code=themeStyle, value=null, createTime=1762150085897, updateTime=1762150085897, creator=18614031015, updator=18614031015)]), Website(id=1192106106018218929, webName=null, webTitle=null, webDomain=null, webCopyrigh=null, webIpcNo=null, seoTitle=null, seoKeywords=null, seoDescription=null, tenantJournalId=null, journalId=1192105938417971205, journalNameCn=null, journalNameEn=null, grayFlag=null, tenantId=1146029695717560320, platformId=null, journalGroupId=null, journalGroupNameCn=null, journalGroupNameEn=null, type=1, domain=https://castjournals.cast.org.cn/joweb/wswxb/EN, language=EN, createTime=1762149843935, createBy=18614031015, updateTime=1762149925242, updateBy=18614031015, name=微生物学报-英文, tplId=1146101810881728533, title=Acta Microbiologica Sinica, delFlag=0, indexPage=/home, props=[WebsiteProps(id=1192107140455220192, tenantId=1146029695717560320, journalId=null, journalGroupId=null, siteId=1192106106018218929, code=articleTextType, value=kx, createTime=1762150090564, updateTime=1762150090564, creator=18614031015, updator=18614031015), WebsiteProps(id=1192107140434248669, tenantId=1146029695717560320, journalId=null, journalGroupId=null, siteId=1192106106018218929, code=banner, value=null, createTime=1762150090559, updateTime=1762150090559, creator=18614031015, updator=18614031015), WebsiteProps(id=1192107140476191715, tenantId=1146029695717560320, journalId=null, journalGroupId=null, siteId=1192106106018218929, code=grayFlag, value=0, createTime=1762150090569, updateTime=1762150090569, creator=18614031015, updator=18614031015), WebsiteProps(id=1192107140425860060, tenantId=1146029695717560320, journalId=null, journalGroupId=null, siteId=1192106106018218929, code=logo, value=https://castjournals.cast.org.cn/joweb/wswxb/EN/file/pic?fileId=FOz4Ks7dC79FYnCEBIlMdw==, createTime=1762150090557, updateTime=1762150090557, creator=18614031015, updator=18614031015), WebsiteProps(id=1192107140484580325, tenantId=1146029695717560320, journalId=null, journalGroupId=null, siteId=1192106106018218929, code=minRunFlag, value=0, createTime=1762150090571, updateTime=1762150090571, creator=18614031015, updator=18614031015), WebsiteProps(id=1192107140451025887, tenantId=1146029695717560320, journalId=null, journalGroupId=null, siteId=1192106106018218929, code=picServerUrl, value=https://castjournals.cast.org.cn/joweb/wswxb/EN/file/pic, createTime=1762150090563, updateTime=1762150090563, creator=18614031015, updator=18614031015), WebsiteProps(id=1192107140480386020, tenantId=1146029695717560320, journalId=null, journalGroupId=null, siteId=1192106106018218929, code=silenceFlag, value=0, createTime=1762150090570, updateTime=1762150090570, creator=18614031015, updator=18614031015), WebsiteProps(id=1192107140442637278, tenantId=1146029695717560320, journalId=null, journalGroupId=null, siteId=1192106106018218929, code=staticResourcePath, value=https://castjournals.cast.org.cn/joweb/cast_kjdb_en_623/, createTime=1762150090561, updateTime=1762150090561, creator=18614031015, updator=18614031015), WebsiteProps(id=1192107140463608801, tenantId=1146029695717560320, journalId=null, journalGroupId=null, siteId=1192106106018218929, code=themeColor, value=null, createTime=1762150090566, updateTime=1762150090566, creator=18614031015, updator=18614031015), WebsiteProps(id=1192107140467803106, tenantId=1146029695717560320, journalId=null, journalGroupId=null, siteId=1192106106018218929, code=themeStyle, value=null, createTime=1762150090567, updateTime=1762150090567, creator=18614031015, updator=18614031015)])], journalTitle=微生物学报, weixinUrl=null, journalUrl=https://actamicro.ijournals.cn, iacademicId=null, status=1, seqNo=null, journalTitleEn=Acta Microbiologica Sinica, journalPhotoCn=tNA7JigLZj/rxynSmzKgDQ==, journalPhotoEn=R/d5eSUu8/o5mAGWCF3M5Q==, journalFirstLetter=A, journalRecommend=null, journalNew=null, journalCollection=null, jcrJf=null, cjcrJf=null, jcrJfStr=null, cjcrJfStr=null, submissionFirstDecision=null, sciSubjectClassification=null, casSubjectClassification=null, citeScore=null, totalCitationFrequency=null, icpCode=null, psCode=null, advertisingLicenseCode=null, copyrightInformation=null, country=null, option=, provinceCode=null, provinceName=null, collectFlag=false), detailUrlCn=https://castjournals.cast.org.cn/joweb/wswxb/CN/10.13343/j.cnki.wsxb.20250019, detailUrlEn=https://castjournals.cast.org.cn/joweb/wswxb/EN/10.13343/j.cnki.wsxb.20250019, pdfUrlCn=https://castjournals.cast.org.cn/joweb/wswxb/CN/PDF/10.13343/j.cnki.wsxb.20250019, pdfUrlEn=https://castjournals.cast.org.cn/joweb/wswxb/EN/PDF/10.13343/j.cnki.wsxb.20250019, aliStartDate=null, aliEndDate=null, collectionFlag=false, citedCount=null, citedUrl=null, reference=null)
收藏切换
细菌转录因子调控功能的研究策略
收藏切换
PDF下载
陈玲莉 1 , 李晓飞 2 , 刘莹 1 , 任方哲 2 , 焦新安 3 , 黄金林 1, 2, 3, 4
微生物学报 | 综述 2025,65(7): 2864-2873
收起
收藏切换
微生物学报 | 综述 2025, 65(7): 2864-2873
细菌转录因子调控功能的研究策略
全屏
陈玲莉1, 李晓飞2, 刘莹1, 任方哲2, 焦新安3, 黄金林1, 2, 3, 4
作者信息
  • 1.扬州大学,江苏省人兽共患病学重点实验室,江苏 扬州
  • 2.江苏高校动物重要疫病与人兽共患病防控协同创新中心,江苏 扬州
  • 3.农业农村部农产品质量安全生物性危害因子(动物源)控制重点实验室,江苏 扬州
  • 4.教育部农业与农产品安全国际合作联合实验室,江苏 扬州
Research strategies for the regulatory functions of bacterial transcription factors
Lingli CHEN1, Xiaofei LI2, Ying LIU1, Fangzhe REN2, Xin’an JIAO3, Jinlin HUANG1, 2, 3, 4
Affiliations
  • 1.Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, Jiangsu, China
  • 2.Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, Jiangsu, China
  • 3.Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture and Rural Affairs, Yangzhou, Jiangsu, China
  • 4.Joint International Research Laboratory of Agriculture and Agri-product Safety, Ministry of Education, Yangzhou, Jiangsu, China
出版时间: 2025-07-04 doi: 10.13343/j.cnki.wsxb.20250019
文章导航
收藏切换

转录因子对细菌的生存至关重要,其功能解析有助于推动抗菌药物研发、工业应用以及环境保护等多个领域的发展。目前,转录因子的研究方法与策略种类繁多,在生物信息学和分子生物学等领域均取得了迅速发展。本文从未知转录因子的鉴定方法、转录因子调控功能的鉴定方法、转录因子调控网络的构建方法以及转录因子调控基因的验证方法等4个方面进行综述,为细菌转录因子调控功能的分析与验证提供了新策略与新思路。

细菌  /  转录因子  /  调控  /  生物信息学

Transcription factors are essential for the survival of bacteria, and revealing their functions is conducive to the development of antimicrobials, industrial applications, and environmental protection. At present, there are many methods and strategies for the research on transcription factors, which have been developed rapidly in the fields of bioinformatics and molecular biology. This paper summarizes the methods for identifying unknown transcription factors, unveiling the regulatory functions of transcription factors, constructing regulatory networks of transcription factors, and validating the regulatory genes of transcription factors. This review aims to provide new strategies and new ideas for the analysis and verification of the regulatory functions of bacterial transcription factors.

bacteria  /  transcription factors  /  regulation  /  bioinformatics
陈玲莉, 李晓飞, 刘莹, 任方哲, 焦新安, 黄金林. 细菌转录因子调控功能的研究策略. 微生物学报, 2025 , 65 (7) : 2864 -2873 . DOI: 10.13343/j.cnki.wsxb.20250019
Lingli CHEN, Xiaofei LI, Ying LIU, Fangzhe REN, Xin’an JIAO, Jinlin HUANG. Research strategies for the regulatory functions of bacterial transcription factors[J]. Acta Microbiologica Sinica, 2025 , 65 (7) : 2864 -2873 . DOI: 10.13343/j.cnki.wsxb.20250019
细菌在面对不同的环境刺激时会调控相关靶基因的表达,从而使体内代谢过程适应环境刺激。每种细菌中都含有多种转录因子,而细菌转录调控是其确保自身繁殖与生存的主要机制之一[1-2]。根据调控范围的不同,转录因子可分为全局转录因子(global transcription factor)和局部转录因子(local transcription factor)[3]。目前,关于转录因子调控机制的探索已经取得了较为深入的进展,细菌转录因子的研究已成为热点领域[4-5]。本文基于研究现状,综合阐述了细菌转录因子调控功能的研究策略,以期为细菌转录因子的研究提供思路(图1)。
基因组序列信息的完善和生物信息学技术的快速发展使生物信息学工具成为挖掘未知转录因子的重要方法,高效识别转录因子对研究其调控功能至关重要[6]
序列比对是生物信息学中最常用的基本技术之一,已成为对细菌中潜在的转录因子进行分类和预测的绝佳工具。蛋白质家族(protein family analysis and modeling, PFAM)数据库(http://pfam.xfam.org/)是一个汇总并归类蛋白质家族的生物信息学数据库,用于分类和分析蛋白质家族的结构和功能;该数据库使用隐马尔可夫模型对蛋白质家族的序列进行建模,并利用序列比对方法预测目标序列的蛋白质家族分类;除此之外,PFAM数据库可与其他生物信息学数据库,如UniProt数据库(https://www.uniprot.org/)、InterPro数据库(https://www.ebi.ac.uk/interpro/)、PDB数据库(https://www.rcsb.org/)等进行数据整合,以便进一步了解蛋白质家族的背景和应用[7]。PFAM数据库中收录了一些全局转录因子蛋白家族的信息,例如GntR家族蛋白、FIS家族蛋白等,可以通过该数据库查询未知转录因子的家族分类及PFAM数据库注释、结构域等信息,初步了解其是否可能为全局转录因子。PFAM数据库因物种覆盖广、定期更新、信息全面等优点广泛运用于转录因子的挖掘与鉴定[7]
首先从NCBI数据库(https://www.ncbi.nlm.nih.gov/)中获得原核生物基因组,从DBD数据库(http://www.transcriptionfactor.org)、RegulonDB数据库(https://regulondb.ccg.unam.mx)、DBTBS数据库(http://dbtbs.hgc.jp)等转录调控数据库中获取具有实验证据的转录因子数据集[8-10]。然后使用Proteinortho程序(http://www.bioinf.uni-leipzig.de/Software/proteinortho/)与转录因子数据集进行序列比较,识别与鉴别转录因子同源蛋白[11]。同时,使用PFAM数据库中人工整理的与DNA结合相关的模型扫描基因组序列,检索与基因调控有关的蛋白质[6]。2020年,Flores-Bautista等[12]利用PFAM数据库分析等方法确定细菌和古细菌中的转录因子库。
转录因子中的DNA结合结构域主要包括螺旋-转角-螺旋、锌指结构、碱性-亮氨酸拉链等类型,约80%的转录因子包含螺旋-转角-螺旋结构域,这些特征已被用于预测转录因子[12]。识别螺旋-转角-螺旋结构的经典程序是Dodd-Egan程序,同时可以配合局部序列比对检索基本工具(basic local alignment search tool, BLAST),以排除与基因调控功能无关的蛋白质[13]。2015年,Reuter等[14]运用基因组序列分析和结构域分析,在空肠弯曲杆菌(Campylobacter jejuni)中发现保守的Per-Arnt-Sim (PAS)结构域,进一步分析表明菌体包含具有螺旋-转角-螺旋结构域的转录因子,并对其功能进行研究。可以利用BLASTp工具(https://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastp&PAGE_TYPE=BlastSearch&LINK_LOC=blasthome)搜索同源蛋白,进一步通过InterPro数据库和MotifFinder工具(https://www.genome.jp/tools/motif/)分析未知转录因子的蛋白家族;2022年,Li等[15]通过BLASTp、InterPro数据库和MotifFinder工具分析发现副溶血弧菌(Vibrio parahaemolyticus)中HutC属于GntR全局转录因子蛋白家族,并研究了其调控功能。此外,还可以通过构建系统发育树的方法研究局部转录因子。2024年,Abd-El-Haleem[16]通过构建系统发育树等方法鉴定了局部转录因子AraC的同源基因,并研究了其功能。
转录因子种类繁多,对于与已知转录因子不具有同源性的未知转录因子,预测难度较大。DeepTFactor (https://bitbucket.org/kaistsystemsbio logy/deeptfactor)是基于深度学习模型的转录因子预测工具,它采用具有3个并行子网络的卷积神经网络(convolutional neural network, CNN)[17]。与其他转录因子预测工具相比,DeepTFactor工具表现出更高的预测性能,面对以前未见过的序列数据,深度学习模型表现更好,而且预测转录因子的速度也更快[17]
细菌转录因子的功能复杂多样,涵盖了多种生物学过程,对生物体的生存至关重要。转录因子的功能不仅与转录因子本身有关,还与相邻基因编码的蛋白相关[12]。因此,可以对转录因子进行体内失活和过表达,通过表型变化或生理生化特性改变的分析,直观地了解该转录因子可能的调控功能。同时,通过对相邻基因编码的蛋白功能分析,推测该转录因子可能的功能,为后续解析调控网络奠定基础。
通过观察缺失转录因子后的生物学表型和生理变化,能够深入探索该转录因子的功能,并进一步揭示转录调控作用。全局转录因子和局部转录因子皆可用此方法探究其调控功能。在细菌中,常用的基因敲除技术有Red同源重组技术、自杀质粒载体敲除技术和CRISPR/Cas9技术[18]。这3种方法均通过非同源末端或同源末端修复机制诱导DNA双链断裂来替代靶基因[18]。通过将含有高效调控表达元件和目的转录因子的载体转入缺失株中,可以实现转录因子在体内的过表达。观察转录因子缺失株和过表达菌株的生物学表型变化,并分析两者之间的内在关系,可以推测该转录因子在体内发挥的功能与作用。2022年,Zhao等[19]通过基因敲除等技术观察丁香假单胞菌(Pseudomonas syringae) OmpR-like转录因子缺失株和过表达菌株的生物学表型,探究了其生物学功能和转录调控机制。
在细菌的进化过程中,具有相似功能的基因会在基因组上趋向于共同定位并协同工作,从而增强细菌应对环境变化的能力。编码转录因子的基因和靶基因通常以相反的方向转录,例如LysR家族[20]。2020年,Flores-Bautista等[12]通过PFAM数据库的功能注释,对转录因子编码基因的相邻基因功能进行评估,发现MarR家族成员与对药物、压力和非生物刺激反应的相关基因相邻,这一发现支持了MarR家族在适应性和抗药性方面的作用;同时,通过蛋白质序列比较和毒力因子数据库分析发现,包含高比例毒力蛋白的OmpR家族和FIS家族的相邻基因也与毒力相关。
高通量测序技术被广泛应用于转录因子调控功能的研究,其中染色质免疫沉淀测序(chromatin immunoprecipitation sequencing, ChIP-seq)技术和转录组测序(RNA sequencing, RNA-seq)技术深受研究者的青睐。ChIP-seq和RNA-seq均基于下一代测序(next generation sequencing, NGS)技术,通过结合RNA-seq数据与ChIP-seq数据可以高效识别转录因子与其候选基因的结合位点,从而构建复杂的调控网络[21-22]。近年来,蛋白组学技术,如质谱技术(mass spectrometry, MS)也被运用于细菌转录因子的研究。
转录组是指细胞中所有由基因转录产生的RNA的总和,其相对丰度反映了在特定发育阶段或生理条件下相应基因的表达水平[21]。由于具有高通量、高灵敏度和广泛的检测范围等优势,该技术已成为研究生物分子机制的重要工具,尤其在批量筛选与挖掘功能基因方面发挥着独特的优势[23]。可以通过火山图、散点图、热图、维恩图和主成分分析(principal component analysis, PCA)图来可视化差异表达基因的结果,并利用基因本体论(gene ontology, GO)分析和京都基因与基因组百科全书(Kyoto encyclopedia of genes and genomes, KEGG)分析,挖掘差异基因富集的信号通路,进而揭示潜在的调控网络。2020年,Wang等[24]通过RNA-seq分析揭示了全局转录因子GntR家族MpaR的调控功能,完善了转录因子MpaR的调控网络。2023年,Sun等[25]通过RNA-seq分析揭示了类鼻疽伯克霍尔德氏菌(Burkholderia pseudomallei)转录因子SapR对Sap1的调控作用,完善了SapR的调控网络。
ChIP-seq是一种在全基因组范围内分析DNA结合蛋白、组蛋白修饰或核小体的技术[26]。染色质免疫沉淀(chromatin immunoprecipitation, ChIP)法用于富集与特定蛋白质或核小体结合的DNA片段,通过与下一代测序结合,可以将ChIP捕获的DNA片段进行高效的可视化分析[26]。可以使用DAVID数据库(http://david.abcc.ncifcrf.gov/)对基因组进行注释,将ChIP-seq实验获得的峰位与已知的基因组注释信息进行比较,然后利用GO分析和KEGG分析,之后使用STRING在线工具(https://cn.string-db.org/)和Cytoscape软件等工具构建可视化的调控网络[27]。2022年,Liang等[28]利用ChIP-seq揭示了恰菲埃里希氏体(Ehrlichia chaffeensis)全局转录因子CtrA在抵抗氧化应激方面的作用。2022年,Rivas-Solano等[29]通过ChIP-seq发现马耳他布鲁氏菌(Brucella melitensis)双组分系统BvrR/BvrS的直接调控靶点,这对于阐明马耳他布鲁氏菌如何调控其生理反应至关重要。ChIP-seq具有高灵敏度、高分辨率、高灵活性等优势,被广泛运用于转录因子的研究,但其局限性在于需要ChIP级的高特异性抗体,否则易出现假阳性,不利于后续实验[30]。此外,ChIP可能会忽略远端相互作用[31]
质谱技术是蛋白质组学的核心技术之一。与转录组测序技术和染色质免疫沉淀测序技术相比,蛋白质组学技术可以在蛋白质水平上反映转录因子的调控功能,可能涉及基因的转录后调控、转录调控复合物的组成分析、蛋白质的翻译后修饰等。然而,蛋白质组学的数据精确度和数量可能比转录组学数据低,因为现有技术无法检测到细胞内一些表达丰度低的蛋白质[32]。可以使用DAVID数据库对差异表达的蛋白质进行GO分析和KEGG分析,并使用R语言软件中的GOplot包对结果进行可视化,然后通过STRING在线工具预测蛋白质的相互作用,利用Cytoscape软件绘制蛋白质相互作用的可视化网络图[33]。2021年,Li等[34]利用质谱技术阐述了转录因子SlyA在调节嗜水气单胞菌(Aeromonas hydrophila)生理功能中的重要性。
RNA-seq能够筛选出转录因子调控的基因,但无法直接判断其是否通过直接结合的方式调控基因表达;而ChIP-seq能够检测到转录因子的具体结合序列,但无法确认是否真正调控相应基因的表达[35]。因此,将RNA-seq数据与ChIP-seq数据联合分析,通过分析转录因子结合位点与基因表达水平之间的关系,可以明确哪些基因受到目标转录因子的直接调控,并揭示这种调控如何影响基因的表达水平,从而更有利于探索基因的调控关系,构建复杂的调控网络。首先,可以根据ChIP-seq的峰值数据确定转录因子结合位点的位置,分析其是否位于基因启动子等关键区域,以及是否与基因表达水平相关。其次,根据RNA-seq数据筛选出在特定实验条件下表达量显著变化的基因,并结合ChIP-seq数据及在线工具如MEME工具(http://meme-suite.org/)进行预测,分析这些基因中是否存在转录因子结合位点。最后,对与转录因子结合且差异表达的基因进行功能富集分析,挖掘这些基因参与的信号通路,进而构建调控网络。2016年,Lobel等[36]利用RNA-seq和ChIP-seq证明全局转录因子CodY调控单核增生李斯特氏菌(Listeria monocytogenes)代谢、运动和毒力等生物学过程。2024年,Gerges等[37]利用RNA-seq和ChIP-seq,阐明转录因子Lsr2在脓肿分枝杆菌(Mycobacterium abscessus)中的分子作用,揭示Lsr2的多效调控作用。
基因和蛋白质的表达信息可以更清晰地反映细菌体内的生理特征,因此联合分析RNA-seq和质谱2种组学技术能够更好地分析转录因子在mRNA和蛋白质水平的调控功能[38]。2019年,Liu等[39]联合分析转录组学和蛋白质组学的数据,揭示了荧光假单胞菌(Pseudomonas fluorescens)转录因子RpoS在食物腐败中的作用。
高通量大规模测序可以快速获取大量的基因数据,但不同样本之间的测序差异可能导致错误,因此需要运用检测蛋白-DNA相互作用的技术进行验证。可以根据表型分析以及组学联合分析的结果,选取感兴趣通路中的靶标基因进行验证。以下列举的4种方法均适用于全局转录因子和局部转录因子。
凝胶滞缓实验(electrophoretic mobility shift assay, EMSA)是一种体外检测蛋白质-核酸相互作用的实验。进行该实验时,先将纯化的蛋白质和核酸探针混合孵育,然后通过非变性的聚丙烯酰胺凝胶电泳分离蛋白质-核酸复合物和游离的核酸片段[40]。如果蛋白质和目的探针发生相互作用,则会由于复合物分子量变大,导致其在电泳时迁移速度减慢,从而在自由探针条带后出现结合带型[41]。为了保证实验结果的准确性,通常会设置梯度实验和竞争型实验。2020年,本课题组Li等[42]通过RNA-seq、EMSA等方法发现FlhF直接结合鞭毛合成基因flgIrpoDflgSfliA的启动子,探索FlhF与鞭毛合成基因之间的新相互作用。2023年,Xiao等[43]运用EMSA等方法证实了调控因子ComE调控regR的转录表达。
EMSA因其简单易行、灵敏度高、直观等特点,被广泛应用于研究转录因子与核酸的体外结合,但EMSA也具有局限性,比如不能鉴定复合物中的蛋白质、不能检测蛋白与DNA的具体结合序列、电泳时间过长会导致复合物解离等[40]。因此,常用其他方法与EMSA联合验证。
脱氧核糖核酸酶(deoxyribonuclease, DNase)足迹法可以检测蛋白质和核酸的结合位点,常与EMSA方法结合应用于体外转录因子结合位点的探究。在该方法中,用适量的DNase消化蛋白质-核酸探针复合物,由于蛋白质与核酸片段的结合位点不会被DNase降解,所以酶切后结合位点的片段会被保留,即“足迹”[44]。通过变性的聚丙烯酰胺凝胶图分析,在显影后蛋白结合位点对应的位置不会有放射性标记的条带[45]
与EMSA技术相比,DNase足迹法可以精准地展示蛋白质与核酸片段的结合位点,且能精确到单个碱基,并能比较结合蛋白与其多个结合片段的亲和力,但也存在缺点,比如对蛋白的纯度和浓度要求很高、需要摸索DNase的最佳使用浓度、需要特殊设备和原材料等[46]。2020年,Palombo等[47]利用DNase足迹法证明转录因子HspR和HrcA共同调控主要热休克基因的表达。2021年,Kelley等[48]通过DNase足迹法证明转录因子HeuR能够结合ridA的启动子区域。2021年,Park等[49]用DNase足迹法证明转录因子CosR结合perR的启动子区域,为空肠弯曲杆菌氧化应激防御调控机制的研究提供新的见解。
LacZ报告基因是一种外源基因,其编码产物β-半乳糖苷酶能够催化半乳糖苷键的水解,将底物X-gal分解为蓝色的产物。可以将LacZ报告基因插入目的基因启动子下游,通过测定β-半乳糖苷酶的活性来检测体内启动子的转录活性,从而揭示基因调控的细节[50]
LacZ报告基因具有操作简单、高灵敏度、易检测、不需要使用放射性同位素等优点,被广泛应用于基因表达调控的研究。2022年,Long等[51]运用LacZ报告基因融合实验方法、EMSA等技术证明铜绿假单胞菌(Pseudomonas aeruginosa)转录因子LfsT通过结合gp71和几个重要噬菌体基因的启动子区域,抑制噬菌体PP9W2的溶原发育,从而促进噬菌体的裂解周期。2023年,Li等[52]运用LacZ报告基因融合实验方法等技术证明副溶血弧菌转录因子QsvR和OpaR协同间接激活cpsScpsR的转录,完善了副溶血弧菌生物膜形成的调控网络。
ChIP-qPCR是一种将染色质免疫沉淀与定量聚合酶链式反应相结合的实验方法。在转录因子的研究中,可通过设计qPCR引物来验证候选靶基因上的结合位点[53]。该方法的具体步骤包括:首先固定并随机切断细胞中的染色质,形成蛋白质-DNA复合物;随后利用特异性抗体识别并沉淀这些复合物,从而富集转录因子结合的DNA片段;最后通过qPCR对这些富集的DNA片段进行定量分析,以此研究蛋白质与DNA的相互作用[54]
ChIP-qPCR具有高灵敏度和特异性的特点,且成本相对较低,但其引物设计比其他qPCR引物设计更为复杂[55]。2019年,Liu等[56]通过DNase足迹法和ChIP-qPCR等方法证实了天蓝色链霉菌(Streptomyces coelicolor)转录因子MacR的靶基因结合位点。2023年,Zhang等[57]证明嗜水气单胞菌转录因子ORF02889直接调控corC的启动子,揭示了其生物学功能。
细菌转录因子的研究方法在多个领域都取得了迅速发展,但仍存在一些问题有待解决。首先,生物信息学技术广泛应用于破译复杂且动态的转录调控网络,但由于缺乏标准化的计算模型,可能导致不准确的预测数据集,进而产生错误的转录调控模型。此外,预测工具在可应用物种方面存在一定局限性,且预测转录因子结合位点的深度学习模型和基于机器学习的算法有待优化,缺乏深入理解,相关的在线工具也较少。其次,细菌转录因子具有多重调控功能,而每种分子生物学技术都存在局限性,例如非特异性结合、实验技术要求较高、受到体内复杂环境的限制等。综上所述,细菌转录因子的研究领域仍有很大的发展空间。未来可从模型设计、数据源和数据分辨率等方面优化深度学习模型的性能,改进卷积神经网络的功能,整合多层网络结构开发混合模型,并开发更多在线预测工具。此外,利用实时成像技术和分子探针技术动态监测与分析转录因子在体内的活性和分布情况,揭示其在不同生理或病理状态下的时空变化,也是重要的发展方向。相信在不久的将来,随着互联网技术和分子生物学技术的不断发展,人工智能与成熟的实验技术相互配合,有望实现动态模拟和预测调控网络的变化、自动化联合分析多组学数据等功能,为转录因子的研究提供新途径和巨大的便利,从而推动生物学领域的发展。
作者声明不存在任何可能会影响本文所报告工作的已知经济利益或个人关系。
  • 国家自然科学基金(32473117)
  • 国家自然科学基金(32172939)
  • 国家重点研发计划(2024YFC2310300)
参考文献 引证文献
排序方式:
[1]
DIESER M, SMITH HJ, RAMARAJ T, FOREMAN CM. Janthinobacterium CG23_2: comparative genome analysis reveals enhanced environmental sensing and transcriptional regulation for adaptation to life in an Antarctic supraglacial stream[J]. Microorganisms, 2019, 7(10): 454.
[2]
ORTET P, de LUCA G, WHITWORTH DE, BARAKAT M. P2TF: a comprehensive resource for analysis of prokaryotic transcription factors[J]. BMC Genomics, 2012, 13: 628.
[3]
MEJÍA-ALMONTE C, BUSBY SJW, WADE JT, van HELDEN J, ARKIN AP, STORMO GD, EILBECK K, PALSSON BO, GALAGAN JE, COLLADO-VIDES J. Redefining fundamental concepts of transcription initiation in bacteria[J]. Nature Reviews Genetics, 2020, 21(11): 699-714.
[4]
POUNTAIN AW, JIANG PE, YAO TY, HOMAEE E, GUAN YC, McDONALD KJC, PODKOWIK M, SHOPSIN B, TORRES VJ, GOLDING I, YANAI I. Transcription-replication interactions reveal bacterial genome regulation[J]. Nature, 2024, 626(7999): 661-669.
[5]
FORSTER ER, YANG XL, TAI AK, HANG HC, SHEN A. Identification of a bile acid-binding transcription factor in Clostridioides difficile using chemical proteomics[J]. ACS Chemical Biology, 2022, 17(11): 3086-3099.
[6]
LEDESMA L, HERNANDEZ-GUERRERO R, PEREZ-RUEDA E. Prediction of DNA-binding transcription factors in bacteria and Archaea genomes[M]//Prokaryotic Gene Regulation. New York, NY: Springer US, 2022: 103-112.
[7]
MISTRY J, CHUGURANSKY S, WILLIAMS L, QURESHI M, SALAZAR GA, SONNHAMMER ELL, TOSATTO SCE, PALADIN L, RAJ S, RICHARDSON LJ, FINN RD, BATEMAN A. Pfam: the protein families database in 2021[J]. Nucleic Acids Research, 2021, 49(D1): D412-D419.
[8]
KUMMERFELD SK, TEICHMANN SA. DBD: a transcription factor prediction database[J]. Nucleic Acids Research, 2006, 34(Database issue): D74-D81.
[9]
SIERRO N, MAKITA Y, de HOON M, NAKAI KT. DBTBS: a database of transcriptional regulation in Bacillus subtilis containing upstream intergenic conservation information[J]. Nucleic Acids Research, 2008, 36(Database issue): D93-D96.
[10]
GAMA-CASTRO S, SALGADO H, SANTOS-ZAVALETA A, LEDEZMA-TEJEIDA D, MUÑIZ-RASCADO L, GARCÍA-SOTELO JS, ALQUICIRA-HERNÁNDEZ K, MARTÍNEZ-FLORES I, PANNIER L, CASTRO-MONDRAGÓN JA, MEDINA-RIVERA A, SOLANO-LIRA H, BONAVIDES-MARTÍNEZ C, PÉREZ-RUEDA E, ALQUICIRA-HERNÁNDEZ S, PORRÓN-SOTELO L, LÓPEZ-FUENTES A, HERNÁNDEZ-KOUTOUCHEVA A, del MORAL-CHÁVEZ V, RINALDI F, et al. RegulonDB version 9.0: high-level integration of gene regulation, coexpression, motif clustering and beyond[J]. Nucleic Acids Research, 2016, 44(D1): D133-D143.
[11]
LECHNER M, FINDEISS S, STEINER L, MARZ M, STADLER PF, PROHASKA SJ. Proteinortho: detection of (co-)orthologs in large-scale analysis[J]. BMC Bioinformatics, 2011, 12: 124.
[12]
FLORES-BAUTISTA E, HERNANDEZ-GUERRERO R, HUERTA-SAQUERO A, TENORIO-SALGADO S, RIVERA-GOMEZ N, ROMERO A, IBARRA JA, PEREZ-RUEDA E. Deciphering the functional diversity of DNA-binding transcription factors in bacteria and archaea organisms[J]. PLoS One, 2020, 15(8): e0237135.
[13]
DODD IB, EGAN JB. Improved detection of helix-turn-helix DNA-binding motifs in protein sequences[J]. Nucleic Acids Research, 1990, 18(17): 5019-5026.
[14]
REUTER M, PERIAGO PM, MULHOLLAND F, BROWN HL, van VLIET AHM. A PAS domain-containing regulator controls flagella-flagella interactions in Campylobacter jejuni [J]. Frontiers in Microbiology, 2015, 6: 770.
[15]
LI YY, SUN WD, WANG Q, YU Y, WAN Y, ZHOU K, GUO R, HAN XG, CHEN ZG, FANG WH, JIANG W. The GntR-like transcriptional regulator HutC involved in motility, biofilm-forming ability, and virulence in Vibrio parahaemolyticus [J]. Microbial Pathogenesis, 2022, 167: 105546.
[16]
ABD-EL-HALEEM D. AraC transcriptional regulator, aspartate semialdehyde dehydrogenase and acyltransferase: three putative genes in phenol catabolic pathway of Acinetobacter sp. strain DF4[J]. Journal of Genetic Engineering and Biotechnology, 2024, 22(1): 100349.
[17]
KIM GB, GAO Y, PALSSON BO, LEE SY. DeepTFactor: a deep learning-based tool for the prediction of transcription factors[J]. Proceedings of the National Academy of Sciences of the United States of America, 2021, 118(2): e2021171118.
[18]
TONG CY, LIANG YM, ZHANG ZL, WANG S, ZHENG XH, LIU Q, SONG BC. Review of knockout technology approaches in bacterial drug resistance research[J]. PeerJ, 2023, 11: e15790.
[19]
ZHAO F, ZHI TH, HU RJ, FAN R, LONG YH, TIAN FH, ZHAO ZB. The OmpR-like transcription factor as a negative regulator of hrpR/S in Pseudomonas syringae pv. actinidiae [J]. International Journal of Molecular Sciences, 2022, 23(20): 12306.
[20]
OLIVER P, PERALTA-GIL M, TABCHE ML, MERINO E. Molecular and structural considerations of TF-DNA binding for the generation of biologically meaningful and accurate phylogenetic footprinting analysis: the LysR-type transcriptional regulator family as a study model[J]. BMC Genomics, 2016, 17(1): 686.
[21]
FINOTELLO F, di CAMILLO B. Measuring differential gene expression with RNA-seq: challenges and strategies for data analysis[J]. Briefings in Functional Genomics, 2015, 14(2): 130-142.
[22]
DO E, CHO YJ, KIM D, KRONSTAD JW, JUNG WH. A transcriptional regulatory map of iron homeostasis reveals a new control circuit for capsule formation in Cryptococcus neoformans [J]. Genetics, 2020, 215(4): 1171-1189.
[23]
SUDHAGAR A, KUMAR G, EL-MATBOULI M. Transcriptome analysis based on RNA-seq in understanding pathogenic mechanisms of diseases and the immune system of fish: a comprehensive review[J]. International Journal of Molecular Sciences, 2018, 19(1): 245.
[24]
WANG TT, QI YH, WANG ZH, ZHAO JR, JI LX, LI J, CAI Z, YANG L, WU M, LIANG HH. Coordinated regulation of anthranilate metabolism and bacterial virulence by the GntR family regulator MpaR in Pseudomonas aeruginosa [J]. Molecular Microbiology, 2020, 114(5): 857-869.
[25]
SUN ZX, HEACOCK-KANG Y, McMILLAN IA, CABANAS D, ZARZYCKI-SIEK J, HOANG TT. A virulence activator of a surface attachment protein in Burkholderia pseudomallei acts as a global regulator of other membrane-associated virulence factors[J]. Frontiers in Microbiology, 2023, 13: 1063287.
[26]
NAKATO R, SHIRAHIGE K. Recent advances in ChIP-seq analysis: from quality management to whole-genome annotation[J]. Briefings in Bioinformatics, 2017, 18(2): 279-290.
[27]
BAI Y, LI WL, XU GY, CUI GH. A bioinformatics approach revealed the transcription factors of Helicobacter pylori pathogenic genes and their regulatory network nodes[J]. Electronic Journal of Biotechnology, 2020, 45: 53-59.
[28]
LIANG QA, YAN JQ, ZHANG SW, YANG N, LI MF, JIN YX, BAI F, WU WH, CHENG ZH. CtrA activates the expression of glutathione S-transferase conferring oxidative stress resistance to Ehrlichia chaffeensis [J]. Frontiers in Cellular and Infection Microbiology, 2022, 12: 1081614.
[29]
RIVAS-SOLANO O, van der HENST M, CASTILLO-ZELEDÓN A, SUÁREZ-ESQUIVEL M, MUÑOZ-VARGAS L, CAPITAN-BARRIOS Z, THOMSON NR, CHAVES-OLARTE E, MORENO E, de BOLLE X, GUZMÁN-VERRI C. The regulon of Brucella abortus two-component system BvrR/BvrS reveals the coordination of metabolic pathways required for intracellular life[J]. PLoS One, 2022, 17(9): e0274397.
[30]
PARK PJ. ChIP-seq: advantages and challenges of a maturing technology[J]. Nature Reviews Genetics, 2009, 10(10): 669-680.
[31]
BADIA-I-MOMPEL P, WESSELS L, MÜLLER-DOTT S, TRIMBOUR R, RAMIREZ FLORES RO, ARGELAGUET R, SAEZ-RODRIGUEZ J. Gene regulatory network inference in the era of single-cell multi-omics[J]. Nature Reviews Genetics, 2023, 24: 739-754.
[32]
王娟红, 臧明, 郑毛亮, 常卫华. 绵羊繁殖调控的转录组学和蛋白组学研究进展[J]. 中国草食动物科学, 2018, 38(1): 49-52.
WANG JH, ZANG M, ZHENG ML, CHANG WH. Progress and prospects in the research on sheep transcriptomics and proteomics[J]. China Herbivore Science, 2018, 38(1): 49-52 (in Chinese).
[33]
WALTER W, SÁNCHEZ-CABO F, RICOTE M. GOplot: an R package for visually combining expression data with functional analysis[J]. Bioinformatics, 2015, 31(17): 2912-2914.
[34]
LI Z, ZHANG LS, SUN LN, WANG YQ, CHEN JZ, TANG HM, LIN L, LIN XM. Proteomics analysis reveals the importance of transcriptional regulator slyA in regulation of several physiological functions in Aeromonas hydrophila [J]. Journal of Proteomics, 2021, 244: 104275.
[35]
WADE JT. Mapping transcription regulatory networks with ChIP-seq and RNA-seq[M]//Prokaryotic Systems Biology. Cham: Springer International Publishing, 2015: 119-134.
[36]
LOBEL L, HERSKOVITS AA. Systems level analyses reveal multiple regulatory activities of CodY controlling metabolism, motility and virulence in Listeria monocytogenes [J]. PLoS Genetics, 2016, 12(2): e1005870.
[37]
GERGES E, RODRÍGUEZ-ORDOÑEZ MD, DURAND N, HERRMANN JL, CRÉMAZY F. Lsr2, a pleiotropic regulator at the core of the infectious strategy of Mycobacterium abscessus [J]. Microbiology Spectrum, 2024, 12(3): e0352823.
[38]
BASSEY AP, YE KP, LI CB, ZHOU GH. Transcriptomic-proteomic integration: a powerful synergy to elucidate the mechanisms of meat spoilage in the cold chain[J]. Trends in Food Science & Technology, 2021, 113: 12-25.
[39]
LIU XX, XU J, ZHU JL, DU P, SUN AH. Combined transcriptome and proteome analysis of RpoS regulon reveals its role in spoilage potential of Pseudomonas fluorescens [J]. Frontiers in Microbiology, 2019, 10: 94.
[40]
HELLMAN LM, FRIED MG. Electrophoretic mobility shift assay (EMSA) for detecting protein-nucleic acid interactions[J]. Nature Protocols, 2007, 2(8): 1849-1861.
[41]
孙宇航, 王宇祥. DNA与蛋白质的相互作用及其生物学研究方法[J]. 生命科学, 2018, 30(5): 585-592.
SUN YH, WANG YX. Interaction and biological research methods of DNA-protein[J]. Chinese Bulletin of Life Sciences, 2018, 30(5): 585-592 (in Chinese).
[42]
LI XF, REN FZ, CAI GQ, HUANG PY, CHAI QW, GUNDOGDU O, JIAO XN, HUANG JL. Investigating the role of FlhF identifies novel interactions with genes involved in flagellar synthesis in Campylobacter jejuni [J]. Frontiers in Microbiology, 2020, 11: 460.
[43]
XIAO JM, ZHANG YP, ZHANG JH, LIU BC, WANG HY, YANG R, YIN YB, ZHANG XM. Identification of Cis-acting elements upstream of regR gene in Streptococcus pneumoniae [J]. Microbial Pathogenesis, 2023, 182: 106263.
[44]
王秋岩, 何淑雅, 马云, 李俐娟, 李斌元. 启动子分析方法的研究进展[J]. 现代生物医学进展, 2015, 15(14): 2794-2800.
WANG QY, HE SY, MA Y, LI LJ, LI BY. Advances in analytical methods of promoter[J]. Progress in Modern Biomedicine, 2015, 15(14): 2794-2800 (in Chinese).
[45]
CARDEW AS, FOX KR. DNase I footprinting[M]//Drug-DNA Interaction Protocols. Totowa, NJ: Humana Press, 2009: 153-172.
[46]
LEBLANC BP, MOSS T. In vitro DNase I footprinting[M]//DNA-Protein Interactions. New York, NY: Springer New York, 2015: 17-27.
[47]
PALOMBO M, SCARLATO V, RONCARATI D. Cooperative regulation of Campylobacter jejuni heat-shock genes by HspR and HrcA[J]. Microorganisms, 2020, 8(8): 1161.
[48]
KELLEY BR, CALLAHAN SM, JOHNSON JG. Transcription of cystathionine β-lyase (MetC) is repressed by HeuR in Campylobacter jejuni, and methionine biosynthesis facilitates colonocyte invasion[J]. Journal of Bacteriology, 2021, 203(15): e0016421.
[49]
PARK M, HWANG S, RYU S, JEON B. CosR regulation of perR transcription for the control of oxidative stress defense in Campylobacter jejuni [J]. Microorganisms, 2021, 9(6): 1281.
[50]
HUGHES KT, MALOY SR. Use of operon and gene fusions to study gene regulation in Salmonella [M]//Advanced Bacterial Genetics: Use of Transposons and Phage for Genomic Engineering. Amsterdam: Elsevier, 2007: 140-158.
[51]
LONG X, WANG XL, MAO DQ, WU WH, LUO Y. A novel XRE-type regulator mediates phage lytic development and multiple host metabolic processes in Pseudomonas aeruginosa [J]. Microbiology Spectrum, 2022, 10(6): e0351122.
[52]
LI X, LIAN W, ZHANG MM, LUO X, ZHANG YQ, LU RF. QsvR and OpaR coordinately regulate the transcription of cpsS and cpsR in Vibrio parahaemolyticus [J]. Canadian Journal of Microbiology, 2024, 70(4): 128-134.
[53]
KIM TH, DEKKER J. ChIP-quantitative polymerase chain reaction (ChIP-qPCR)[J]. Cold Spring Harbor Protocols, 2018, 2018(5): 10.1101/pdb.prot082628.
[54]
GE PZ, RASHID FM, CRÉMAZY FGE, DAME RT. ChIP-qPCR of FLAG-tagged proteins in bacteria[M]//Bacterial Chromatin. New York, NY: Springer US, 2024: 55-75.
[55]
KURTENBACH S, REDDY R, WILLIAM HARBOUR J. ChIPprimersDB: a public repository of verified qPCR primers for chromatin immunoprecipitation (ChIP)[J]. Nucleic Acids Research, 2019, 47(D1): D46-D49.
[56]
LIU M, ZHANG PP, ZHU YP, LU T, WANG YM, CAO GX, SHI M, CHEN XL, TAO MF, PANG XH. Novel two-component system MacRS is a pleiotropic regulator that controls multiple morphogenic membrane protein genes in Streptomyces coelicolor [J]. Applied and Environmental Microbiology, 2019, 85(4): e02178-18.
[57]
ZHANG LS, SUN LN, SRINIVASAN R, LIN MZ, GONG LQ, LIN XM. Unveiling a virulence-regulating mechanism in Aeromonas hydrophila: a quantitative exoproteomic analysis of an AraC-like protein[J]. Frontiers in Immunology, 2023, 14: 1191209.
2025年第65卷第7期
PDF下载
171
69
引用本文
BibTeX
文章信息
doi: 10.13343/j.cnki.wsxb.20250019
  • 接收时间:2025-01-08
  • 首发时间:2026-02-06
  • 出版时间:2025-07-04
补充材料
相关文章
文章信息
作者
出版历史
  • 收稿日期:2025-01-08
  • 录用日期:2025-02-11
基金
National Natural Science Foundation of China(32473117)
国家自然科学基金(32473117)
国家自然科学基金(32172939)
National Key Research and Development Program of China(2024YFC2310300)
国家重点研发计划(2024YFC2310300)
作者信息
    1.扬州大学,江苏省人兽共患病学重点实验室,江苏 扬州
    2.江苏高校动物重要疫病与人兽共患病防控协同创新中心,江苏 扬州
    3.农业农村部农产品质量安全生物性危害因子(动物源)控制重点实验室,江苏 扬州
    4.教育部农业与农产品安全国际合作联合实验室,江苏 扬州
参考文献
分享链接
https://castjournals.cast.org.cn/joweb/wswxb/CN/10.13343/j.cnki.wsxb.20250019
分享至
全文二维码

扫描看全文

引用本文
BibTeX
本文的引用情况
2种不同金属材料的力学参数

Family
属数
Number of
genus
种数
Number of
species
占总种数比例
Percentage of
total species (%)

Genus
种数
Number of
species
占总种数比例
Percentage of total
species (%)
鹅膏菌科Amanitaceae 2 11 5.26 鹅膏菌属 Amanita 10 4.78
小菇科 Mycenaceae 2 12 5.74 丝盖伞属 Inocybe 5 2.39
多孔菌科 Polyporaceae 8 14 6.70 蜡蘑属 Laccaria 5 2.39
红菇科 Russulaceae 3 23 11.00 小皮伞属 Marasmius 6 2.87
小菇属 Mycena 11 5.26
光柄菇属 Pluteus 5 2.39
红菇属 Russula 17 8.13
栓菌属 Trametes 5 2.39
关闭全屏