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SHAPE-seq reveals the typical 5′mRNA structure of Escherichia coli and its effect on gene expression
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Jinpeng ZHANG1, 2, Jiawei REN1, 2, Zilun MEI1, 2, Xiaomei ZHANG3, Guoqiang XU1, 2, Hui LI3, Jinsong SHI3, Zhenghong XU4, Xiaojuan ZHANG1, 2, *
Acta Microbiologica Sinica | 2024, 64(11) : 4440 - 4454
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Acta Microbiologica Sinica | 2024, 64(11): 4440-4454
• Technology and Method •
SHAPE-seq reveals the typical 5′mRNA structure of Escherichia coli and its effect on gene expression
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Jinpeng ZHANG1, 2, Jiawei REN1, 2, Zilun MEI1, 2, Xiaomei ZHANG3, Guoqiang XU1, 2, Hui LI3, Jinsong SHI3, Zhenghong XU4, Xiaojuan ZHANG1, 2, *
Affiliations
  • 1 Key Laboratory of Industrial Biotechnology of Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, China
  • 2 National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214122, Jiangsu, China
  • 3 School of Life Sciences and Health Engineering, Jiangnan University, Wuxi 214122, Jiangsu, China
  • 4 College of Biomass Science and Engineering, Sichuan University, Chengdu 610065, Sichuan, China
Published: 2024-09-10 doi: 10.13343/j.cnki.wsxb.20240378
Outline
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[Objective] Due to the short half-life of mRNA transcript, their anti-degradation ability and ability to recruit ribosomes to initiate translation have significant effects on the gene expression in prokaryotes. However, the multiple functional regions in the 5′ end, of mRNA can affect the half-life and thus the expression of target genes, including the Shine-Dalgarno (SD) sequence and its upstream and downstream translational standby sites (TSSs) and the N-terminal coding sequence (NCS). The own and cross-regional structural differences will affect gene expression. Therefore, it is important to analyze the structure-activity relationship of each functional region. [Methods] We employed primer extension sequencing (SHAPE-seq) to analyze the structural characteristics of seven different 5′mRNAs in Escherichia coli and collected the mRNA abundance and protein level information under their regulation. [Results] Under the regulation of unstructured NCS, the mRNA abundance and protein level were increased by10 and 19 times, respectively. The formation of secondary structure TSS with a stem length of 10 nt increased the mRNA abundance. When the SD sequence was wrapped to form a secondary structure, the efficiency of translation initiation mediated by the SD sequence was affected (protein level downregulation by 10%). The combination of TSS and NCS significantly increased the mRNA abundance and protein level by 11 and 60 folds, respectively. [Conclusion] We characterized the structure of each region of 5′mRNA conducive to prokaryotic gene expression and revealed the structure-activity relationship of each functional region, providing a new regulatory element for target gene expression in industrial microorganisms.

translational standby site  /  N-terminal coding sequence  /  SD sequence  /  SHAPE-seq  /  structure-activity relationship
Jinpeng ZHANG, Jiawei REN, Zilun MEI, Xiaomei ZHANG, Guoqiang XU, Hui LI, Jinsong SHI, Zhenghong XU, Xiaojuan ZHANG. SHAPE-seq reveals the typical 5′mRNA structure of Escherichia coli and its effect on gene expression[J]. Acta Microbiologica Sinica, 2024 , 64 (11) : 4440 -4454 . DOI: 10.13343/j.cnki.wsxb.20240378
Funding
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  • National Natural Science Foundation of China(32171421)
Appendix
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Year 2024 volume 64 Issue 11
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Article Info
doi: 10.13343/j.cnki.wsxb.20240378
  • Receive Date：2024-06-20
  • Online Date：2026-03-21
  • Published：2024-09-10
Article Data
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History
  • Received：2024-06-20
  • Accepted：2024-08-29
Funding
National Natural Science Foundation of China(32171421)
Affiliations
    1 Key Laboratory of Industrial Biotechnology of Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, China
    2 National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214122, Jiangsu, China
    3 School of Life Sciences and Health Engineering, Jiangnan University, Wuxi 214122, Jiangsu, China
    4 College of Biomass Science and Engineering, Sichuan University, Chengdu 610065, Sichuan, China

Corresponding:

*ZHANG Xiaojuan, E-mail:
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表12种不同金属材料的力学参数
科
Family		 属数
Number of
genus		 种数
Number of
species		 占总种数比例
Percentage of
total species (%)		 属
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
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