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Transcriptomics-proteomics conjoint analysis of differentially expressed genes/proteins between wild type and ultraviolet radiation-mutated Halomonas campaniensis strains
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Jinzi CUI1, Rui HAN2, Lijuan QIAO1, Yongzhen LI1, Jiangwa XING1, Rong WANG1, Guoping SHEN1, *, Derui ZHU1
Acta Microbiologica Sinica | 2025, 65(4) : 1601 - 1615
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Acta Microbiologica Sinica | 2025, 65(4): 1601-1615
• New technologies and methods for microbial resources •
Transcriptomics-proteomics conjoint analysis of differentially expressed genes/proteins between wild type and ultraviolet radiation-mutated Halomonas campaniensis strains
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Jinzi CUI1, Rui HAN2, Lijuan QIAO1, Yongzhen LI1, Jiangwa XING1, Rong WANG1, Guoping SHEN1, *, Derui ZHU1
Affiliations
  • 1.Research Center of Basic Medical Science, Medical College, Qinghai University, Xining, Qinghai, China
  • 2.Key Laboratory of Vegetable Genetics and Physiology, Academy of Agriculture and Forestry Sciences, Qinghai University, Xining, Qinghai, China
Published: 2025-04-04 doi: 10.13343/j.cnki.wsxb.20240477
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A mutant strain G9-72 with a high yield of ectoine was obtained from wild type Halomonas campaniensis after nine rounds of ultraviolet mutagenesis. The differentially expressed genes/proteins (DEGs/DEPs) and the molecular mechanism underlying the excessive increase in the ectoine yield remain to be explored for the mutant strain. [Objective] To explore the DEGs/DEPs between the wild type strain XH26 and G9-72 and decipher the molecular mechanism of efficient ectoine production by conjoint analysis. [Methods] A non-salt (NS, 0 mol/L NaCl) group and a high-salt (HS, 1.5 mol/L NaCl) group were designed for the culture of XH26 and G9-72. Illumina HiSeq and quantitative mass spectrometry were employed to identify the DEGs/DEPs between the two strains by transcriptomics-proteomics conjoint analysis. Furthermore, RT-qPCR was carried out to verify the expression of significant DEGs. [Results] The transcriptomics analysis revealed 11 amino acid metabolic pathways (44 DEGs) associated with ectoine anabolism, and the proteomics analysis revealed ten amino acid metabolic pathways (50 DEPs) associated with ectoine anabolism. The transcriptomics-proteomics conjoint analysis identified 15 significant DEGs, including seven genes (ectB, betB, betA, asd, doeD, doeC, and gabD) with up-regulated mRNA and protein level, four genes (ItaE, gdhA, gabT, and acnB) with down-regulated mRNA and protein levels, three genes (gltD, atoB, and narG) with down-regulated mRNA levels and up-regulated protein levels, and one gene narK with up-regulated mRNA level and no protein level. Additionally, the RT-qPCR results were consistent with the transcriptomics analysis. [Conclusion] The excessive increase in the ectoine yield of the mutant strain was associated with key genes in the ectoine metabolic pathway (including the synthesis genes asd and ectB and the catabolism genes doeD and doeC) and indirectly associated with several genes (betB, betA, ItaE, gltD, gadA, and acnB) in the upstream metabolic pathway. Notably, ectoine biosynthesis was highly associated with the Ala/Asp/Glu/His metabolic pathway (gabD, gdhA, gabT, and atoB) and nitrogen source metabolism (narK and narG).

Halomonas campaniensis  /  ectoine  /  transcriptomics  /  proteomics  /  differentially expressed genes
Jinzi CUI, Rui HAN, Lijuan QIAO, Yongzhen LI, Jiangwa XING, Rong WANG, Guoping SHEN, Derui ZHU. Transcriptomics-proteomics conjoint analysis of differentially expressed genes/proteins between wild type and ultraviolet radiation-mutated Halomonas campaniensis strains[J]. Acta Microbiologica Sinica, 2025 , 65 (4) : 1601 -1615 . DOI: 10.13343/j.cnki.wsxb.20240477
Funding
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  • National Natural Science Foundation of China(32260019)
  • Qinghai Central Government Guide Local Science and Technology Development Fund(2024ZY015)
Appendix
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Year 2025 volume 65 Issue 4
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Article Info
doi: 10.13343/j.cnki.wsxb.20240477
  • Receive Date：2024-08-01
  • Online Date：2026-02-06
  • Published：2025-04-04
Article Data
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History
  • Received：2024-08-01
  • Accepted：2024-10-15
Funding
National Natural Science Foundation of China(32260019)
Qinghai Central Government Guide Local Science and Technology Development Fund(2024ZY015)
Affiliations
    1.Research Center of Basic Medical Science, Medical College, Qinghai University, Xining, Qinghai, China
    2.Key Laboratory of Vegetable Genetics and Physiology, Academy of Agriculture and Forestry Sciences, Qinghai University, Xining, Qinghai, China

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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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