Differential analysis of transcriptome of Glutamicibacter arilaitensis under different culture temperatures
DOI:
https://doi.org/10.5564/mjas.v17i41.1466Keywords:
transcriptome analysis, GO enrichment analysis, KEGG, psychrophilic mechanismAbstract
Low-temperature adaptation is a critical physiological process in mesophilic bacteria, yet its molecular mechanisms remain unclear. To investigate how Glutamicibacter arilaitensis strain F9 adapts to cold stress, the strain was cultured at 5°C (F9_5), 10°C (F9_10), and 25°C (F9_25). High-throughput transcriptome sequencing was performed to analyze differentially expressed genes (DEGs) across these conditions. Gene expression differences were identified and subjected to Gene Ontology (GO) enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis. A total of 731 DEGs were identified between the F9_25 and F9_10 groups, 747 between F9_25 and F9_5, and 265 between F9_10 and F9_5, with 65 shared DEGs across all comparisons. GO enrichment analysis revealed that the DEGs were primarily associated with cellular energy metabolism, amino acid biosynthesis, and membrane components. KEGG pathway analysis identified 20 significantly enriched pathways, with key differences observed in: dicarboxylate metabolism, ABC transporters, and two-component systems in the F9_25 and F9_10 comparison; two-component systems, pyruvate metabolism, and glyoxylate/dicarboxylate metabolism in the F9_25 and F9_5 comparison; and fatty acid degradation, tryptophan metabolism, and two-component systems in the F9_10 and F9_5 comparison. To survive low-temperature stress, strain F9 modulated gene expression to counteract the reduction in enzyme activity and protein efficiency. This regulation helped maintain membrane fluidity, ensuring proper substance exchange and signal transduction, while also securing sufficient energy and biosynthetic precursors for essential cellular functions.
Downloads
19
References
[1] R. Y. Morita, “Psychrophilic bacteria,” Bacteriol. Rev., vol. 39, no. 2, pp. 144–167, 1975. http://doi.org/10.1128/br.39.2.144-167.1975
[2] R. Margesin and V. Miteva, “Diversity and ecology of psychrophilic microorganisms,” Res. Microbiol., vol. 162, no. 3, pp. 346–361, 2011. http://doi.org/10.1016/j.resmic.2010.12.004
[3] A. Ramón et al., “A general overview of the multifactorial adaptation to cold: biochemical mechanisms and strategies,” Braz. J. Microbiol., vol. 54, no. 3, pp. 2259–2287, 2023. http://doi.org/10.1007/s42770-023-01057-4
[4] S. Y. Zhang et al., “Research progress and applications on mechanisms of cold adaptation in psychrophilic bacteria,” Shandong Chem. Ind., vol. 46, no. 17, pp. 63–65+69, 2017.
[5] X. Y. Li, “Research on the cold-adaptation mechanism of β-Glycosidase from Pseudomonas putida,” M.S. thesis, Dali Univ., Dali, 2023.
[6] G. J. Hu, “Comparative analysis of structural parameters of temperature-adaptive enzymes,” M.S. thesis, Yunnan Univ., Kunming, 2022.
[7] R. Cavicchioli, “On the concept of a psychrophile,” ISME J., vol. 10, no. 4, pp. 793–795, 2016.
http://doi.org/10.1038/ismej.2015.160
[8] G. Horn et al., “Structure and function of bacterial cold shock proteins,” Cell. Mol. Life Sci., vol. 64, no. 12, pp. 1457–1470, 2007. http://doi.org/10.1007/s00018-007-6388-4
[9] Z. J. Chen et al., “The genome and transcriptome of a newly described psychrophilic archaeon, Methanolobus psychrophilus R15, reveal its cold adaptive characteristics,” Environ. Microbiol. Rep., vol. 4, no. 6, pp. 633–641, 2012. http://doi.org/10.1111/j.1758-2229.2012.00389.x
[10] H. C. Gao et al., “Global transcriptome analysis of the heat shock response of Shewanella oneidensis,” J. Mycobact., vol. 186, no. 22, pp. 7796–7803, 2004.
http://doi.org/10.1128/JB.186.22.7796-7803.2004
[11] S. Frank et al., “Functional genomics of the initial phase of cold adaptation of Pseudomonas putida KT2440,” FEMS Microbiol. Lett., vol. 318, no. 1, pp. 47–54, 2011. http://doi.org/10.1111/j.1574-6968.2011.02237.x
[12] F. M. Lauro et al., “Large-scale transposon mutagenesis of Photobacterium profundum SS9 reveals new genetic loci important for growth at low temperature and high pressure,” J. Mycobact., vol. 190, no. 5, pp. 1699–1709, 2008. http://doi.org/10.1128/JB.01176-07
[13] G. Cacace et al., “Proteomics for the elucidation of cold adaptation mechanisms in Listeria monocytogenes,” J. Proteomics, vol. 73, no. 10, pp. 2021–2030, 2010.
http://doi.org/10.1016/j.jprot.2010.06.011
[14] P. De Maayer et al., “Some like it cold: understanding the survival strategies of psychrophiles,” EMBO Rep., vol. 15, no. 5, pp. 508–517, 2014. http://doi.org/10.1002/embr.201338170
[15] G. J. Wang, “Mechanisms of LisK/R two-component system in regulating flagellar gene expression to affect Listeria monocytogenes low-temperature growth,” M.S. thesis, Huazhong Agric. Univ., Wuhan, 2022.
[16] Q. Wang et al., “Integration of DSF and temperature signals for RpfC/RpfG two-component system modulating protease production in Stenotrophomonas maltophilia FF11,” Curr. Microbiol., vol. 79, no. 2, p. 54, 2022. http://doi.org/10.1007/s00284-021-02731-2
Xu Chun-Guang et al. MJAS Vol 17 No.41 (2024)
[17] P. S. Aguilar et al., “Molecular basis of thermosensing: a two-component signal transduction thermometer in Bacillus subtilis,” EMBO J., vol. 20, no. 7, pp. 1681–1691, 2001. http://doi.org/10.1093/emboj/20.7.1681
[18] S. E. Diomand et al., “The CasKR two-component system is required for the growth of mesophilic and psychrotolerant Bacillus cereus strains at low temperatures,” Appl. Environ. Microbiol., vol. 80, no. 8, pp. 2493–2503, 2014. http://doi.org/10.1128/AEM.00090-14
[19] Y. Derman et al., “The two-component system CBO2306/CBO2307 is important for cold adaptation of Clostridium botulinum ATCC3502,” Int. J. Food Microbiol., vol. 167, no. 1, pp. 87–91, 2013. http://doi.org/10.1016/j.ijfoodmicro.2013.06.004
[20] E. Palonen et al., “Expression of signal transduction system encoding genes of Yersinia pseudotuberculosis IP32953 at 28 °C and 3 °C,” PLoS One, vol. 6, no. 9, p. e25063, 2011. http://doi.org/10.1371/journal.pone.0025063
[21] Y. B. Wang et al., “Roles of proline and soluble sugars in the cold adaptation mechanisms of Antarctic diatoms,” Biotechnol. Bull., vol. 32, no. 2, pp. 198–202, 2016.
[22] Y. P. Li et al., “Trehalose in fungi and its functions under cold stress,” J. Edible Fungi, vol. 20, no. 4, pp. 71–77, 2013.
[23] Z. Q. Shen et al., “Effects of exogenous EBR and H₂O₂ spray on cold stress resistance in tobacco seedlings,” J. Yunnan Agric. Univ. (Nat. Sci.), vol. 37, no. 4, pp. 623–629, 2022.
[24] L. X. Hou, “H₂O₂ impacts on physiological indices of rape seedlings under low temperatures,” Hubei Agric. Sci., vol. 52, no. 21, pp. 5144–5146+5152, 2013.
[25] Q. J. Lai et al., “Exogenous H₂O₂ pretreatment enhances cold resistance and improves yield and quality of Sedum adolphii,” Chin. Mater. Med., vol. 53, no. 21, pp. 6874–6880, 2022.
Published
How to Cite
Issue
Section
License
Copyright (c) 2024 XU Chun-guang, YANG Li-xia , WANG Ji-chun, MA Yu-jiao, YU Bao-li
This work is licensed under a Creative Commons Attribution 4.0 International License.
Copyright on any research article in the Mongolian Journal of Agricultural Sciences is retained by the author(s).
The authors grant the Mongolian Journal of Agricultural Sciences a license to publish the article and identify itself as the original publisher.
Articles in the Mongolian Journal of Agricultural Sciences are Open Access articles published under a Creative Commons Attribution 4.0 International License CC BY.
This license permits use, distribution and reproduction in any medium, provided the original work is properly cited.
