Abstract
The differential gene expression under phosphate stress conditions leads to cross-talk between the global regulator, pho regulon, and metabolic genes. Promoter activity analysis of the selected 23 genes reveals the dynamic nature of real-time gene expression under different phosphate conditions. The expression profiles of the global regulator (rpoD, soxR, soxS, arcB, and fur), pho regulon (phoH, phoR, phoB, and ugpB), and metabolic genes (sdh, pfkA, ldh) varied significantly on phosphate level variation. Under stress conditions, soxR switches expression partners and co-expresses with rpoS instead of soxS. The partner-switching behavior of the genes under a challenging environment represents the intelligence of functional execution and ensures cell survival. The dynamic expression profile of the selected genes applies a time-lagged correlation to provide insight into the differential gene interaction between time-shifted expression profiles. Under different phosphate conditions, the minimum spanning tree graph revealed a different clustering pattern of selected genes depending on the computed distance and its proximity to other promoters.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
Data availability
The datasets generated during and/or analyzed during the current study are available from the corresponding author upon reasonable request.
Code availability
NA.
References
Bougdour A, Gottesman S (2007) ppGpp regulation of RpoS degradation via anti-adaptor protein IraP. Proc Natl Acad Sci 104:12896–12901
Derrick TR, Thomas JM (2004) Time series analysis: the cross-correlation function
Deshpande OA, Mohiuddin SS (2021) Biochemistry, oxidative phosphorylation. In StatPearls [Internet]. StatPearls Publishing, Treasure Island (FL)
Emmert-Streib F, Glazko GV (2011) Pathway analysis of expression data: deciphering functional building blocks of complex diseases. PLoS Comput Biol 7:e1002053
Girard ME, Gopalkrishnan S, Grace ED, Halliday JA, Gourse RL, Herman C (2018) DksA and ppGpp regulate the σS stress response by activating promoters for the small RNA DsrA and the anti-adapter protein IraP. J Bacteriol 200:e00463-e517
Gottesman S (2019) Trouble is coming: signaling pathways that regulate general stress responses in bacteria. J Biol 294:11685–11700
Jha V, Tikariha H, Dafale NA, Purohit HJ (2018) Exploring the rearrangement of sensory intelligence in proteobacteria: insight of Pho regulon. World J Microb Biot 34:172
Jha V, Dafale NA, Purohit HJ (2019) Regulatory rewiring through global gene regulations by PhoB and alarmone (p) ppGpp under various stress conditions. Microbiol Res 126309
Kearney EB, Ackrell BA, Mayr M, Singer TP (1974) Activation of succinate dehydrogenase by anions and pH. J Biol Chem 249:2016–2020
Marzan LW, Shimizu K (2011) Metabolic regulation of Escherichia coli and its phoB and phoR genes knockout mutants under phosphate and nitrogen limitations as well as at acidic condition. Microb Cell Fact 10:39
McKenzie AT, Katsyv I, Song WM, Wang M, Zhang B (2016) DGCA: a comprehensive R package for differential gene correlation analysis. BMC Syst Biol 10:106
Puranik S, Purohit HJ (2015) Dynamic interactive events in gene regulation using E. coli dehydrogenase as a model. Funct Integr Genomic 15:175–188
Rahmatallah Y, Emmert-Streib F, Glazko G (2014) Gene Sets Net Correlations Analysis (GSNCA): a multivariate differential co-expression test for gene sets. Bioinformatics 30:360–368
Ruiz N, Silhavy TJ (2003) Constitutive activation of the Escherichia coli Pho regulon upregulates rpoS translation in an Hfq-dependent fashion. J Bacteriol 185:5984–5992
Rutter J, Winge DR, Schiffman JD (2010) Succinate dehydrogenase–assembly, regulation and role in human disease. Mitochondrion 10:393–401
Santos-Beneit F (2015) The Pho regulon: a huge regulatory network in bacteria. Front Microbiol 6:402
Shaik F, Bezawada S, Goveas N (2015) CySpanningTree: minimal spanning tree computation in cytoscape. F1000Research 4:476
Shimizu K (2013) Metabolic regulation of a bacterial cell system with emphasis on Escherichia coli metabolism. ISRN Biochem 2013
Taschner NP, Yagil E, Spira B (2004) A differential effect of σS on the expression of the PHO regulon genes of Escherichia coli. Microbiology 150:2985–2992
Wanner BL (1996) Phosphorus assimilation and control of the phosphate regulon. Escherichia coli and Salmonella: cellular and molecular biology, 2nd edn. ASM Press, Washington, DC pp 1357–1381
Woldesemayat AA, Ntwasa M (2018) Pathways and network based analysis of candidate genes to reveal cross-talk and specificity in the Sorghum (Sorghum bicolor (L.) Moench) responses to drought and it’s co-occurring stresses. Front Genet 9:557
Xu Y, Olman V, Xu D (2002) Clustering gene expression data using a graph-theoretic approach: an application of minimum spanning trees. Bioinformatics 18:536–545
Zaslaver A, Bren A, Ronen M, Itzkovitz S, Kikoin I, Shavit S, Alon U (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat Methods 3:623–628
Acknowledgements
Varsha Jha is grateful to the University Grant Commission (UGC) for the Senior Research Fellow (SRF) award. The authors highly acknowledge the Director, CSIR-NEERI, Nagpur, for providing facilities to successfully carry this work [KRC No. CSIR-NEERI/KRC/2020/AUG/EBGD/2].
Author information
Authors and Affiliations
Corresponding author
Ethics declarations
Ethics approval
NA
Consent to participate
All authors have read and approved the final version of the manuscript.
Consent for publication
All the work reported in the manuscript is original and has not yet been submitted to other journals. The authors agree to transfer the copyright of manuscript to the Journal of Applied Genetics upon acceptance for publication.
Conflict of interest
The authors declare no competing interests.
Additional information
Communicated by: Agnieszka Szalewska-Palasz
Publisher’s note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Supplementary Information
Below is the link to the electronic supplementary material.
Rights and permissions
Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.
About this article
Cite this article
Jha, V., Dafale, N.A. & Purohit, H.J. Differential expression and cross-correlation between global regulator and pho regulon genes involved in decision-making under phosphate stress. J Appl Genetics 64, 173–183 (2023). https://doi.org/10.1007/s13353-022-00735-7
Received:
Revised:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s13353-022-00735-7