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Regulation of metabolic pathways by MarR family transcription factors.
Open accessAbstract
Bacteria have evolved sophisticated mechanisms for regulation of metabolic pathways. Such regulatory circuits ensure that anabolic pathways remain repressed unless final products are in short supply and that catabolic enzymes are not produced in absence of their substrates. The precisely tuned gene activity underlying such circuits is in the purview of transcription factors that may bind pathway intermediates, which in turn modulate transcription factor function and therefore gene expression. This review focuses on the role of ligand-responsive MarR family transcription factors in controlling expression of genes encoding metabolic enzymes and the mechanisms by which such control is exerted. Prospects for exploiting these transcription factors for optimization of gene expression for metabolic engineering and for the development of biosensors are considered.
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Mj223 is predicted to recognize its unknown operator sequence via a winged-helix-turn-helix DNA-binding motif.
“Mj223 is predicted to recognize its (unknown) operator sequence via a winged-helix-turn-helix DNA-binding motif (Ray et al., 2003; Grove, 2017).”
From Two MarR-Type Repressors Balance Precursor Uptake and Glycine Betaine Synthesis in Bacillus subtilis to Provide Cytoprotection Against Sustained Osmotic Stress (2020) · cites this paper as Grove, 2017
The MarR Protein Family section (page unavailable) says MarR proteins use a winged helix-turn-helix motif to bind DNA. Our copy does not mention Mj223 or establish that its operator sequence is unknown, so it supports the general mechanism but not its application to Mj223. (LLM, conf=0.84)
Experimental — accuracy not yet measuredGbsR and OpcR belong to the same sub-family of MarR-type transcriptional regulators.
“These two amino acid-sequence-related proteins (Nau-Wagner et al., 2012; Lee et al., 2013) belong to the same sub-family of MarR-type transcriptional regulators (Grove, 2017; Ronzheimer et al., 2018).”
From Two MarR-Type Repressors Balance Precursor Uptake and Glycine Betaine Synthesis in Bacillus subtilis to Provide Cytoprotection Against Sustained Osmotic Stress (2020) · cites this paper as Grove, 2017
The MarR Protein Family section describes MarR regulators generally but does not identify GbsR or OpcR or place them in a shared sub-family. Searches for both protein names and their proposed relationship found no passage addressing that classification in our copy; page numbers were unavailable. (LLM, conf=0.74)
Experimental — accuracy not yet measured
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Research works printed but not linked: 49
- 10.1093/jmcb/mjq021 · DOI
- 10.1074/jbc.R115.685032 · DOI
- 10.1111/j.1574-6976.2010.00227.x · DOI
- Philips S.J., Canalizo-Hernandez M., Yildirim I., Schatz G.C., Mondragon A. and O'Halloran T.V.: TRANSCRIPTION. Allosteric transcriptional regulation via changes in the overall topology of the core promoter. Science 2015; 349: 877. · DOI
- Deochand D.K., Meariman J.K. and Grove A.: pH-dependent DNA distortion and repression of gene expression by Pectobacterium atrosepticum PecS. ACS Chem Biol 2016; 11: 2049. · DOI
- 10.1016/j.tim.2010.12.001 · DOI
- 10.1128/MMBR.00018-13 · DOI
- Wilkinson S.P. and Grove A.: Ligand-responsive transcriptional regulation by members of the MarR family of winged helix proteins. Curr Issues Mol Biol 2006; 8: 51.
- 10.1016/j.compbiolchem.2004.09.004 · DOI
- Ibarra J.A., Perez-Rueda E., Carroll R.K. and Shaw L.N.: Global analysis of transcriptional regulators in Staphylococcus aureus. BMC Genomics 2013; 14: 126. · DOI
- Ellison D.W. and Miller V.L.: Regulation of virulence by members of the MarR/SlyA family. Curr Opin Microbiol 2006; 9: 153. · DOI
- 10.1074/jbc.M115.712067 · DOI
- 10.1039/C6MB00304D · DOI
- Gupta A. and Grove A.: Ligand-binding pocket bridges DNA-binding and dimerization domains of the urate-responsive MarR homologue MftR from Burkholderia thailandensis. Biochemistry 2014; 53: 4368. · DOI
- Andresen C., Jalal S., Aili D., Wang Y., Islam S., Jarl A. et al: Critical biophysical properties in the Pseudomonas aeruginosa efflux gene regulator MexR are targeted by mutations conferring multidrug resistance. Protein Sci 2010; 19: 680. · DOI
- Zhu R., Hao Z., Lou H., Song Y., Zhao J., Chen Y. et al: Structural characterization of the DNA-binding mechanism underlying the copper(II)-sensing MarR transcriptional regulator. J Biol Inorg Chem 2017; .
- 10.1038/nrmicro1932 · DOI · Paper page
- Carmona M., Zamarro M.T., Blazquez B., Durante-Rodriguez G., Juarez J.F., Valderrama J.A. et al: Anaerobic catabolism of aromatic compounds: a genetic and genomic view. Microbiol Mol Biol Rev 2009; 73: 71. · DOI
- Diaz E., Jimenez J.I. and Nogales J.: Aerobic degradation of aromatic compounds. Curr Opin Biotechnol 2013; 24: 431. · DOI
- Fuchs G., Boll M. and Heider J.: Microbial degradation of aromatic compounds — from one strategy to four. Nat Rev Microbiol 2011; 9: 803. · DOI
- Parke D. and Ornston L.N.: Hydroxycinnamate (hca) catabolic genes from Acinetobacter sp. strain ADP1 are repressed by HcaR and are induced by hydroxycinnamoyl-coenzyme A thioesters. Appl Environ Microbiol 2003; 69: 5398. · DOI
- 10.1371/journal.ppat.1005557 · DOI
- Anandapadamanaban M., Pilstal R., Andresen C., Trewhella J., Moche M., Wallner B. et al: Mutation-induced population shift in the MexR conformational ensemble disengages DNA binding: a novel mechanism for MarR family derepression. Structure 2016; 24: 1311. · DOI
- Otani H., Stogios P.J., Xu X., Nocek B., Li S.N., Savchenko A. et al: The activity of CouR, a MarR family transcriptional regulator, is modulated through a novel molecular mechanism. Nucleic Acids Res 2016; 44: 595. · DOI
- Kasai D., Kamimura N., Tani K., Umeda S., Abe T., Fukuda M. et al: Characterization of FerC, a MarR-type transcriptional regulator, involved in transcriptional regulation of the ferulate catabolic operon in Sphingobium sp. strain SYK-6. FEMS Microbiol Lett 2012; 332: 68. · DOI
- Hirakawa H., Schaefer A.L., Greenberg E.P. and Harwood C.S.: Anaerobic p-coumarate degradation by Rhodopseudomonas palustris and identification of CouR, a MarR repressor protein that binds p-coumaroyl coenzyme A. J Bacteriol 2012; 194: 1960. · DOI
- 10.1128/MMBR.68.3.474-500.2004 · DOI
- 10.1093/nar/gkt009 · DOI
- Jerga A. and Rock C.O.: Acyl-acyl carrier protein regulates transcription of fatty acid biosynthetic genes via the FabT repressor in Streptococcus pneumoniae. J Biol Chem 2009; 284: 15364. · DOI
- Zhu D., Wang Y., Zhang M., Ikeda H., Deng Z. and Cane D.E.: Product-mediated regulation of pentalenolactone biosynthesis in Streptomyces species by the MarR/SlyA family activators PenR and PntR. J Bacteriol 2013; 195: 1255. · DOI
- 10.1146/annurev.micro.62.081307.162903 · DOI
- Huang H. and Grove A.: The transcriptional regulator TamR from Streptomyces coelicolor controls a key step in central metabolism during oxidative stress. Mol Microbiol 2013; 87: 1151. · DOI
- Huang H., Sivapragasam S. and Grove A.: The regulatory role of Streptomyces coelicolor TamR in central metabolism. Biochem J 2015; 466: 347. · DOI
- Ramsay R.R., Dreyer J.L., Schloss J.V., Jackson R.H., Coles C.J., Beinert H. et al: Relationship of the oxidation state of the iron-sulfur cluster of aconitase to activity and substrate binding. Biochemistry 1981; 20: 7476. · DOI
- 10.1126/science.1193990 · DOI
- Mahr R. and Frunzke J.: Transcription factor-based biosensors in biotechnology: current state and future prospects. Appl Microbiol Biotechnol 2016; 100: 79. · DOI
- 10.1038/nature07190 · DOI
- 10.1038/nrmicro.2016.32 · DOI
- 10.1016/j.cbpa.2015.06.009 · DOI
- 10.1126/science.1137016 · DOI
- 10.1038/nbt.1591 · DOI · Paper page
- 10.1038/nmeth.3696 · DOI · Paper page
- 10.1038/nbt.1617 · DOI
- Geraths C., Daoud-El Baba M., Charpin-El Hamri G. and Weber W.: A biohybrid hydrogel for the urate-responsive release of urate oxidase. J Control Release 2013; 171: 57. · DOI
- 10.1074/jbc.M405586200 · DOI
- Perera I.C., Lee Y.H., Wilkinson S.P. and Grove A.: Mechanism for attenuation of DNA binding by MarR family transcriptional regulators by small molecule ligands. J Mol Biol 2009; 390: 1019. · DOI
- Li S., Zhou L., Yao Y., Fan K., Li Z., Zhang L. et al: A platform for the development of novel biosensors by configuring allosteric transcription factor recognition with amplified luminescent proximity homogeneous assays. Chem Commun (Camb) 2016; 53: 99. · DOI
- Pundir C.S. and Devi R.: Biosensing methods for xanthine determination: a review. Enzyme Microb Technol 2014; 57: 55. · DOI
- Perera I.C. and Grove A.: Urate is a ligand for the transcriptional regulator PecS. J Mol Biol 2010; 402: 539. · DOI
Cited by
Sorted by citations
Warmbold, B., Ronzheimer, S., Freibert, S.-A., Seubert, A., Hoffmann, T., & Bremer, E. (2020) · Frontiers in Microbiology · doi:10.3389/fmicb.2020.01700 · Cited by 17
“…should recognize their cognate operators in a fashion similar to other structurally and biochemically well studied MarR-type regulatory proteins (Grove, 2013, 2017) [see Supplementary Figure S2 for an extended amino acid sequence alignment of GbsR-, OpcR- and YvaV-type proteins in Bacilli].”
BackgroundInfluential
Metadata
- Authors
- Grove, A.
- Affiliations
- Louisiana State University (US)
- Corresponding author
- Grove, Anne
- ORCID
- Grove, Anne
- Venue
- Computational and Structural Biotechnology Journal
- Published
- 2017-01
- Volume
- 15
- Pages
- 366-371
- ISSN
- 2001-0370 (ISSN-L)
- PMC
- PMC5487221
- OpenAlex
- W2625036894
- Cited by
- 88
- References
- 0
- Citations by year
- 2026: 10 · 2025: 11 · 2024: 10 · 2023: 4 · 2022: 7 · 2021: 12 · 2020: 16 · 2019: 9 · 2018: 8 · 2017: 1
- FWCI
- 1.19
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Computational and Structural Biotechnology Journal (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Civil War Book Review (submittedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
- Funders
- National Science Foundation (MCB-1515349)
- National Institutes of Health (1R15GM107825)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Bacterial Genetics and Biotechnology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Microbial Metabolic Engineering and Bioproduction
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene Regulatory Network Analysis
- Keywords
- metabolic pathway regulation, pathway intermediates, catabolite repression, gene expression regulation, metabolic engineering, biosensors, bacterial gene regulation
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