Bacterial Transcription Factors in Gene Expression Regulation
WANG Xue-Ying1), SUN Ze-Min1), FENG Yong-Jun1),2)*
1)School of Life Sciences, Beijing Institute of Technology, Beijing 100081, China; 2)Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, Guangdong China
Abstract:Transcription factors (TFs) are key proteins that regulate gene expression by guiding RNA polymerases to bind to specific DNA sequences in cells, thus enabling organisms to respond to environmental changes rapidly and achieving better survival adaptability. Most bacterial transcription factors are composed of two parts: a DNA-binding domain and a regulatory domain, but some transcription factors have only one DNA-binding domain. According to the functional profile, they can be classified as activating transcription factors and repressive transcription factors. The important function of bacterial transcription factors is to sense changes in environmental conditions and to adjust the expression of related genes accordingly, at same time they are also affected by other signaling molecules. They often form a complex regulatory network with each other and jointly manage the expression of genes to cope with the environmental signals. Due to the importance of bacterial transcription factors in gene regulation, it has become a hot spot in molecular biology research. In this review, we summarize the study of bacterial transcription factors in recent years, focusing on their structures and function mechanisms and roles in stress response, in order to provide ideas for a systematic understanding of the topic.
[1] Browning DF, Busby SJ. The regulation of bacterial transcription initiation [J]. Nat Rev Microbiol, 2004, 2(1): 57-65
[2] Demple B. Redox signaling and gene control in the Escherichia coli soxRS oxidative stress regulon—a review[J]. Gene, 1996, 179(1): 53-57
[3] Swint-Kruse L, Matthews KS. Allostery in the LacI/GalR family: variations on a theme [J]. Curr Opin Microbiol, 2009, 12(2): 129-137
[4] Stock AM, Robinson VL, Goudreau PN. Two-component signal transduction [J]. Annu Rev Biochem, 2000, 69: 183-215
[5] Nikaido E, Shirosaka I, Yamaguchi A, et al. Regulation of the AcrAB multidrug efflux pump in Salmonella enterica serovar Typhimurium in response to indole and paraquat [J]. Microbiology, 2011, 157(3):648-655
[6] Perez-Rueda E, Hernandez-Guerrero R, Martinez-Nunez MA, et al. Abundance, diversity and domain architecture variability in prokaryotic DNA-binding transcription factors [J]. PLoS One, 2018, 13(4): e0195332
[7] Ali F, Seshasayee ASN. Dynamics of genetic variation in transcription factors and its implications for the evolution of regulatory networks in bacteria [J]. Nucleic Acids Res, 2020, 48(8): 4100-4114
[8] Chávez J, Devos DP, Merino E. Complementary tendencies in the use of regulatory elements (transcription factors, sigma factors, and riboswitches) in bacteria and archaea [J]. J Bacteriol, 2020, 203(2): e00413-20
[9] Busby SJW. Transcription activation in bacteria: ancient and modern [J]. Microbiology, 2019, 165(4): 386-395
[10] Reitzer LJ, Magasanik B. Transcription of glnA in E. coli is stimulated by activator bound to sites far from the promoter.[J]. Cell, 1986, 45(6): 785-792
[11] Zurawski G, Elseviers D, Stauffer VG, et al. Translational control of transcription termination at the attenuator of the Escherichia coli tryptophan operon[J]. Proc Natl Acad Sci, 1978, 75(12): 5988-5992
[12] Mejía-Almonte C, Busby SJW, Wade JT, et al. Redefining fundamental concepts of transcription initiation in bacteria[J]. Nat Rev Genet, 2020, 21(11): 699-714
[13] Kolesov G, Wunderlich Z, Laikova ON, et al. How gene order is influenced by the biophysics of transcription regulation [J]. Proc Natl Acad Sci USA, 2007, 104(35): 13948-13953
[14] Browning DF, Busby SJW. Local and global regulation of transcription initiation in bacteria [J]. Nat Rev Microbiol, 2016, 14(10): 638-650
[15] Balleza E, López-Bojorquez LN, Martínez-Antonio A, et al. Regulation by transcription factors in bacteria: beyond description [J]. FEMS Microbiol Rev, 2009, 33(1): 133-151
[16] Martinez-Antonio A, Collado-Vides J. Identifying global regulators in transcriptional regulatory networks in bacteria [J]. Curr Opin Microbiol, 2003, 6(5): 482-489
[17] Nosho K, Fukushima H, Asai T, et al. cAMP-CRP acts as a key regulator for the viable but non-culturable state in Escherichia coli[J]. Microbiology, 2018, 164(3): 410-419
[18] Fernández PA, Velásquez F, Garcias-Papayani H, et al. Fnr and ArcA regulate lipid a hydroxylation in Salmonella enteritidis by controlling lpxO expression in response to oxygen availability [J]. Front Microbiol, 2018, 9: 1220
[19] Landgraf JR, Wu J, Calvo JM. Effects of nutrition and growth rate on Lrp levels in Escherichia coli [J]. J Bacteriol, 1996, 178(23): 6930-6936
[20] Monteiro LMO, Sanches-Medeiros A, Westmann CA, et al. Unraveling the complex interplay of Fis and IHF through synthetic promoter engineering [J]. Front Bioeng Biotechnol, 2020, 8: 510
[21] Scott S, Busby S, Beacham I. Transcriptional co-activation at the ansB promoters: involvement of the activating regions of CRP and FNR when bound in tandem [J]. Mol Microbiol, 1995, 18(3): 521-531
[22] Chahla M, Wooll J, Laue TM, et al. Role of protein - protein bridging interactions on cooperative assembly of DNA - bound CRP - CytR - CRP complex and regulation of the Escherichia Coli CytR regulon[J]. Biochemistry, 2003, 42(13): 3812-3825
[23] Jacob, F. La Logique du Vivant, Une Histoire de L'Hérédité, 1st edn, Gallimard, 1970
[24] Browning DF, Butala M, Busby SJW. Bacterial transcription factors: regulation by pick “N” mix[J]. J Mol Biol, 2019, 431(20): 4067-4077
[25] Martin RG, Gillette WK, Martin NI, et al. Complex formation between activator and RNA polymerase as the basis for transcriptional activation by MarA and SoxS in Escherichia coli[J]. Mol Microbiol, 2002, 43(2): 355-370
[26] Pérez-Rueda E, Janga SC. Identification and genomic analysis of transcription factors in archaeal genomes exemplifies their functional architecture and evolutionary origin[J]. Mol Biol Evol, 2010, 27(6): 1449-1459
[27] Bintu L, Buchler NE, Garcia HG, et al. Transcriptional regulation by the numbers: applications[J]. Curr Opin Genet Dev, 2005, 15(2): 125-135
[28] Busby S, Ebright RH. Promoter structure, promoter recognition, and transcription activation in prokaryotes [J]. Cell, 1994, 79(5): 743-746
[29] Brown NL, Stoyanov JV, Kidd SP, et al. The MerR family of transcriptional regulators [J]. FEMS Microbiol Rev, 2003, 27(2-3): 145-163
[30] Wade JT, Grainger DC. Pervasive transcription: illuminating the dark matter of bacterial transcriptomes [J]. Nat Rev Microbiol, 2014, 12(9): 647-653
[31] Barnard A, Wolfe A, Busby S. Regulation at complex bacterial promoters: how bacteria use different promoter organizations to produce different regulatory outcomes [J]. Curr Opin Microbiol, 2004, 7(2): 102-108
[32] Yang Y, Darbari VC, Zhang N, et al. Structures of the RNA polymerase-σ54 reveal new and conserved regulatory strategies [J]. Science, 2015, 349(6250): 882-885
[33] Buck M, Gallegos MT, Studholme DJ, et al. The bacterial enhancer-dependent sigma(54) (sigma(N)) transcription factor[J]. J Bacteriol, 2000, 182(15): 4129-4136
[34] Pan X, Wu J, Xu S, et al. Contribution of OxyR towards differential sensitivity to antioxidants in Xanthomonas oryzae pathovars oryzae and oryzicola[J]. Mol Plant Microbe Interact, 2018, 31(12): 1244-1256
[35] Lim D, Kim K, Song M, et al. Transcriptional regulation of Salmochelin glucosyltransferase by Fur in Salmonella[J]. Biochem Biophys Res Commun, 2020, 529(1): 70-76
[36] Phelps TJ, Palumbo AV, Beliaev AS. Metabolomics and microarrays for improved understanding of phenotypic characteristics controlled by both genomics and environmental constraints[J]. Curr Opin Biotechnol, 2002, 13(1): 20-24
[37] Lee HH, Molla MN, Cantor CR, et al. Bacterial charity work leads to population-wide resistance[J]. Nature, 2010, 467(7311): 82-85
[38] Zheng J, Yu J, Jia M, et al. Indole enhances the survival of Pantoea ananatis YJ76 in face of starvation conditions [J]. J Basic Microbiol, 2017, 57(7): 633-639
[39] Barbier CS, Short SA, Senear DF. Allosteric mechanism of induction of CytR-regulated gene expression [J]. J Biol Chem, 1997, 272(27): 16962-16971
[40] Weickert MJ, Adhya S. A family of bacterial regulators homologous to Gal and Lac repressors [J]. J Biol Chem, 1992, 267(22): 15869-15874
[41] Jia M, Yu X, Jiang J, et al. The cytidine repressor participates in the regulatory pathway of indole in Pantoea agglomerans[J]. Res Microbiol, 2017, 168(7): 636-643
[42] Yu J, Jia M, Feng Y. The cytidine repressor regulates the survival of Pantoea agglomerans YS19 under oxidative stress and sulfur starvation conditions [J]. J Gen Appl Microbiol, 2021, doi: 10.2323/jgam. 2020.07.001
[43] Mongkolsuk S, Helmann JD. Regulation of inducible peroxide stress response[J]. Mol Microbiol, 2002, 45(1): 9-15
[44] Quadroni M, Staudenmann W, Kertesz M, et al. Analysis of global responses by protein and peptide fingerprinting of proteins isolated by two-dimensional gel electrophoresis[J]. Eur J Biochem, 1996, 239(3): 773-781
[45] Wu HC, Tyson KL, Cole JA, et al. Regulation of transcription initiation at the Escherichia coli nir operon promoter: a new mechanism to account for co-dependence on two transcription factors [J]. Mol Microbiol, 1998, 27(2): 493-505