Abstract
Transcriptional initiation is arguably the most important control point for gene expression. It is regulated by a combination of factors, including DNA sequence and its three-dimensional topology, proteins and small molecules. In this chapter, we focus on the trans-acting factors of bacterial regulation. Initiation begins with the recruitment of the RNA polymerase holoenzyme to a specific locus upstream of the gene known as its promoter. The sigma factor, which is a component of the holoenzyme, provides the most fundamental mechanisms for orchestrating broad changes in gene expression state. It is responsible for promoter recognition as well as recruiting the holoenzyme to the promoter. Distinct sigma factors compete with for binding to a common pool of RNA polymerases, thus achieving condition-dependent differential expression. Another important class of bacterial regulators is transcription factors, which activate or repress transcription of target genes typically in response to an environmental or cellular trigger. These factors may be global or local depending on the number of genes and range of cellular functions that they target. The activities of both global and local transcription factors may be regulated either at a post-transcriptional level via signal-sensing protein domains or at the level of their own expression. In addition to modulating polymerase recruitment to promoters, several global factors are considered as “nucleoid-associated proteins” that impose structural constraints on the chromosome by altering the conformation of the bound DNA, thus influencing other processes involving DNA such as replication and recombination. This chapter concludes with a discussion of how regulatory interactions between transcription factors and their target genes can be represented as a network.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Browning DF, Busby SJ (2004) The regulation of bacterial transcription initiation. Nat Rev Microbiol 2:57–65
Goldman SR, Ebright RH, Nickels BE (2009) Direct detection of abortive RNA transcripts in vivo. Science 324:927–928
Gruber TM, Gross CA (2003) Multiple sigma subunits and the partitioning of bacterial transcription space. Annu Rev Microbiol 57:441–466
Pérez-Rueda E, Janga SC, Martínez-Antonio A (2009) Scaling relationship in the gene content of transcriptional machinery in bacteria. Mol Biosyst 5:1494–1501
Holland AM, Rather PN (2008) Evidence for extracellular control of RpoS proteolysis in Escherichia coli. FEMS Microbiol Lett 286:50–59
Balandina A, Claret L, Hengge-Aronis R, et al (2001) The Escherichia coli histone-like protein HU regulates rpoS translation. Mol Microbiol 39:1069–1079
Zhou Y, Gottesman S, Hoskins JR, et al (2001) The RssB response regulator directly targets sigma (S) for degradation by ClpXP. Genes Dev 15:627–637
Yamashino T, Ueguchi C, Mizuno T (1995) Quantitative control of the stationary phase-specific sigma factor, sigma S, in Escherichia coli: involvement of the nucleoid protein H-NS. EMBO J 14:594–602
Jishage M, Ishihama A (1998) A stationary phase protein in Escherichia coli with binding activity to the major sigma subunit of RNA polymerase. Proc Natl Acad Sci U S A 95:4953–4958
Jishage M, Kvint K, Shingler V, et al (2002) Regulation of sigma factor competition by the alarmone ppGpp. Genes Dev 16:1260–1270
Wassarman KM, Storz G (2000) 6S RNA regulates E. coli RNA polymerase activity. Cell 101:613–623
Shin M, Song M, Rhee JH, et al (2005) DNA looping-mediated repression by histone-like protein H-NS: specific requirement of Esigma70 as a cofactor for looping. Genes Dev 19:2388–2398
Typas A, Hengge R (2006) Role of the spacer between the -35 and -10 regions in sigmas promoter selectivity in Escherichia coli. Mol Microbiol 59:1037–1051
Typas A, Becker G, Hengge R (2007) The molecular basis of selective promoter activation by the sigmaS subunit of RNA polymerase. Mol Microbiol 63:1296–1306
Wade JT, Roa DC, Grainger DC, et al (2006) Extensive functional overlap between sigma factors in Escherichia coli. Nat Struct Mol Biol 13:806–814
Waldminghaus T, Skarstad K (2010) ChIP on Chip: surprising results are often artifacts. BMC Genomics 11:414
Hansen UM, McClure WR (1980) Role of the sigma subunit of Escherichia coli RNA polymerase in initiation. II. Release of sigma from ternary complexes. J Biol Chem 255:9564–9570
Travers AA, Burgess RR (1969) Cyclic re-use of the RNA polymerase sigma factor. Nature 222:537–540
Straney DC, Crothers DM (1985) Intermediates in transcription initiation from the E. coli lac UV5 promoter. Cell 43:449–459
Kapanidis AN, Margeat E, Laurence TA, et al (2005) Retention of transcription initiation factor sigma70 in transcription elongation: single-molecule analysis. Mol Cell 20:347–356
Mukhopadhyay J, Kapanidis AN, Mekler V, et al (2001) Translocation of sigma (70) with RNA polymerase during transcription: fluorescence resonance energy transfer assay for movement relative to DNA. Cell 106:453–463
Reppas NB, Wade JT, Church GM, et al (2006) The transition between transcriptional initiation and elongation in E. coli is highly variable and often rate limiting. Mol Cell 24:747–757
Mooney RA, Landick R (2003) Tethering sigma70 to RNA polymerase reveals high in vivo activity of sigma factors and sigma70-dependent pausing at promoter-distal locations. Genes Dev 17:2839–2851
Ring BZ, Yarnell WS, Roberts JW (1996) Function of E. coli RNA polymerase sigma factor sigma 70 in promoter-proximal pausing. Cell 86:485–493
Salgado H, Martínez-Antonio A, Janga SC (2007) Conservation of transcriptional sensing systems in prokaryotes: a perspective from Escherichia coli. FEBS Lett 581:3499–3506
Finn RD, Mistry J, Tate J, et al (2010) The Pfam protein families database. Nucleic Acids Res 38:D211–D222
Altschul SF, Madden TL, Schäffer AA, et al (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389–3402
Pfreundt U, James DP, Tweedie S, et al (2010) FlyTF: improved annotation and enhanced functionality of the Drosophila transcription factor database. Nucleic Acids Res 38:D443–D447
Gama-Castro S, Jiménez-Jacinto V, Peralta-Gil M, et al (2008) RegulonDB (version 6.0): gene regulation model of Escherichia coli K-12 beyond transcription, active (experimental) annotated promoters and Textpresso navigation. Nucleic Acids Res 36:D120–D124
Charoensawan V, Wilson D, Teichmann SA (2010) Genomic repertoires of DNA-binding transcription factors across the tree of life. Nucleic Acids Res 38:7364–7377
van Nimwegen E (2003) Scaling laws in the functional content of genomes. Trends Genet 19:479–484
Ranea JA, Grant A, Thornton JM, et al (2005) Microeconomic principles explain an optimal genome size in bacteria. Trends Genet 21:21–25
Madan Babu M, Teichmann SA (2003) Evolution of transcription factors and the gene regulatory network in Escherichia coli. Nucleic Acids Res 31:1234–1244
Madan Babu M, Teichmann SA, Aravind L (2006) Evolutionary dynamics of prokaryotic transcriptional regulatory networks. J Mol Biol 358:614–633
Cole ST, Eiglmeier K, Parkhill J, et al (2001) Massive gene decay in the leprosy bacillus. Nature 409:1007–1011
Andersson SG, Zomorodipour A, Andersson JO, et al (1998) The genome sequence of Rickettsia prowazekii and the origin of mitochondria. Nature 396:133–140
Anantharaman V, Koonin EV, Aravind L (2001) Regulatory potential, phyletic distribution and evolution of ancient, intracellular small-molecule-binding domains. J Mol Biol 307:1271–1292
Keseler IM, Bonavides-Martínez C, Collado-Vides J, et al (2009) EcoCyc: a comprehensive view of Escherichia coli biology. Nucleic Acids Res 37:D464–D470
Sellick CA, Reece RJ (2005) Eukaryotic transcription factors as direct nutrient sensors. Trends Biochem Sci 30:405–412
Martínez-Antonio A, Collado-Vides J (2003) Identifying global regulators in transcriptional regulatory networks in bacteria. Curr Opin Microbiol 6:482–489
Kahramanoglou C, Seshasayee ASN, Prieto AI, et al (2011) Direct and indirect effects of H-NS and Fis on global gene expression control in Escherichia coli. Nucleic Acids Res 39:2073–2091
Seshasayee AS, Fraser GM, Babu MM, et al (2009) Principles of transcriptional regulation and evolution of the metabolic system in E. coli. Genome Res 19:79–91
Anderson JJ, Quay SC, Oxender DL (1976) Mapping of two loci affecting the regulation of branched-chain amino acid transport in Escherichia coli K-12. J Bacteriol 126:80–90
Lin R, D’Ari R, Newman EB (1992) Lambda placMu insertions in genes of the leucine regulon: extension of the regulon to genes not regulated by leucine. J Bacteriol 174:1948–1955
Chen S, Hao Z, Bieniek E, et al (2001) Modulation of Lrp action in Escherichia coli by leucine: effects on non-specific binding of Lrp to DNA. J Mol Biol 314:1067–1075
Cho BK, Barrett CL, Knight EM, et al (2008) Genome-scale reconstruction of the Lrp regulatory network in Escherichia coli. Proc Natl Acad Sci U S A 105:19462–19467
Calvo JM, Matthews RG (1994) The leucine-responsive regulatory protein, a global regulator of metabolism in Escherichia coli. Microbiol Rev 58:466–490
Chen S, Rosner MH, Calvo JM (2001) Leucine-regulated self-association of leucine-responsive regulatory protein (Lrp) from Escherichia coli. J Mol Biol 312:625–635
McFarland KA, Lucchini S, Hinton JC, et al (2008) The leucine-responsive regulatory protein, Lrp, activates transcription of the fim operon in Salmonella enterica serovar typhimurium via the fimZ regulatory gene. J Bacteriol 190:602–612
Tapias A, López G, Ayora S (2000) Bacillus subtilis LrpC is a sequence-independent DNA-binding and DNA-bending protein which bridges DNA. Nucleic Acids Res 28:552–559
Beloin C, Jeusset J, Revet B, et al (2003) Contribution of DNA conformation and topology in right-handed DNA wrapping by the Bacillus subtilis LrpC protein. J Biol Chem 278:5333–5342
Zheng D, Constantinidou C, Hobman JL, et al (2004) Identification of the CRP regulon using in vitro and in vivo transcriptional profiling. Nucleic Acids Res 32:5874–5893
Soutourina O, Kolb A, Krin E, et al (1999) Multiple control of flagellum biosynthesis in Escherichia coli: role of H-NS protein and the cyclic AMP-catabolite activator protein complex in transcription of the flhDC master operon. J Bacteriol 181:7500–7508
Liu M, Durfee T, Cabrera JE, et al (2005) Global transcriptional programs reveal a carbon source foraging strategy by Escherichia coli. J Biol Chem 280:15921–15927
Grainger DC, Hurd D, Harrison M, et al (2005) Studies of the distribution of Escherichia coli cAMP-receptor protein and RNA polymerase along the E. coli chromosome. Proc Natl Acad Sci U S A 102:17693–17698
Lin SH, Lee JC (2003) Determinants of DNA bending in the DNA-cyclic AMP receptor protein complexes in Escherichia coli. Biochemistry 42:4809–4818
Napoli AA, Lawson CL, Ebright RH, et al (2006) Indirect readout of DNA sequence at the primary-kink site in the CAP-DNA complex: recognition of pyrimidine-purine and purine-purine steps. J Mol Biol 357:173–183
Schneider R, Travers A, Muskhelishvili G (1997) FIS modulates growth phase-dependent topological transitions of DNA in Escherichia coli. Mol Microbiol 26:519–530
Ali Azam T, Iwata A, Nishimura A, et al (1999) Growth phase-dependent variation in protein composition of the Escherichia coli nucleoid. J Bacteriol 181:6361–6370
Browning DF, Cole JA, Busby SJ (2008) Regulation by nucleoid-associated proteins at the Escherichia coli nir operon promoter. J Bacteriol 190:7258–7267
Grainger DC, Goldberg MD, Lee DJ, et al (2008) Selective repression by Fis and H-NS at the Escherichia coli dps promoter. Mol Microbiol 68:1366–1377
Squire DJ, Xu M, Cole JA, et al (2009) Competition between NarL-dependent activation and Fis-dependent repression controls expression from the Escherichia coli yeaR and ogt promoters. Biochem J 420:249–257
Bradley MD, Beach MB, de Koning AP, et al (2007) Effects of Fis on Escherichia coli gene expression during different growth stages. Microbiology 153:2922–2940
Cho BK, Knight EM, Barrett CL, et al (2008) Genome-wide analysis of Fis binding in Escherichia coli indicates a causative role for A-/AT-tracts. Genome Res 18:900–910
Maurer S, Fritz J, Muskhelishvili G (2009) A systematic in vitro study of nucleoprotein complexes formed by bacterial nucleoid-associated proteins revealing novel types of DNA organization. J Mol Biol 387:1261–1276
Schneider R, Lurz R, Lüder G, et al (2001) An architectural role of the Escherichia coli chromatin protein FIS in organising DNA. Nucleic Acids Res 29:5107–5114
Dorman CJ (2004) H-NS: a universal regulator for a dynamic genome. Nat Rev Microbiol 2:391–400
Dame RT, Luijsterburg MS, Krin E, et al (2005) DNA bridging: a property shared among H-NS-like proteins. J Bacteriol 187:1845–1848
Dame RT, Noom MC, Wuite GJ (2006) Bacterial chromatin organization by H-NS protein unravelled using dual DNA manipulation. Nature 444:387–390
Dorman CJ (2007) Probing bacterial nucleoid structure with optical tweezers. Bioessays 29:212–216
Noom MC, Navarre WW, Oshima T, Wuite GJ, Dame RT (2007) H-NS promotes looped domain formation in the bacterial chromosome. Curr Biol 17:R913–R914
Oshima T, Ishikawa S, Kurokawa K, et al (2006) Escherichia coli histone-like protein H-NS preferentially binds to horizontally acquired DNA in association with RNA polymerase. DNA Res 13:141–153
Doyle M, Fookes M, Ivens A, et al (2007) An H-NS-like stealth protein aids horizontal DNA transmission in bacteria. Science 315:251–252
Lucchini S, Rowley G, Goldberg MD, et al (2006) H-NS mediates the silencing of laterally acquired genes in bacteria. PLoS Pathog 2:e81
Schechter LM, Jain S, Akbar S, et al (2003) The small nucleoid-binding proteins H-NS, HU, and Fis affect hilA expression in Salmonella enterica serovar Typhimurium. Infect Immun 71:5432–5435
Hinton JC, Santos DS, Seirafi A, et al (1992) Expression and mutational analysis of the nucleoid-associated protein H-NS of Salmonella typhimurium. Mol Microbiol 6:2327–2337
Baños RC, Vivero A, Aznar S, et al (2009) Differential regulation of horizontally acquired and core genome genes by the bacterial modulator H-NS. PLoS Genet 5:e1000513
Barth M, Marschall C, Muffler A, et al (1995) Role for the histone-like protein H-NS in growth phase-dependent and osmotic regulation of sigma S and many sigma S-dependent genes in Escherichia coli. J Bacteriol 177:3455–3464
Stoebel DM, Free A, Dorman CJ (2008) Anti-silencing: overcoming H-NS-mediated repression of transcription in Gram-negative enteric bacteria. Microbiology 154:2533–2545
Grillo AO, Brown MP, Royer CA (1999) Probing the physical basis for trp repressor-operator recognition. J Mol Biol 287:539–554
Hartwell LH, Hopfield JJ, Leibler S, et al (1999) From molecular to modular cell biology. Nature 402:C47–C52
Ma HW, Kumar B, Ditges U, et al (2004) An extended transcriptional regulatory network of Escherichia coli and analysis of its hierarchical structure and network motifs. Nucleic Acids Res 32:6643–6649
Balázsi G, Barabási AL, Oltvai ZN (2005) Topological units of environmental signal processing in the transcriptional regulatory network of Escherichia coli. Proc Natl Acad Sci U S A 102:7841–7846
Freyre-González JA, Alonso-Pavón JA, Treviño-Quintanilla LG, et al (2008) Functional architecture of Escherichia coli: new insights provided by a natural decomposition approach. Genome Biol 9:R154
Resendis-Antonio O, Freyre-González JA, Menchaca-Méndez R, et al (2005) Modular analysis of the transcriptional regulatory network of E. coli. Trends Genet 21:16–20
Shen-Orr SS, Milo R, Mangan S, et al (2002) Network motifs in the transcriptional regulation network of Escherichia coli. Nat Genet 31:64–68
Martínez-Antonio A, Janga SC, Thieffry D (2008) Functional organisation of Escherichia coli transcriptional regulatory network. J Mol Biol 381:238–247
Cerca N, Jefferson KK (2008) Effect of growth conditions on poly-N-acetylglucosamine expression and biofilm formation in Escherichia coli. FEMS Microbiol Lett 283:36–41
Romeo T (1998) Global regulation by the small RNA-binding protein CsrA and the non-coding RNA molecule CsrB. Mol Microbiol 29:1321–1330
Kaplan S, Bren A, Zaslaver A, et al (2008) Diverse two-dimensional input functions control bacterial sugar genes. Mol Cell 29:786–792
Lozada-Chávez I, Janga SC, Collado-Vides J (2006) Bacterial regulatory networks are extremely flexible in evolution. Nucleic Acids Res 34:3434–3445
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2011 Springer Science+Business Media B.V.
About this chapter
Cite this chapter
Seshasayee, A.S.N., Sivaraman, K., Luscombe, N.M. (2011). An Overview of Prokaryotic Transcription Factors. In: Hughes, T. (eds) A Handbook of Transcription Factors. Subcellular Biochemistry, vol 52. Springer, Dordrecht. https://doi.org/10.1007/978-90-481-9069-0_2
Download citation
DOI: https://doi.org/10.1007/978-90-481-9069-0_2
Published:
Publisher Name: Springer, Dordrecht
Print ISBN: 978-90-481-9068-3
Online ISBN: 978-90-481-9069-0
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)