Chapter 1 : Structure and Evolution of Transcriptional Regulatory Networks

MyBook is a cheap paperback edition of the original book and will be sold at uniform, low price.

Preview this chapter:
Zoom in

Structure and Evolution of Transcriptional Regulatory Networks, Page 1 of 2

| /docserver/preview/fulltext/10.1128/9781555816841/9781555816216_Chap01-1.gif /docserver/preview/fulltext/10.1128/9781555816841/9781555816216_Chap01-2.gif


Regulation of transcription is mediated through proteins called transcription factors (TFs). TFs are DNA binding proteins that bind to specific regions, the -regulatory elements, in the promoter regions of certain genes and eventually influence gene expression. The binding of a TF to a promoter region can either result in an increased or decreased transcription of the regulated target gene (TG). The first part of this chapter discusses the main characteristics of the structure of prokaryotic transcriptional regulatory networks (TRNs). The second part discusses the various forces that influence their evolution, and finally the chapter discusses how the understanding gained is being exploited in biotechnology and medicine. Horizontal gene transfer (HGT) requires the physical incorporation of foreign DNA into the receiver organism, its integration into the host regulatory network, and eventually its selection through the bacterial population. The incorporation of DNA during HGT is driven by three distinct mechanisms referred to as conjugation, transduction, and transformation. Approaches used to address the problem of the inference of TRN from other prokaryotes can broadly be grouped into two categories, depending on whether one focuses on orthology or on sequence similarity of TF binding sites.

Citation: Chalancon G, Babu M. 2011. Structure and Evolution of Transcriptional Regulatory Networks, p 3-16. In Storz G, Hengge R (ed), Bacterial Stress Responses, Second Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816841.ch1
Highlighted Text: Show | Hide
Loading full text...

Full text loading...


Image of Figure 1.
Figure 1.

Structure of a TRN. (A) The basic unit consists of a TF, which recognizes specific regulatory sequence upstream of its TG. (B) At the local level, the basic units assemble to form network motifs (FFM, SIM, and MIM). (C) At the global level, TRNs display a scale-free topology, which is characterized by the presence of a few TFs (hubs or global regulators) that regulate many genes and many TFs that regulate a few genes.

Citation: Chalancon G, Babu M. 2011. Structure and Evolution of Transcriptional Regulatory Networks, p 3-16. In Storz G, Hengge R (ed), Bacterial Stress Responses, Second Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816841.ch1
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 2.
Figure 2.

The major evolutionary forces that drive TRN evolution.

Citation: Chalancon G, Babu M. 2011. Structure and Evolution of Transcriptional Regulatory Networks, p 3-16. In Storz G, Hengge R (ed), Bacterial Stress Responses, Second Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816841.ch1
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 3.
Figure 3.

General principles of evolution at three distinct levels of network organization.

Citation: Chalancon G, Babu M. 2011. Structure and Evolution of Transcriptional Regulatory Networks, p 3-16. In Storz G, Hengge R (ed), Bacterial Stress Responses, Second Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816841.ch1
Permissions and Reprints Request Permissions
Download as Powerpoint


1. Acar, M.,, J. T. Mettetal, and, A. van Oudenaarden. 2008. Stochastic switching as a survival strategy in fluctuating environments. Nat. Genet. 40: 471475.
2. Ahmed, N.,, U. Dobrindt,, J. Hacker, and, S. E. Hasnain. 2008. Genomic fluidity and pathogenic bacteria: applications in diagnostics, epidemiology and intervention. Nat. Rev. Microbiol. 6: 387394.
3. Alon, U. 2007. Network motifs: theory and experimental approaches. Nat. Rev. Genet. 8: 450461.
4. Alper, H.,, C. Fischer,, E. Nevoigt, and, G. Stephanopoulos. 2005. Tuning genetic control through promoter engineering. Proc. Natl. Acad. Sci. USA 102: 1267812683.
5. An, W., and, J. W. Chin. 2009. Synthesis of orthogonal transcription-translation networks. Proc. Natl. Acad. Sci. USA 106: 84778482.
6. Anderson, J. C.,, E. J. Clarke,, A. P. Arkin, and, C. A. Voigt. 2006. Environmentally controlled invasion of cancer cells by engineered bacteria. J. Mol. Biol. 355: 619627.
7. Babu, M. M. 2008. Computational approaches to study transcriptional regulation. Biochem. Soc. Trans. 36: 758765.
8. Babu,, M. M.,, N. M. Luscombe,, L. Aravind,, M. Gerstein, and, S. A. Teichmann. 2004. Structure and evolution of transcriptional regulatory networks. Curr. Opin. Struct. Biol. 14: 283291.
9. Balaban,, N. Q.,, J. Merrin,, R. Chait,, L. Kowalik, and, S. Leibler. 2004. Bacterial persistence as a phenotypic switch. Science 305: 16221625.
10. Balaji, S.,, M. M. Babu, and, L. Aravind. 2007. Interplay between network structures, regulatory modes and sensing mechanisms of transcription factors in the transcriptional regulatory network of E. coli. J. Mol. Biol. 372: 11081122.
11. Barabasi, A. L., and, R. Albert. 1999. Emergence of scaling in random networks. Science 286: 509512.
12. Barabasi, A. L., and, Z. N. Oltvai. 2004. Network biology: understanding the cell’s functional organization. Nat. Rev. Genet. 5: 101113.
13. Becq,, J.,, M. C. Gutierrez,, V. Rosas-Magallanes,, J. Rauzier,, B. Gicquel,, O. Neyrolles, and, P. Deschavanne. 2007. Contribution of horizontally acquired genomic islands to the evolution of the tubercle bacilli. Mol. Biol. Evol. 24: 18611871.
14. Berger,, M.,, A. Farcas,, M. Geertz,, P. Zhelyazkova,, K. Brix,, A. Travers, and, G. Muskhelishvili. 2010. Coordination of genomic structure and transcription by the main bacterial nucleoid-associated protein HU. EMBO Rep. 11: 5964.
15. Brenner, S. E.,, T. Hubbard,, A. Murzin, and, C. Chothia. 1995. Gene duplications in H. influenzae. Nature 378: 140.
16. Brochet,, M.,, C. Rusniok,, E. Couve,, S. Dramsi,, C. Poyart,, P. Trieu-Cuot,, F. Kunst, and, P. Glaser. 2008. Shaping a bacterial genome by large chromosomal replacements, the evolutionary history of Streptococcus agalactiae. Proc. Natl. Acad. Sci. USA 105: 1596115966.
17. Browning, D. F., and, S. J. Busby. 2004. The regulation of bacterial transcription initiation. Nat. Rev. Microbiol. 2: 5765.
18. Brzuszkiewicz,, E.,, H. Bruggemann,, H. Liesegang,, M. Emmerth,, T. Olschlager,, G. Nagy,, K. Albermann,, C. Wagner,, C. Buchrieser,, L. Emody,, G. Gottschalk,, J. Hacker, and, U. Dobrindt. 2006. How to become a uropathogen: comparative genomic analysis of extraintestinal pathogenic Escherichia coli strains. Proc. Natl. Acad. Sci. USA 103: 1287912884.
19. Cagatay,, T.,, M. Turcotte,, M. B. Elowitz,, J. Garcia-Ojalvo, and, G. M. Suel. 2009. Architecture-dependent noise discriminates functionally analogous differentiation circuits. Cell 139: 512522.
20. Chen, I.,, P. J. Christie, and, D. Dubnau. 2005. The ins and outs of DNA transfer in bacteria. Science 310: 14561460.
21. Chin, J. W. 2006. Modular approaches to expanding the functions of living matter. Nat. Chem. Biol. 2: 304311.
22. Chothia, C., and, J. Gough. 2009. Genomic and structural aspects of protein evolution. Biochem. J. 419: 1528.
23. Conant, G. C., and, A. Wagner. 2003. Convergent evolution of gene circuits. Nat. Genet. 34: 264266.
24. Cosentino Lagomarsino, M.,, P. Jona,, B. Bassetti, and, H. Isambert. 2007. Hierarchy and feedback in the evolution of the Escherichia coli transcription network. Proc. Natl. Acad. Sci. USA 104: 55165520.
25. Dantas, G., M. O. Sommer,, R. D. Oluwasegun, and, G. M. Church. 2008. Bacteria subsisting on antibiotics. Science 320: 100103.
26. Davies, J., and, F. Jacob. 1968. Genetic mapping of the regulator and operator genes of the lac operon. J. Mol. Biol. 36: 413417.
27. Dekel, E., and, U. Alon. 2005. Optimality and evolutionary tuning of the expression level of a protein. Nature 436: 588592.
28. Dillon, S. C., and, C. J. Dorman. 2010. Bacterial nucleoid-associated proteins, nucleoid structure and gene expression. Nat. Rev. Microbiol. 8: 185195.
29. Dorman, C. J. 2007. H-NS, the genome sentinel. Nat. Rev. Microbiol. 5: 157161.
30. Dorman, C. J. 2009a. Nucleoid-associated proteins and bacterial physiology. Adv. Appl. Microbiol. 67: 4764.
31. Dorman, C. J. 2009b. Regulatory integration of horizontally-transferred genes in bacteria. Front. Biosci. 14: 41034112.
32. Doyle,, M.,, M. Fookes,, A. Ivens,, M. W. Mangan,, J. Wain, and, C. J. Dorman. 2007. An H-NS-like stealth protein aids horizontal DNA transmission in bacteria. Science 315: 251252.
33. Foster, P. L. 2007. Stress-induced mutagenesis in bacteria. Crit. Rev. Biochem. Mol. Biol. 42: 373397.
34. Gama-Castro,, S.,, V. Jimenez-Jacinto,, M. Peralta-Gil,, A. Santos-Zavaleta,, M. I. Penaloza-Spinola,, B. Contreras-Moreira,, J. Segura-Salazar,, L. Muniz-Rascado,, I. Martinez-Flores,, H. Salgado,, C. Bonavides-Martinez,, C. Abreu-Goodger,, C. Rodriguez-Penagos,, J. Miranda-Rios,, E. Morett,, E. Merino,, A. M. Huerta,, L. Trevino-Quintanilla, and, J. Collado-Vides. 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:D 120124.
35. Gelfand, M. S. 2006. Evolution of transcriptional regulatory networks in microbial genomes. Curr. Opin. Struct. Biol. 16: 420429.
36. Grainger,, D. C.,, D. Hurd,, M. Harrison,, J. Holdstock, and, S. J. Busby. 2005. Studies of the distribution of Escherichia coli cAMP-receptor protein and RNA polymerase along the E. coli chromosome. Proc. Natl. Acad. Sci. USA 102: 1769317698.
37. Grainger, D. C.,, D. J. Lee, and, S. J. Busby. 2009. Direct methods for studying transcription regulatory proteins and RNA polymerase in bacteria. Curr. Opin. Microbiol. 12: 531535.
38. Hengge, R. 2009. Principles of c-di-GMP signalling in bacteria. Nat. Rev. Microbiol. 7: 263273.
39. Hershberg, R., and, H. Margalit. 2006. Co-evolution of transcription factors and their targets depends on mode of regulation. Genome Biol. 7: R62.
40. Isalan,, M.,, C. Lemerle,, K. Michalodimitrakis,, C. Horn,, P. Beltrao,, E. Raineri,, M. Garriga-Canut, and, L. Serrano. 2008. Evolvability and hierarchy in rewired bacterial gene networks. Nature 452: 840845.
41. Janga, S. C., and, J. Collado-Vides. 2007. Structure and evolution of gene regulatory networks in microbial genomes. Res. Microbiol. 158: 787794.
42. Janga, S. C.,, H. Salgado,, J. Collado-Vides, and, A. Martinez-Antonio. 2007a. Internal versus external effector and transcription factor gene pairs differ in their relative chromosomal position in Escherichia coli. J. Mol. Biol. 368: 263272.
43. Janga, S. C.,, H. Salgado,, A. Martinez-Antonio, and, J. Collado-Vides. 2007b. Coordination logic of the sensing machinery in the transcriptional regulatory network of Escherichia coli. Nucleic Acids Res. 35: 69636972.
44. Janky, R.,, J. Helden, and, M. M. Babu. 2009. Investigating transcriptional regulation: from analysis of complex networks to discovery of cis-regulatory elements. Methods 48: 277286.
45. Jayaraman, R. 2008. Bacterial persistence: some new insights into an old phenomenon. J. Biosci. 33: 795805.
46. Jothi,, R.,, S. Balaji,, A. Wuster,, J. A. Grochow,, J. Gsponer,, T. M. Przytycka,, L. Aravind, and, M. M. Babu. 2009. Genomic analysis reveals a tight link between transcription factor dynamics and regulatory network architecture. Mol. Syst. Biol. 5: 294.
47. Juhas,, M.,, J. R. van der Meer,, M. Gaillard,, R. M. Harding,, D. W. Hood, and, D. W. Crook. 2009. Genomic islands: tools of bacterial horizontal gene transfer and evolution. FEMS Microbiol. Rev. 33: 376393.
48. Kalir,, S.,, J. McClure,, K. Pabbaraju,, C. Southward,, M. Ronen,, S. Leibler,, M. G. Surette, and, U. Alon. 2001. Ordering genes in a flagella pathway by analysis of expression kinetics from living bacteria. Science 292: 20802083.
49. Kiel, C.,, E. Yus, and, L. Serrano. 2010. Engineering signal transduction pathways. Cell 140: 3347.
50. Kitano, H. 2004. Biological robustness. Nat. Rev. Genet. 5: 826837.
51. Koonin, E. V.,, K. S. Makarova, and, L. Aravind. 2001. Horizontal gene transfer in prokaryotes: quantification and classification. Annu. Rev. Microbiol. 55: 709742.
52. Kunin, V.,, L. Goldovsky,, N. Darzentas, and, C. A. Ouzounis. 2005. The net of life: reconstructing the microbial phylogenetic network. Genome Res. 15: 954959.
53. Lee,, T. I.,, N. J. Rinaldi,, F. Robert,, D. T. Odom,, Z. Bar-Joseph,, G. K. Gerber,, N. M. Hannett,, C. T. Harbison,, C. M. Thompson,, I. Simon,, J. Zeitlinger,, E. G. Jennings,, H. L. Murray,, D. B. Gordon,, B. Ren,, J. J. Wyrick,, J. B. Tagne,, T. L. Volkert,, E. Fraenkel,, D. K. Gifford, and, R. A. Young. 2002. Transcriptional regulatory networks in Saccharomyces cerevisiae. Science 298: 799804.
54. Leonard, E.,, D. Nielsen,, K. Solomon, and, K. J. Prather. 2008. Engineering microbes with synthetic biology frameworks. Trends Biotechnol. 26: 674681.
55. Lerat, E.,, V. Daubin,, H. Ochman, and, N. A. Moran. 2005. Evolutionary origins of genomic repertoires in bacteria. PLoS Biol. 3: e130.
56. Lercher, M. J., and, C. Pal. 2008. Integration of horizontally transferred genes into regulatory interaction networks takes many million years. Mol. Biol. Evol. 25: 559567.
57. Losick, R., and, C. Desplan. 2008. Stochasticity and cell fate. Science 320: 6568.
58. Lozada-Chavez, I.,, S. C. Janga, and, J. Collado-Vides. 2006. Bacterial regulatory networks are extremely flexible in evolution. Nucleic Acids Res. 34: 34343445.
59. Lu,, T. K.,, A. S. Khalil, and, J. J. Collins. 2009. Next-generation synthetic gene networks. Nat. Biotechnol. 27: 11391150.
60. Luijsterburg, M. S.,, M. C. Noom,, G. J. Wuite, and, R. T. Dame. 2006. The architectural role of nucleoid-associated proteins in the organization of bacterial chromatin: a molecular perspective. J. Struct. Biol. 156: 262272.
61. Luijsterburg,, M. S.,, M. F. White,, R. van Driel, and, R. T. Dame. 2008. The major architects of chromatin: architectural proteins in bacteria, archaea and eukaryotes. Crit. Rev. Biochem. Mol. Biol. 43: 393418.
62. Luscombe,, N. M.,, M. M. Babu,, H. Yu,, M. Snyder,, S. A. Teichmann, and, M. Gerstein. 2004. Genomic analysis of regulatory network dynamics reveals large topological changes. Nature 431: 308312.
63. Lynch, M. 2007. The evolution of genetic networks by non-adaptive processes. Nat. Rev. Genet. 8: 803813.
64. Lynch, M., and, J. S. Conery. 2000. The evolutionary fate and consequences of duplicate genes. Science 290: 11511155.
65. Ma, H. W.,, J. Buer, and, A. P. Zeng. 2004. Hierarchical structure and modules in the Escherichia coli transcriptional regulatory network revealed by a new top-down approach. BMC Bioinformatics 5: 199.
66. Maamar, H.,, A. Raj, and, D. Dubnau. 2007. Noise in gene expression determines cell fate in Bacillus subtilis. Science 317: 526529.
67. Madan Babu, M., and, S. A. Teichmann. 2003. Evolution of transcription factors and the gene regulatory network in Escherichia coli. Nucleic Acids Res. 31: 12341244.
68. Madan Babu, M.,, S. A. Teichmann, and, L. Aravind. 2006. Evolutionary dynamics of prokaryotic transcriptional regulatory networks. J. Mol. Biol. 358: 614633.
69. Mangan, S., and, U. Alon. 2003. Structure and function of the feed-forward loop network motif. Proc. Natl. Acad. Sci. USA 100: 1198011985.
70. Mangan, S.,, S. Itzkovitz,, A. Zaslaver, and, U. Alon. 2006. The incoherent feed-forward loop accelerates the response-time of the gal system of Escherichia coli. J. Mol. Biol. 356: 10731081.
71. Marino-Ramirez, L.,, K. C. Lewis,, D. Landsman, and, I. K. Jordan. 2005. Transposable elements donate lineage-specific regulatory sequences to host genomes. Cytogenet. Genome Res. 110: 333341.
72. Marr, C.,, M. Geertz,, M. T. Hutt, and, G. Muskhelishvili. 2008. Dissecting the logical types of network control in gene expression profiles. BMC Syst. Biol. 2: 18.
73. Martinez, J. L. 2008. Antibiotics and antibiotic resistance genes in natural environments. Science 321: 365367.
74. Martinez-Antonio, A.,, S. C. Janga, and, D. Thieffry. 2008. Functional organisation of Escherichia coli transcriptional regulatory network. J. Mol. Biol. 381: 238247.
75. McAdams, H. H.,, B. Srinivasan, and, A. P. Arkin. 2004. The evolution of genetic regulatory systems in bacteria. Nat. Rev. Genet. 5: 169178.
76. Milo,, R.,, S. Shen-Orr,, S. Itzkovitz,, N. Kashtan,, D. Chklovskii, and, U. Alon. 2002. Network motifs: simple building blocks of complex networks. Science 298: 824827.
77. Molle,, V.,, Y. Nakaura,, R. P. Shivers,, H. Yamaguchi,, R. Losick,, Y. Fujita, and, A. L. Sonenshein. 2003. Additional targets of the Bacillus subtilis global regulator CodY identified by chromatin immunoprecipitation and genome-wide transcript analysis. J. Bacteriol. 185: 19111922.
78. Monot,, M.,, N. Honore,, T. Garnier,, N. Zidane,, D. Sherafi,, A. Paniz-Mondolfi,, M. Matsuoka,, G. M. Taylor,, H. D. Donoghue,, A. Bouwman,, S. Mays,, C. Watson,, D. Lockwood,, A. Khamispour,, Y. Dowlati,, S. Jianping,, T. H. Rea,, L. Vera-Cabrera,, M. M. Stefani,, S. Banu,, M. Macdonald,, B. R. Sapkota,, J. S. Spencer,, J. Thomas,, K. Harshman,, P. Singh,, P. Busso,, A. Gattiker,, J. Rougemont,, P. J. Brennan, and, S. T. Cole. 2009. Comparative genomic and phylogeographic analysis of Mycobacterium leprae. Nat. Genet. 41: 12821289.
79. Montange, R. K., and, R. T. Batey. 2008. Riboswitches: emerging themes in RNA structure and function. Annu. Rev. Biophys. 37: 117133.
80. Nakamura, Y.,, T. Itoh,, H. Matsuda, and, T. Gojobori. 2004. Biased biological functions of horizontally transferred genes in prokaryotic genomes. Nat. Genet. 36: 760766.
81. Navarre, W. W.,, M. McClelland,, S. J. Libby, and, F. C. Fang. 2007. Silencing of xenogeneic DNA by H-NS-facilitation of lateral gene transfer in bacteria by a defense system that recognizes foreign DNA. Genes Dev. 21: 14561471.
82. Navarre,, W. W.,, S. Porwollik,, Y. Wang,, M. McClelland,, H. Rosen,, S. J. Libby, and, F. C. Fang. 2006. Selective silencing of foreign DNA with low GC content by the H-NS protein in Salmonella. Science 313: 236238.
83. Ooka,, T., Y. Ogura,, M. Asadulghani,, M. Ohnishi,, K. Nakayama,, J. Terajima,, H. Watanabe, and, T. Hayashi. 2009. Inference of the impact of insertion sequence (IS) elements on bacterial genome diversification through analysis of small-size structural polymorphisms in Escherichia coli O157 genomes. Genome Res. 19: 18091816.
84. Osborne,, S. E.,, D. Walthers,, A. M. Tomljenovic,, D. T. Mulder,, U. Silphaduang,, N. Duong,, M. J. Lowden,, M. E. Wickham,, R. F. Waller,, L. J. Kenney, and, B. K. Coombes. 2009. Pathogenic adaptation of intracellular bacteria by rewiring a cis regulatory input function. Proc. Natl. Acad. Sci. USA 106: 39823987.
85. Osbourn, A. E., and, B. Field. 2009. Operons. Cell. Mol. Life Sci. 66: 37553775.
86. Perez, J. C., and, E. A. Groisman. 2009a. Evolution of transcriptional regulatory circuits in bacteria. Cell 138: 233244.
87. Perez, J. C., and, E. A. Groisman. 2009b. Transcription factor function and promoter architecture govern the evolution of bacterial regulons. Proc. Natl. Acad. Sci. USA 106: 43194324.
88. Pesavento, C., and, R. Hengge. 2009. Bacterial nucleotide-based second messengers. Curr. Opin. Microbiol. 12: 170176.
89. Price, M. N.,, P. S. Dehal, and, A. P. Arkin. 2007. Orthologous transcription factors in bacteria have different functions and regulate different genes. PLoS Comput. Biol. 3: 17391750.
90. Purnick, P. E., and, R. Weiss. 2009. The second wave of synthetic biology: from modules to systems. Nat. Rev. Mol. Cell Biol. 10: 410422.
91. Raj, A., and, A. van Oudenaarden. 2008. Nature, nurture, or chance: stochastic gene expression and its consequences. Cell 135: 216226.
92. Ronen, M.,, R. Rosenberg,, B. I. Shraiman, and, U. Alon. 2002. Assigning numbers to the arrows: parameterizing a gene regulation network by using accurate expression kinetics. Proc. Natl. Acad. Sci. USA 99: 1055510560.
93. Schirmer, T., and, U. Jenal. 2009. Structural and mechanistic determinants of c-di-GMP signalling. Nat. Rev. Microbiol. 7: 724735.
94. Sharma,, C. M.,, S. Hoffmann,, F. Darfeuille,, J. Reignier,, S. Findeiss,, A. Sittka,, S. Chabas,, K. Reiche,, J. Hackermuller,, R. Reinhardt,, P. F. Stadler, and, J. Vogel. 2010. The primary transcriptome of the major human pathogen Helicobacter pylori. Nature 464: 250255.
95. Shen-Orr, S. S.,, R. Milo,, S. Mangan, and, U. Alon. 2002. Network motifs in the transcriptional regulation network of Escherichia coli. Nat. Genet. 31: 6468.
96. Sorek,, R., Y. Zhu,, C. J. Creevey,, M. P. Francino,, P. Bork, and, E. M. Rubin. 2007. Genome-wide experimental determination of barriers to horizontal gene transfer. Science 318: 14491452.
97. Steen,, E. J.,, Y. Kang,, G. Bokinsky,, Z. Hu,, A. Schirmer,, A. McClure,, S. B. Del Cardayre, and, J. D. Keasling. 2010. Microbial production of fatty-acid-derived fuels and chemicals from plant biomass. Nature 463: 559562.
98. Steidler,, L., W. Hans,, L. Schotte,, S. Neirynck,, F. Obermeier,, W. Falk,, W. Fiers, and, E. Remaut. 2000. Treatment of murine colitis by Lactococcus lactis secreting interleukin-10. Science 289: 13521355.
99. Stoebel, D. M., A. Free, and, C. J. Dorman. 2008. Anti-silencing: overcoming H-NS-mediated repression of transcription in Gram-negative enteric bacteria. Microbiology 154: 25332545.
100. Storz, G., S. Altuvia, and, K. M. Wassarman. 2005. An abundance of RNA regulators. Annu. Rev. Biochem. 74: 199217.
101. Studier,, F. W.,, P. Daegelen,, R. E. Lenski,, S. Maslov, and, J. F. Kim. 2009. Understanding the differences between genome sequences of Escherichia coli B strains REL606 and BL21(DE3) and comparison of the E. coli B and K-12 genomes. J. Mol. Biol. 394: 653680.
102. Suel,, G. M., J. Garcia-Ojalvo,, L. M. Liberman, and, M. B. Elowitz. 2006. An excitable gene regulatory circuit induces transient cellular differentiation. Nature 440: 545550.
103. Suel,, G. M.,, R. P. Kulkarni,, J. Dworkin,, J. Garcia-Ojalvo, and, M. B. Elowitz. 2007. Tunability and noise dependence in differentiation dynamics. Science 315: 17161719.
104. Taoka,, M., Y. Yamauchi,, T. Shinkawa,, H. Kaji,, W. Motohashi,, H. Nakayama,, N. Takahashi, and, T. Isobe. 2004. Only a small subset of the horizontally transferred chromosomal genes in Escherichia coli are translated into proteins. Mol. Cell. Proteomics 3: 780787.
105. Teichmann, S. A., and, M. M. Babu. 2004. Gene regulatory network growth by duplication. Nat. Genet. 36: 492496.
106. Teichmann, S. A.,, J. Park, and, C. Chothia. 1998. Structural assignments to the Mycoplasma genitalium proteins show extensive gene duplications and domain rearrangements. Proc. Natl. Acad. Sci. USA 95: 1465814663.
107. Thieffry, D.,, A. M. Huerta,, E. Perez-Rueda, and, J. Collado-Vides. 1998. From specific gene regulation to genomic networks: a global analysis of transcriptional regulation in Escherichia coli. Bioessays 20: 433440.
108. Venancio, T. M., and, L. Aravind. 2009. Reconstructing prokaryotic transcriptional regulatory networks: lessons from actinobacteria. J. Biol. 8: 29.
109. Waters, L. S., and, G. Storz. 2009. Regulatory RNAs in bacteria. Cell 136: 615628.
110. Weber, H.,, C. Pesavento,, A. Possling,, G. Tischendorf, and, R. Hengge. 2006. Cyclic-di-GMP-mediated signalling within the sigma network of Escherichia coli. Mol. Microbiol. 62: 10141034.
111. Weber,, H., T. Polen,, J. Heuveling,, V. F. Wendisch,, and R. Hengge. 2005. Genome-wide analysis of the general stress response network in Escherichia coli: sigmaS-dependent genes, promoters, and sigma factor selectivity. J. Bacteriol. 187: 15911603.
112. Xu, J., and, D. A. Lavan. 2008. Designing artificial cells to harness the biological ion concentration gradient. Nat. Nanotechnol. 3: 666670.
113. Yu, H., and, M. Gerstein. 2006. Genomic analysis of the hierarchical structure of regulatory networks. Proc. Natl. Acad. Sci. USA 103: 1472414731.
114. Zaslaver,, A., A. Bren,, M. Ronen,, S. Itzkovitz,, I. Kikoin,, S. Shavit,, W. Liebermeister,, M. G. Surette, and, U. Alon. 2006. A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat. Methods 3: 623628.
115. Zaslaver,, A.,, A. E. Mayo,, R. Rosenberg,, P. Bashkin,, H. Sberro,, M. Tsalyuk,, M. G. Surette, and, U. Alon. 2004. Just-in-time transcription program in metabolic pathways. Nat. Genet. 36: 486491.


Generic image for table
Table 1.

Databases and computer programs for investigating transcriptional regulatory networks

Citation: Chalancon G, Babu M. 2011. Structure and Evolution of Transcriptional Regulatory Networks, p 3-16. In Storz G, Hengge R (ed), Bacterial Stress Responses, Second Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816841.ch1

This is a required field
Please enter a valid email address
Please check the format of the address you have entered.
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error