Adaptation in bacterial flagellar and motility systems: From regulon members to 'foraging'-like behavior in E. coli

Nucleic Acids Research

Volumn 35, Issue 13, 2007, Pages 4441-4452

  Zhao, Kai ^a   Liu, Mingzhu ^b,c,d   Burgess, Richard R ^a  

^a UNIVERSITY OF WISCONSIN MADISON   (United States)

^b UNIVERSITY OF WISCONSIN MADISON   (United States)

^c University of Wisconsin Madison   (United States)

^d UNIVERSITY OF WISCONSIN SCHOOL OF MEDICINE AND PUBLIC HEALTH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL PROTEIN; C REACTIVE PROTEIN; PROTEIN FLHDC; UNCLASSIFIED DRUG; CARBON; CRP PROTEIN, E COLI; CYCLIC AMP BINDING PROTEIN; DNA BINDING PROTEIN; ESCHERICHIA COLI PROTEIN; FLHC PROTEIN, E COLI; FLHD PROTEIN, E COLI; SIGMA E FACTOR; SIGMA FACTOR; SIGMA-E FACTOR; TRANSACTIVATOR PROTEIN; TRANSCRIPTION FACTOR;

ARTICLE; BACTERIAL FLAGELLUM; BACTERIAL GENOME; CARBON SOURCE; CELL MOTILITY; CHEMOTAXIS; CONTROLLED STUDY; ESCHERICHIA COLI; EVOLUTIONARY ADAPTATION; FORAGING BEHAVIOR; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; NONHUMAN; PRIORITY JOURNAL; REGULATORY MECHANISM; REGULON; ADAPTATION; BINDING SITE; FLAGELLUM; GENETICS; METABOLISM; MOVEMENT (PHYSIOLOGY); PHYSIOLOGY;

BACTERIA (MICROORGANISMS); ESCHERICHIA COLI; NEGIBACTERIA;

ADAPTATION, PHYSIOLOGICAL; BINDING SITES; CARBON; CHEMOTAXIS; CYCLIC AMP RECEPTOR PROTEIN; DNA-BINDING PROTEINS; ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; FLAGELLA; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, BACTERIAL; MOVEMENT; REGULON; SIGMA FACTOR; TRANS-ACTIVATORS; TRANSCRIPTION FACTORS;

EID: 34547851781     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkm456     Document Type: Article

References (59)

1. Burgess,R.R., Travers,A.A., Dunn,J.J. and Bautz,E.K. (1969) Factor stimulating transcription by RNA polymerase. Nature, 221, 43-46.
2. Wosten,M.M. (1998) Eubacterial sigma-factors. FEMS Microbiol. Rev. 22, 127-150.
3. Haldenwang,W.G. (1995) The sigma factors of Bacillus subtilis. Microbiol. Rev., 59, 1-30.
4. Sauer,U., Santangelo,J.D., Treuner,A., Buchholz,M. and Durre,P. (1995) Sigma factor and sporulation genes in Clostridium. FEMS Microbiol. Rev. 17, 331-340.
5. Gomez,J.E. Chen,J.M. and Bishai,W.R. (1997) Sigma factors of Mycobacterium tuberculosis. Tuber. Lung Dis., 78, 175-183.
6. Burgess,R.R. and Travers,A.A. (1970) Escherichia coli RNA polymerase: purification, subunit structure, and factor requirements. Fed. Proc. 29, 1164-1169.
7. Aiyar,S.E., McLeod,S.M., Ross,W., Hirvonen,C.A., Thomas,M.S., Johnson,R.C. and Gourse,R.L. (2002) Architecture of Fis-activated transcription complexes at the Escherichia coli rrnB P1 and rrnE P1 promoters. J. Mol. Biol., 316, 501-516.
8. McLeod,S.M., Aiyar,S.E., Gourse,R.L. and Johnson,R.C. (2002) The C-terminal domains of the RNA polymerase alpha subunits: Contact site with Fis and localization during co-activation with CRP at the Escherichia coli proP P2 promoter. J. Mol. Biol., 316, 517-529.
9. Attey,A., Belyaeva,T., Savery,N., Hoggett,J., Fujita,N., Ishihama,A. and Busby,S. (1994) Interactions between the cyclic AMP receptor protein and the alpha subunit of RNA polymerase at the Escherichia coli galactose operon P1 promoter. Nucleic Acids Res., 22, 4375-4380.
10. Blazy,B., Takahashi,M. and Baudras,A. (1980) Binding of CRP to DNA-dependent RNA polymerase from E. coli: Modulation by cAMP of the interactions with free and DNA-bound holo and core enzyme. Mol. Biol. Rep., 6, 39-43.
11. Macnab,R.M. (1996) Flagella and Motility. ASM Press, Washington, DC.
12. Chilcott,G.S. and Hughes,K.T. (2000) Coupling of flagellar gene expression to flagellar assembly in Salmonella enterica serovar typhimurium and Escherichia coli. Microbiol. Mol. Biol. Rev., 64, 694-708.
13. Silverman,M. and Simon,M. (1973) Genetic analysis of flagellar mutants in Escherichia coli. J. Bacteriol., 113, 105-113.
14. Silverman,M. and Simon,M. (1973) Genetic analysis of bacteriophage Mu-induced flagellar mutants in Escherichia coli. J. Bacteriol., 116, 114-122.
15. Silverman,M. and Simon,M. (1974) Positioning flagellar genes in Escherichia coli by deletion analysis. J. Bacteriol., 117, 73-79.
16. Silverman,M., Matsumura,P. and Simon,M. (1976) The identification of the mot gene product with Escherichia coli-lambda hybrids. Proc. Natl Acad. Sci. USA, 73, 3126-3130.
17. Komeda,Y., Kutsukake,K. and Iino,T. (1980) Definition of additional flagellar genes in Escherichia coli K12. Genetics, 94, 277-290.
18. Frye,J., Karlinsey,J.E., Felise,H.R., Marzolf,B., Dowidar,N., McClelland,M. and Hughes,K.T. (2006) Identification of new flagellar genes of Salmonella enterica. serovar Typhimurium. J. Bacteriol., 188, 2233-2243.
19. Hughes,K.T., Gillen,K.L., Semon,M.J. and Karlinsey,J.E. (1993) Sensing structural intermediates in bacterial flagellar assembly by export of a negative regulator. Science, 262, 1277-1280.
20. Liu,M., Durfee,T., Cabrera,J.E., Zhao,K., Jin,D.J. and Blattner,F.R. (2005) Global transcriptional programs reveal a carbon source foraging strategy by Escherichia coli. J. Biol. Chem., 280, 15921-15927.
21. Hastjarjo,T., Silberberg,A. and Hursh,S.R. (1990) Risky choice as a function of amount and variance in food supply. J. Exp. Anal. Behav. 53, 155-161.
22. Houston,A.I. (1991) Risk-sensitive foraging theory and operant psychology. J. Exp. Anal. Behav., 56, 585-589.
23. Neidhardt,F.C., Bloch,P.L. and Smith,D.F. (1974) Culture medium for enterobacteria. J. Bacteriol., 119, 736-747.
24. Blattner,F.R., Plunkett,G.3rd., Bloch,C.A., Perna,N.T., Burland,V., Riley,M., Collado-Vides,J., Glasner,J.D., Rode,C.K. et al. (1997) The complete genome sequence of Escherichia coli K-12. Science, 277, 1453-1474.
25. Datsenko,K.A. and Wanner,B.L. (2000) One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. Proc. Natl Acad. Sci. USA, 97, 6640-6645.
26. Kang,Y., Durfee,J., Glasner,J.D., Qiu,Y., Frisch,D., Winterberg,K.M. and Blattner,F.R. (2004) Systematic mutagenesis of the Escherichia coli genome. J. Bacteriol., 186, 4921-4930.
27. Zhao,K., Liu,M. and Burgess,R.R. (2005) The global transcriptional response of Escherichia coli to induced sigma32 protein ivolves sigma32 regulon activation followed by inactivation and degradation of sigma32 in vivo. J. Biol. Chem., 280, 17758-17768.
28. Winer,J., Jung,C.K., Shackel,I. and Williams,P.M. (1999) Development and validation of real-time quantitative reverse transcriptase-polymerase chain reaction for monitoring gene expression in cardiac myocytes in vitro. Anal. Biochem., 270, 41-49.
29. Tisa,L.S. and Adler,J. (1995) Cytoplasmic free-Ca2+ level rises with repellents and falls with attractants in Escherichia coli chemotaxis. Proc. Natl Acad. Sci. USA, 92, 10777-10781.
30. Stafford,G.P., Ogi,T. and Hughes,C. (2005) Binding and transcriptional activation.of non-flagellar genes by the Escherichia coli flagellar master regulator FlhD2C2. Microbiology, 151, 1779-1788.
31. Claret,L. and Hughes,C. (2002) Interaction of the atypical prokaryotic transcription activator FlhD2C2 with early promoters of the flagellar gene hierarchy. J. Mol. Biol., 321, 185-199.
32. Jishage,M., Iwata,A., Ueda,S. and Ishihama,A. (1996) Regulation of RNA polymerase sigma subunit synthesis in Escherichia coli: Intracellular levels of four species of sigma subunit under various growth conditions. J. Bacteriol., 178, 5447-5451.
33. Ide,N. and Kutsukake,K. (1997) Identification of a novel Escherichia coli gene whose expression is dependent on the flagellum-specific sigma factor, FliA, but dispensable for motility development. Gene, 199, 19-23.
34. Ko,M. and Park,C. (2000) Two novel flagellar components and H-NS are involved in the motor function of Escherichia coli. J. Mol. Biol., 303, 371-382.
35. Lipinska,B., King,J., Ang,D. and Georgopoulos,C. (1988) Sequence analysis and transcriptional regulation of the Escherichia coli grpE gene, encoding a heat shock protein. Nucleic Acids Res., 16, 7545-7562.
36. Liu,X, Brutlag,D.L. and Liu,J.S. (2001) BioProspector: Discovering conserved DNA motifs in upstream regulatory regions of co-expressed genes. Pac. Symp. Biocomput., 127-138.
37. Eddy,S.R. (1998) Profile hidden Markov models. Bioinformatics, 14, 755-763.
38. Karlinsey,J.E., Lonner,J., Brown,K.L. and Hughes,K.T. (2000) Translation/ secretion coupling by type III secretion systems. Cell, 102, 487-497.
39. Kubori,T., Matsushima,Y., Nakamura,D., Uralil,J., Lara-Tejero,M., Sukhan,A., Galan,J.E. and Aizawa,S.I. (1998) Supramolecular structure of the Salmonella typhimurium type III protein secretion system. Science 280, 602-605.
40. Cheng,L.W. and Schneewind,O. (2000) Type III machines of Gram-negative bacteria: Delivering the goods. Trends Microbiol., 8, 214-220.
41. Adler,J. and Templeton,B. (1967) The effect of environmental conditions on the motility of Escherichia coli. J. Gen. Microbiol., 46, 175-184.
42. Yokota,T. and Gots,J.S. (1970) Requirement of adenosine 3′, 5′-cyclic phosphate for flagella formation in Escherichia coli and Salmonella typhimurium. J. Bacteriol., 103, 513-516.
43. Crasnier,M. (1996) Cyclic AMP and catabolite repression. Res. Microbiol., 147, 479-482.
44. Soutourina,O., Kolb,A., Krin,E., Laurent-Winter,C., Rimsky,S., Danchin,A. and Bertin,P. (1999) Multiple control of flagellum biosynthesis in Escherichia coli. J. Bacteriol., 181, 7500-7508.
45. Soutourina,O.A. and Bertin,P.N. (2003) Regulation cascade of flagellar expression in Gram-negative bacteria. FEMS Microbiol. Rev., 27 505-523.
46. Holland,M.M., Leib,T.K. and Gerit,J.A. (1988) Isolation and characterization of a small catalytic domain released from the adenylate cyclase from Escherichia, coli by digestion with trypsin. J. Biol. Chem., 263, 14661-14668.
47. de Crombrugghe,B., Busby,S. and Buc,H. (1984) Cyclic AMP receptor protein:.Role in transcription activation. Science, 224, 831-838.
48. Kim,J., Adhya,S. and Garges,S. (1992) Allosteric changes in the cAMP receptor protein of Escherichia coli: Hinge reorientation. Proc. Natl Acad. Sci. USA, 89, 9700-9704.
49. Makman,R.S. and Sutherland,E.W. (1965) Adenosine 3′,5′-Phosphate in Escherichia Coli. J. Biol. Chem., 240, 1309-1314.
50. Adler,J. (1969) Chemoreceptors in bacteria. Science, 166, 1588-1597.
51. Spripger,M.S., Goy,M.F. and Adler,J. (1977) Sensory transduction in Escherichia coli: Two complementary pathways of information processing that involve methylated proteins. Proc. Natl Acad. Sci. USA, 74 3312-3316.
52. Springer,M.S., Goy,M.F. and Adler,J. (1979) Protein methylation in behavioural control mechanisms and in signal transduction. Nature 280, 279-284.
53. Aldridge,P., Gnerer,J., Karlinsey,J.E. and Hughes,K.T. (2006) Transcriptional and translational control of the Salmonella fliC gene. J. Bacteriol., 188, 4487-4496.
54. Rosu,V., Chevance,F.F., Karlinsey,J.E., Hirano,T. and Hughes,K.T. (2006) Translation inhibition of the Salmonella fliC gene by the fliC 5′ untranslated region, fliC coding sequences, and FlgM. J. Bacteriol. 188, 4497-4507.
55. Herring,C.D., Raffaelle,M., Allen,T.E., Kanin,E.I., Landick,R., Ansari,A.Z. and Palsson,B.O. (2005) Immobilization of Escherichia coli RNA polymerase and location of binding sites by use of chromatin immunoprecipitation and microarrays. J. Bacteriol., 187, 6166-6174.
56. Raffaelle,M., Kanin,E.I., Vogt,J., Burgess,R.R. and Ansari,A.Z. (2005) Holoenzyme switching and stochastic release of sigma factors from RNA polymerase in vivo. Mol. Cell, 20, 357-366.
57. Neidhardt,F.C. and Umbarger,H.E. (1987) Chemical Composition of E. coli. ASM Press, Washington, DC.
58. Stragier,P. (2006) To kill but not be killed: A delicate balance. Cell, 124, 461-463.
59. Schneider,T.D. and Stephens,R.M. (1990) Sequence logos: A new way to display consensus sequences. Nucleic Acids Res., 18, 6097-6100.