Evolution and dynamics of regulatory architectures controlling polymyxin B resistance in enteric bacteria

PLoS Genetics

Volumn 4, Issue 10, 2008, Pages

  Mitrophanov, Alexander Y ^a,b   Jewett, Mollie W ^b,c   Hadley, Tricia J ^b   Groisman, Eduardo A ^a,b  

^a WASHINGTON UNIVERSITY   (United States)

^b WASHINGTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

^c NATIONAL INSTITUTES OF HEALTH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

POLYMYXIN B; ANTIINFECTIVE AGENT; BACTERIAL PROTEIN;

ANTIBIOTIC RESISTANCE; ARTICLE; BACTERIAL GENE; CONTROLLED STUDY; GENE EXPRESSION; KLEBSIELLA PNEUMONIAE; MATHEMATICAL MODEL; MOLECULAR EVOLUTION; NONHUMAN; PBGP GENE; PHOP GENE; PHYLOGENETIC TREE; PMRA GENE; PMRD GENE; PROTEIN EXPRESSION; PROTEIN PROCESSING; SIGNAL TRANSDUCTION; CLASSIFICATION; DRUG EFFECT; ENTEROBACTERIACEAE; GENE EXPRESSION REGULATION; GENETIC TRANSCRIPTION; GENETICS; METABOLISM; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PHYLOGENY;

ENTEROBACTERIACEAE;

ANTI-BACTERIAL AGENTS; BACTERIAL PROTEINS; BASE SEQUENCE; DRUG RESISTANCE, BACTERIAL; ENTEROBACTERIACEAE; EVOLUTION, MOLECULAR; GENE EXPRESSION REGULATION, BACTERIAL; MOLECULAR SEQUENCE DATA; PHYLOGENY; POLYMYXIN B; TRANSCRIPTION, GENETIC;

EID: 53549120986     PISSN: 15537390     EISSN: 15537404     Source Type: Journal    
DOI: 10.1371/journal.pgen.1000233     Document Type: Article

References (49)

1. Alon U (2007) Network motifs: theory and experimental approaches. Nature Rev Genet 8: 450-461.
2. Kato A, Mitrophanov AY, Groisman EA (2007) A connector of two-component regulatory systems promotes signal amplification and persistence of expression. Proc Natl Acad Sci USA 104: 12063-12068.
3. Mangan S, Alon U (2003) Structure and function of the feed-forward loop network motif. Proc Natl Acad Sci USA 100: 11980-11985.
4. Mitrophanov AY, Groisman EA (2008) Positive feedback in cellular control processes. Bioessays 30: 542-555.
5. Rosenfeld N, Alon U (2003) Response delays and the structure of transcription networks. J Mol Biol 329: 645-654.
6. Appleby JL, Parkinson JS, Bourret RB (1996) Signal transduction via the multistep phosphorelay: Not necessarily a road less traveled. Cell 86: 845-848.
7. Gao R, Mack TR, Stock AM (2007) Bacterial response regulators: versatile regulatory strategies from common domains. Trends Biochem Sci 32: 225-234.
8. Hoch JA (2000) Two-component and phosphorelay signal transduction. Curr Opin Microbiol 3: 165-170.
9. Stock AM, Robinson VL, Goudreau PN (2000) Two-component signal transduction. Annu Rev Biochem 69: 183-215.
10. Mitrophanov AY, Groisman EA (2008) Signal integration in bacterial two-component regulatory systems. Genes Dev: In press.
11. Kato A, Groisman EA (2004) Connecting two-component regulatory systems by a protein that protects a response regulator from dephosphorylation by its cognate sensor. Genes Dev 18: 2302-2313.
12. Kato A, Latifi T, Groisman EA (2003) Closing the loop: The PmrA/PmrB two-component system negatively controls expression of its posttranscriptional activator PmrD. Proc Natl Acad Sci USA 100: 4706-4711.
13. Kox LFF, Wösten MMSM, Groisman EA (2000) A small protein that mediates the activation of a two-component system by another two-component system. EMBO J 19: 1861-1872.
14. Gunn JS, Ryan SS, Van Velkinburgh JC, Ernst RK, Miller SI (2000) Genetic and functional analysis of a PmrA-PmrB-regulated locus necessary for lipopolysaccharide modification, antimicrobial peptide resistance, and oral virulence of Salmonella enterica serovar Typhimurium. Infect Immun 68: 6139-6146.
15. Raetz CRH, Reynolds CM, Trent MS, Bishop RE (2007) Lipid A modification systems in gram-negative bacteria. Annu Rev Biochem 76: 295-329.
16. Gunn JS, Lim KB, Krueger J, Kim K, Guo L, et al. (1998) PmrA-Pmr-Bregulated genes necessary for 4-aminoarabinose lipid A modification and polymyxin resistance. Mol Microbiol 27: 1171-1182.
17. Trent MS, Ribeiro AA, Lin SH, Cotter RJ, Raetz CRH (2001) An inner membrane enzyme in Salmonella and Escherichia coli that transfers 4-amino-4-deoxy-L-arabinose to lipid A. Induction in polymyxin-resistant mutants and role of a novel lipid-linked donor. J Biol Chem 276: 43122-43131.
18. Zhou ZM, Ribeiro AA, Lin SH, Cotter RJ, Miller SI, et al. (2001) Lipid A modifications in polymyxin-resistant Salmonella typhimurium. PmrA-dependent 4-amino-4-deoxy-L-arabinose, and phosphoethanolamine incorporation. J Biol Chem 276: 43111-43121.
19. Groisman EA (2001) The pleiotropic two-component regulatory system PhoP-PhoQ. J Bacteriol 183: 1835-1842.
20. Perez JC, Groisman EA (2007) Acid pH activation of the PmrA/PmrB two-component regulatory system of Salmonella enterica. Mol Microbiol 63: 283-293.
21. 2+ as an extracellular signal: Environmental regulation of Salmonella virulence. Cell 84: 165-174.
22. Winfield MD, Latifi T, Groisman EA (2005) Transcriptional regulation of the 4-amino-4-deoxy-L-arabinose biosynthetic genes in Yersinia pestis. J Biol Chem 280: 14765-14772.
23. Winfield MD, Groisman EA (2004) Phenotypic differences between Salmonella and Escherichia coli resulting from the disparate regulation of homologous genes. Proc Natl Acad Sci USA 101: 17162-17167.
24. Shen-Orr SS, Milo R, Mangan S, Alon U (2002) Network motifs in the transcriptional regulation network of Escherichia coli. Nature Genet 31: 64-68.
25. Ghosh B, Karmakar R, Bose I (2005) Noise characteristics of feed forward loops. Phys Biol 2: 36-45.
26. Kalir S, Mangan S, Alon U (2005) A coherent feed-forward loop with a SUM input function prolongs flagella expression in Escherichia coli. Mol Syst Biol 1: 2005.0006.
27. Mangan S, Zaslaver A, Alon U (2003) The coherent feedforward loop serves as a sign-sensitive delay element in transcription networks. J Mol Biol 334: 197-204.
28. Bijlsma JJE, Groisman EA (2003) Making informed decisions: regulatory interactions between two-component systems. Trends Microbiol 11: 359-366.
29. Hooshangi S, Thiberge S, Weiss R (2005) Ultrasensitivity and noise propagation in a synthetic transcriptional cascade. Proc Natl Acad Sci USA 102: 3581-3586.
30. Kaern M, Elston TC, Blake WJ, Collins JJ (2005) Stochasticity in gene expression: From theories to phenotypes. Nature Rev Genet 6: 451-464.
31. Francino MP (2005) An adaptive radiation model for the origin of new gene functions. Nature Genet 37: 573-577.
32. Ochman H, Lawrence JG, Groisman EA (2000) Lateral gene transfer and the nature of bacterial innovation. Nature 405: 299-304.
33. Perez JC, Latifi T, Groisman EA (2008) Overcoming H-NS-mediated transcriptional silencing of horizontally acquired genes by the PhoP and SlyA proteins in Salmonella enterica. J Biol Chem 283: 10773-10783.
34. Froelich JM, Tran K, Wall D (2006) A PmrA constitutive mutant sensitizes Escherichia coli to deoxycholic acid. J Bacteriol 188: 1180-1183.
35. Tu X, Latifi T, Bougdour A, Gottesman S, Groisman EA (2006) The PhoP/PhoQ two-component system stabilizes the alternative sigma factor RpoS in Salmonella enterica. Proc Natl Acad Sci USA 103: 13503-13508.
36. Tagkopoulos I, Liu YC, Tavazoie S (2008) Predictive behavior within microbial genetic networks. Science 320: 1313-1317.
37. Brisse S, Grimont F, Grimont PAD (2006) The genus Klebsiella. Prokaryotes 6: 159-196.
38. Ellermeier CD, Slauch JM (2006) The genus Salmonella. Prokaryotes 6: 123-158.
39. Brubaker B (2006) Yersinia pestis and bubonic plague. Prokaryotes 6: 399-442.
40. Paulus H, Gray E (1964) The biosynthesis of polymyxin B by growing cultures of Bacillus polymyxa. J Biol Chem 239: 865-871.
41. Nishino K, Hsu FF, Turk J, Cromie MJ, Wösten MMSM, et al. (2006) Identification of the lipopolysaccharide modifications controlled by the Salmonella PmrA/PmrB system mediating resistance to Fe(III) and Al(III). Mol Microbiol 61: 645-654.
42. Raetz CRH, Whitfield C (2002) Lipopolysaccharide endotoxins. Annu Rev Biochem 71: 635-700.
43. Dekel E, Mangan S, Alon U (2005) Environmental selection of the feed-forward loop circuit in gene-regulation networks. Phys Biol 2: 81-88.
44. Kalisky T, Dekel E, Alon U (2007) Cost-benefit theory and optimal design of gene regulation functions. Phys Biol 4: 229-245.
45. Chamnongpol S, Groisman EA (2000) Acetyl phosphate-dependent activation of a mutant PhoP response regulator that functions independently of its cognate sensor kinase. J Mol Biol 300: 291-305.
46. Wertz JE, Goldstone C, Gordon DM, Riley MA (2003) A molecular phylogeny of enteric bacteria and implications for a bacterial species concept. J Evol Biol 16: 1236-1248.
47. Shin D, Lee J, Huang H, Groisman EA (2006) A positive feedback loop promotes transcription surge that jump-starts Salmonella virulence circuit. Science 314: 1607-1609.
48. Mitrophanov AY, Churchward G, Borodovsky M (2007) Control of Streptococcus pyogenes virulence: Modeling of the CovR/S signal transduction system. J Theor Biol 246: 113-128.
49. Alves R, Savageau MA (2000) Systemic properties of ensembles of metabolic networks: application of graphical and statistical methods to simple unbranched pathways. Bioinformatics 16: 534-547.