[1] | Shapiro L (1976) Differentiation in the Caulobacter cell cycle. Annu Rev Microbiol 30: 377–407. pmid:185940 doi: 10.1146/annurev.mi.30.100176.002113
|
[2] | Kaiser D (1986) Control of multicellular development: Dictyostelium and Myxococcus. Annu Rev Genet 20: 539–566. pmid:3028248 doi: 10.1146/annurev.ge.20.120186.002543
|
[3] | Stragier P, Losick R (1996) Molecular genetics of sporulation in Bacillus subtilis. Annu Rev Genet 30: 297–241. pmid:8982457 doi: 10.1146/annurev.genet.30.1.297
|
[4] | Andrewes FW (1922) Studies in group agglutination. I. The Salmonella group and its antigenic structure. J Path Bact 25: 505–524. doi: 10.1002/path.1700250411
|
[5] | Legroux R, Magrou J (1920) état organisé des colonies bactériennes. Ann Inst Pasteur (Paris) 34: 417–431.
|
[6] | Shapiro JA, Higgins NP (1989) Differential activity of a transposable element in Escherichia coli colonies. J Bacteriol 171: 5975–5986. pmid:2553666
|
[7] | Shapiro JA (1998) Thinking about bacterial populations as multicellular organisms. Annu Rev Microbiol 52: 81–104. pmid:9891794 doi: 10.1146/annurev.micro.52.1.81
|
[8] | Zgur-Bertok D (2007) Phenotypic heterogeneity in bacterial populations. Acta Agric Slovenica 90: 17–24.
|
[9] | Dhar N, McKinney JD (2007) Microbial phenotypic heterogeneity and antibiotic tolerance. Curr Opin Microbiol 10: 30–38. pmid:17215163 doi: 10.1016/j.mib.2006.12.007
|
[10] | Davidson CJ, Surette MG (2008) Individuality in bacteria. Annu Rev Genet 42: 253–268. doi: 10.1146/annurev.genet.42.110807.091601. pmid:18652543
|
[11] | Veening JW, Smits WK, Kuipers OP (2008) Bistability, epigenetics, and bet-hedging in bacteria. Annu Rev Microbiol 62: 193–210. doi: 10.1146/annurev.micro.62.081307.163002. pmid:18537474
|
[12] | Casadesus J, Low DA (2013) Programmed heterogeneity: epigenetic mechanisms in bacteria. J Biol Chem 288: 13929–13935. doi: 10.1074/jbc.R113.472274. pmid:23592777
|
[13] | Thattai M, van Oudenaarden A (2004) Stochastic gene expression in fluctuating environments. Genetics 167: 523–530. pmid:15166174 doi: 10.1534/genetics.167.1.523
|
[14] | Kussell E, Leibler S (2005) Phenotypic diversity, population growth, and information in fluctuating environments. Science 309: 2075–2078. pmid:16123265 doi: 10.1126/science.1114383
|
[15] | Wolf DM, Vazirani VV, Arkin AP (2005) Diversity in times of adversity: probabilistic strategies in microbial survival games. J Theor Biol 234: 227–253. pmid:15757681 doi: 10.1016/j.jtbi.2004.11.020
|
[16] | Hernandez SB, Cota I, Ducret A, Aussel L, Casadesus J (2012) Adaptation and preadaptation of Salmonella enterica to bile. PLoS Genet 8: e1002459. doi: 10.1371/journal.pgen.1002459. pmid:22275872
|
[17] | Sanchez-Romero MA, Casadesus J (2014) Contribution of phenotypic heterogeneity to adaptive antibiotic resistance. Proc Natl Acad Sci U S A 111: 355–360. doi: 10.1073/pnas.1316084111. pmid:24351930
|
[18] | Ni M, Decrulle AL, Fontaine F, Demarez A, Taddei F, et al. (2012) Pre-disposition and epigenetics govern variation in bacterial survival upon stress. PLoS Genet 8: e1003148. doi: 10.1371/journal.pgen.1003148. pmid:23284305
|
[19] | Silverman M, Zieg J, Hilmen M, Simon M (1979) Phase variation in Salmonella: genetic analysis of a recombinational switch. Proc Natl Acad Sci U S A 76: 391–395. pmid:370828 doi: 10.1073/pnas.76.1.391
|
[20] | Moxon ER, Rainey PB, Nowak MA, Lenski RE (1994) Adaptive evolution of highly mutable loci in pathogenic bacteria. Curr Biol 4: 24–33. pmid:7922307 doi: 10.1016/s0960-9822(00)00005-1
|
[21] | Moxon R, Bayliss C, Hood D (2006) Bacterial contingency loci: the role of simple sequence DNA repeats in bacterial adaptation. Annu Rev Genet 40: 307–333. pmid:17094739 doi: 10.1146/annurev.genet.40.110405.090442
|
[22] | Dubnau D, Losick R (2006) Bistability in bacteria. Mol Microbiol 61: 564–572. pmid:16879639 doi: 10.1111/j.1365-2958.2006.05249.x
|
[23] | Hernday A, Krabbe M, Braaten B, Low D (2002) Self-perpetuating epigenetic pili switches in bacteria. Proc Natl Acad Sci U S A 99: 16470–16476. pmid:12202745 doi: 10.1073/pnas.182427199
|
[24] | Casadesus J, Low D (2006) Epigenetic gene regulation in the bacterial world. Microbiol Mol Biol Rev 70: 830–856. pmid:16959970 doi: 10.1128/mmbr.00016-06
|
[25] | van der Woude MW (2011) Phase variation: how to create and coordinate population diversity. Curr Opin Microbiol 14: 205–211. doi: 10.1016/j.mib.2011.01.002. pmid:21292543
|
[26] | van der Woude MW, Baumler AJ (2004) Phase and antigenic variation in bacteria. Clin Microbiol Rev 17: 581–611, table of contents. pmid:15258095 doi: 10.1128/cmr.17.3.581-611.2004
|
[27] | van der Woude MW (2006) Re-examining the role and random nature of phase variation. FEMS Microbiol Lett 254: 190–197. pmid:16445745 doi: 10.1111/j.1574-6968.2005.00038.x
|
[28] | Kim M, Ryu S (2012) Spontaneous and transient defence against bacteriophage by phase-variable glucosylation of O-antigen in Salmonella enterica serovar Typhimurium. Mol Microbiol 86: 411–425. doi: 10.1111/j.1365-2958.2012.08202.x. pmid:22928771
|
[29] | Zaleski P, Wojciechowski M, Piekarowicz A (2005) The role of Dam methylation in phase variation of Haemophilus influenzae genes involved in defence against phage infection. Microbiology 151: 3361–3369. pmid:16207918 doi: 10.1099/mic.0.28184-0
|
[30] | Srikhanta YN, Maguire TL, Stacey KJ, Grimmond SM, Jennings MP (2005) The phasevarion: a genetic system controlling coordinated, random switching of expression of multiple genes. Proc Natl Acad Sci U S A 102: 5547–5551. pmid:15802471 doi: 10.1073/pnas.0501169102
|
[31] | Hoskisson PA, Smith MC (2007) Hypervariation and phase variation in the bacteriophage 'resistome'. Curr Opin Microbiol 10: 396–400. pmid:17719266 doi: 10.1016/j.mib.2007.04.003
|
[32] | Cota I, Blanc-Potard AB, Casadesus J (2012) STM2209-STM2208 (opvAB): a phase variation locus of Salmonella enterica involved in control of O-antigen chain length. PLoS One 7: e36863. doi: 10.1371/journal.pone.0036863. pmid:22606300
|
[33] | Ghosh AS, Young KD (2005) Helical disposition of proteins and lipopolysaccharide in the outer membrane of Escherichia coli. J Bacteriol 187: 1913–1922. pmid:15743937 doi: 10.1128/jb.187.6.1913-1922.2005
|
[34] | Murray GL, Attridge SR, Morona R (2003) Regulation of Salmonella typhimurium lipopolysaccharide O antigen chain length is required for virulence; identification of FepE as a second Wzz. Mol Microbiol 47: 1395–1406. pmid:12603743 doi: 10.1046/j.1365-2958.2003.03383.x
|
[35] | Goldman RC, Hunt F (1990) Mechanism of O-antigen distribution in lipopolysaccharide. J Bacteriol 172: 5352–5359. pmid:1697578
|
[36] | Bastin DA, Stevenson G, Brown PK, Haase A, Reeves PR (1993) Repeat unit polysaccharides of bacteria: a model for polymerization resembling that of ribosomes and fatty acid synthetase, with a novel mechanism for determining chain length. Mol Microbiol 7: 725–734. pmid:7682279 doi: 10.1111/j.1365-2958.1993.tb01163.x
|
[37] | Daniels C, Morona R (1999) Analysis of Shigella flexneri Wzz (Rol) function by mutagenesis and cross-linking: Wzz is able to oligomerize. Mol Microbiol 34: 181–194. pmid:10540296 doi: 10.1046/j.1365-2958.1999.01591.x
|
[38] | Batchelor RA, Alifano P, Biffali E, Hull SI, Hull RA (1992) Nucleotide sequences of the genes regulating O-polysaccharide antigen chain length (rol) from Escherichia coli and Salmonella typhimurium: protein homology and functional complementation. J Bacteriol 174: 5228–5236. pmid:1379582
|
[39] | Lindberg AA (1973) Bacteriophage receptors. Annu Rev Microbiol 27: 205–241. pmid:4584686 doi: 10.1146/annurev.mi.27.100173.001225
|
[40] | Kintz E, Davies MR, Hammarlof DL, Canals R, Hinton JC, et al. (2015) A BTP1 prophage gene present in invasive non-typhoidal Salmonella determines composition and length of the O-antigen of the lipopolysaccharide. Mol Microbiol 96: 263–275. doi: 10.1111/mmi.12933. pmid:25586744
|
[41] | Wilkinson RG, Gemski P Jr., Stocker BA (1972) Non-smooth mutants of Salmonella typhimurium: differentiation by phage sensitivity and genetic mapping. J Gen Microbiol 70: 527–554. pmid:4556257 doi: 10.1099/00221287-70-3-527
|
[42] | Casjens SR, Leavitt JC, Hatfull GF, Hendrix RW (2014) Genome sequence of Salmonella phage 9NA. Genome Announc 2: e00531–14 doi: 10.1128/genomeA.00531-14. pmid:25146133
|
[43] | Walter M, Fiedler C, Grassl R, Biebl M, Rachel R, et al. (2008) Structure of the receptor-binding protein of bacteriophage det7: a podoviral tail spike in a myovirus. J Virol 82: 2265–2273. pmid:18077713 doi: 10.1128/jvi.01641-07
|
[44] | Casjens SR, Jacobs-Sera D, Hatfull GF, Hendrix RW (2015) Genome sequence of Salmonella enterica phage Det7. Genome Announc 3: e00279–00215. doi: 10.1128/genomeA.00279-15. pmid:25953168
|
[45] | Smith HO, Levine M (1964) Two sequential repressions of DNA synthesis in the establishment of lysogeny by phage P22 and Its mutants. Proc Natl Acad Sci U S A 52: 356–363. pmid:14206603 doi: 10.1073/pnas.52.2.356
|
[46] | Raetz CR, Whitfield C (2002) Lipopolysaccharide endotoxins. Annu Rev Biochem 71: 635–700. pmid:12045108 doi: 10.1146/annurev.biochem.71.110601.135414
|
[47] | Bravo D, Silva C, Carter JA, Hoare A, Alvarez SA, et al. (2008) Growth-phase regulation of lipopolysaccharide O-antigen chain length influences serum resistance in serovars of Salmonella. J Med Microbiol 57: 938–946. doi: 10.1099/jmm.0.47848-0. pmid:18628492
|
[48] | Beuzon CR, Holden DW (2001) Use of mixed infections with Salmonella strains to study virulence genes and their interactions in vivo. Microbes Infect 3: 1345–1352. pmid:11755424 doi: 10.1016/s1286-4579(01)01496-4
|
[49] | Williams GC (1966) Natural selection, the costs of reproduction, and a refinement of Lack's principle. Am Nat 100: 687–690. doi: 10.1086/282461
|
[50] | Nystrom T (2004) Growth versus maintenance: a trade-off dictated by RNA polymerase availability and sigma factor competition? Mol Microbiol 54: 855–862. pmid:15522072 doi: 10.1111/j.1365-2958.2004.04342.x
|
[51] | Shoval O, Sheftel H, Shinar G, Hart Y, Ramote O, et al. (2012) Evolutionary trade-offs, Pareto optimality, and the geometry of phenotype space. Science 336: 1157–1160. doi: 10.1126/science.1217405. pmid:22539553
|
[52] | Bailly-Bechet M, Benecke A, Hardt WD, Lanza V, Sturm A, et al. (2011) An externally modulated, noise-driven switch for the regulation of SPI1 in Salmonella enterica serovar Typhimurium. J Math Biol 63: 637–662. doi: 10.1007/s00285-010-0385-1. pmid:21107576
|
[53] | Ferenci T, Spira B (2007) Variation in stress responses within a bacterial species and the indirect costs of stress resistance. Ann N Y Acad Sci 1113: 105–113. pmid:17483210 doi: 10.1196/annals.1391.003
|
[54] | Andersson DI, Hughes D (2010) Antibiotic resistance and its cost: is it possible to reverse resistance? Nat Rev Microbiol 8: 260–271. doi: 10.1038/nrmicro2319. pmid:20208551
|
[55] | De Paepe M, Gaboriau-Routhiau V, Rainteau D, Rakotobe S, Taddei F, et al. (2011) Trade-off between bile resistance and nutritional competence drives Escherichia coli diversification in the mouse gut. PLoS Genet 7: e1002107. doi: 10.1371/journal.pgen.1002107. pmid:21698140
|
[56] | Vincent BM, Lancaster AK, Scherz-Shouval R, Whitesell L, Lindquist S (2013) Fitness trade-offs restrict the evolution of resistance to amphotericin B. PLoS Biol 11: e1001692. doi: 10.1371/journal.pbio.1001692. pmid:24204207
|
[57] | Leon M, Bastias R (2015) Virulence reduction in bacteriophage resistant bacteria. Front Microbiol 6: 343. doi: 10.3389/fmicb.2015.00343. pmid:25954266
|
[58] | Taylor VL, Udaskin ML, Islam ST, Lam JS (2013) The D3 bacteriophage alpha-polymerase inhibitor (Iap) peptide disrupts O-antigen biosynthesis through mimicry of the chain length regulator Wzz in Pseudomonas aeruginosa. J Bacteriol 195: 4735–4741. doi: 10.1128/JB.00903-13. pmid:23955007
|
[59] | Susskind MM, Botstein D (1978) Molecular genetics of bacteriophage P22. Microbiol Rev 42: 385–413. pmid:353481
|
[60] | Whitfield C, Trent MS (2014) Biosynthesis and export of bacterial lipopolysaccharides. Annu Rev Biochem 83: 99–128. doi: 10.1146/annurev-biochem-060713-035600. pmid:24580642
|
[61] | Wilson GG, Murray NE (1991) Restriction and modification systems. Annu Rev Genet 25: 585–627. pmid:1812816 doi: 10.1146/annurev.ge.25.120191.003101
|
[62] | Lee DJ, Bingle LE, Heurlier K, Pallen MJ, Penn CW, et al. (2009) Gene doctoring: a method for recombineering in laboratory and pathogenic Escherichia coli strains. BMC Microbiol 9: 252. doi: 10.1186/1471-2180-9-252. pmid:20003185
|
[63] | Datsenko KA, Wanner BL (2000) One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. Proc Natl Acad Sci U S A 97: 6640–6645. pmid:10829079 doi: 10.1073/pnas.120163297
|
[64] | Hautefort I, Proenca MJ, Hinton JC (2003) Single-copy green fluorescent protein gene fusions allow accurate measurement of Salmonella gene expression in vitro and during infection of mammalian cells. Appl Environ Microbiol 69: 7480–7491. pmid:14660401 doi: 10.1128/aem.69.12.7480-7491.2003
|
[65] | Chan RK, Botstein D, Watanabe T, Ogata Y (1972) Specialized transduction of tetracycline by phage P22 in Salmonella typhimurium. II. Properties of a high frequency transducing lysate. Virology 50: 883–898. pmid:4565618 doi: 10.1016/0042-6822(72)90442-4
|
[66] | Torreblanca J, Casadesús J (1996) DNA adenine methylase mutants of Salmonella typhimurium and a novel Dam-regulated locus. Genetics 144: 15–26. pmid:8878670
|
[67] | Buendia-Claveria AM, Moussaid A, Ollero FJ, Vinardell JM, Torres A, et al. (2003) A purL mutant of Sinorhizobium fredii HH103 is symbiotically defective and altered in its lipopolysaccharide. Microbiology 149: 1807–1818. pmid:12855732 doi: 10.1099/mic.0.26099-0
|
[68] | Segura I, Casadesus J, Ramos-Morales F (2004) Use of mixed infections to study cell invasion and intracellular proliferation of Salmonella enterica in eukaryotic cell cultures. J Microbiol Methods 56: 83–91. pmid:14706753 doi: 10.1016/j.mimet.2003.09.004
|