Evolutionary convergence in experimental Pseudomonas populations

ISME Journal

Volumn 11, Issue 3, 2017, Pages 589-600

  Lind, Peter A ^a,b   Farr, Andrew D ^a   Rainey, Paul B ^a,c,d  

^a MASSEY UNIVERSITY   (New Zealand)

^b UMEÅ UNIVERSITY   (Sweden)

^c MAX PLANCK INSTITUTE FOR EVOLUTIONARY BIOLOGY   (Germany)

^d PSL RESEARCH UNIVERSITY   (France)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIUM; CONVERGENT EVOLUTION; EVOLUTIONARY BIOLOGY; EXPERIMENTAL STUDY; FITNESS; GENETIC ANALYSIS; LIFE HISTORY TRAIT; LOCAL ADAPTATION; MUTATION; NICHE; PARALLEL EVOLUTION;

PSEUDOMONAS; PSEUDOMONAS FLUORESCENS;

BETA GLUCAN; CELLULOSE; POLY-N-ACETYL-1-6-GLUCOSAMINE;

ADAPTATION; ENVIRONMENT; EVOLUTION; GENETICS; METABOLISM; MUTATION; PSEUDOMONAS FLUORESCENS; REPRODUCTIVE FITNESS;

ADAPTATION, PHYSIOLOGICAL; BETA-GLUCANS; BIOLOGICAL EVOLUTION; CELLULOSE; ENVIRONMENT; GENETIC FITNESS; MUTATION; PSEUDOMONAS FLUORESCENS;

EID: 85001104709     PISSN: 17517362     EISSN: 17517370     Source Type: Journal    
DOI: 10.1038/ismej.2016.157     Document Type: Article

References (63)

1. Bantinaki E, Kassen R, Knight CG, Robinson Z, Spiers AJ, Rainey PB. (2007). Adaptive divergence in experimental populations of Pseudomonas fluorescens. III. Mutational origins of wrinkly spreader diversity. Genetics 176: 441-453.
2. Barrick JE, Lenski RE. (2013). Genome dynamics during experimental evolution. Nat Rev Genet 14: 827-839.
3. Beaumont HJ, Gallie J, Kost C, Ferguson GC, Rainey PB. (2009). Experimental evolution of bet hedging. Nature 462: 90-93.
4. Bertani G. (1951). Studies on lysogenesis. I. The mode of phage liberation by lysogenic Escherichia coli. J Bacteriol 62: 293-300.
5. Choi AH, Slamti L, Avci FY, Pier GB, Maira-Litran T. (2009). The pgaABCD locus of Acinetobacter baumannii encodes the production of poly-beta-1-6-N-acetylglucosamine, which is critical for biofilm formation. J Bacteriol 191: 5953-5963.
6. Dykhuizen DE. (1990). Experimental studies of natural selection in bacteria. Annu Rev Ecol Syst 21: 373-398.
7. Ferguson GC, Bertels F, Rainey PB. (2013). Adaptive divergence in experimental populations of Pseudomonas fluorescens. V. insight into the niche specialist 'Fuzzy Spreader' compels revision of the model Pseudomonas radiation. Genetics 195: 1319-1335.
8. Flemming HC, Wingender J. (2010). The biofilm matrix. Nat Rev Microbiol 8: 623-633.
9. Fukami T, Beaumont HJ, Zhang XX, Rainey PB. (2007). Immigration history controls diversification in experimental adaptive radiation. Nature 446: 436-439.
10. Gal M, Preston GM, Massey RC, Spiers AJ, Rainey PB. (2003). Genes encoding a cellulosic polymer contribute toward the ecological success of Pseudomonas fluorescens SBW25 on plant surfaces. Mol Ecol 12: 3109-3121.
11. Gallie J, Libby E, Bertels F, Remigi P, Jendresen CB, Ferguson GC et al. (2015). Bistability in a metabolic network underpins the de novo evolution of colony switching in Pseudomonas fluorescens. PLoS Biol 13: e1002109.
12. Gehrig SM. (2005). Adaptation of pseudomonas fluorescens SBW25 to the air-liquid interface: A study in evolutionary genetics. University of Oxford: Oxford, UK.
13. Gerstein AC, Lo DS, Otto SP. (2012). Parallel genetic changes and nonparallel gene-environment interactions characterize the evolution of drug resistance in yeast. Genetics 192: 241-252.
14. Giddens SR, Jackson RW, Moon CD, Jacobs MA, Zhang XX, Gehrig SM et al. (2007). Mutational activation of niche-specific genes provides insight into regulatory networks and bacterial function in a complex environment. Proc Natl Acad Sci USA 104: 18247-18252.
15. Gompel N, Prud'homme B. (2009). The causes of repeated genetic evolution. Dev Biol 332: 36-47.
16. Hengge R. (2009). Principles of c-di-GMP signalling in bacteria. Nat Rev Microbiol 7: 263-273.
17. Herron MD, Doebeli M. (2013). Parallel evolutionary dynamics of adaptive diversification in Escherichia coli. PLoS Biol 11: e1001490.
18. Horton RM, Hunt HD, Ho SN, Pullen JK, Pease LR. (1989). Engineering hybrid genes without the use of restriction enzymes: gene splicing by overlap extension. Gene 77: 61-68.
19. Irie Y, Starkey M, Edwards AN, Wozniak DJ, Romeo T, Parsek MR. (2010). Pseudomonas aeruginosa biofilm matrix polysaccharide Psl is regulated transcriptionally by RpoS and post-transcriptionally by RsmA. Mol Microbiol 78: 158-172.
20. Jessup CM, Kassen R, Forde SE, Kerr B, Buckling A, Rainey PB et al. (2004). Big questions, small worlds: microbial model systems in ecology. Trends Ecol Evol 19: 189-197.
21. Jost MC, Hillis DM, Lu Y, Kyle JW, Fozzard HA, Zakon HH. (2008). Toxin-resistant sodium channels: parallel adaptive evolution across a complete gene family. Mol Biol Evol 25: 1016-1024.
22. King EO, Ward MK, Raney DE. (1954). Two simple media for the demonstration of pyocyanin and fluorescin. J Lab Clin Med 44: 301-307.
23. Knöppel A, Lind PA, Lustig U, Näsvall J, Andersson DI. (2014). Minor fitness costs in an experimental model of horizontal gene transfer in bacteria. Mol Biol Evol 31: 1220-1227.
24. Kojic M, Aguilar C, Venturi V. (2002). TetR family member PsrA directly binds the Pseudomonas rpoS and psrA promoters. J Bacteriol 184: 2324-2330.
25. Kulasekara BR, Kamischke C, Kulasekara HD, Christen M, Wiggins PA, Miller SI. (2013). c-di-GMP heterogeneity is generated by the chemotaxis machinery to regulate flagellar motility. eLife 2: e01402.
26. Lambertsen L, Sternberg C, Molin S. (2004). Mini-Tn7 transposons for site-specific tagging of bacteria with fluorescent proteins. Environ Microbiol 6: 726-732.
27. Lind PA, Tobin C, Berg OG, Kurland CG, Andersson DI. (2010). Compensatory gene amplification restores fitness after inter-species gene replacements. Mol Microbiol 75: 1078-1089.
28. Lind PA, Farr AD, Rainey PB. (2015). Experimental evolution reveals hidden diversity in evolutionary pathways. eLife 4: 07074.
29. Lori C, Ozaki S, Steiner S, Bohm R, Abel S, Dubey BN et al. (2015). Cyclic di-GMP acts as a cell cycle oscillator to drive chromosome replication. Nature 523: 236-239.
30. Malone JG, Jaeger T, Spangler C, Ritz D, Spang A, Arrieumerlou C et al. (2010). YfiBNR mediates cyclic di-GMP dependent small colony variant formation and persistence in Pseudomonas aeruginosa. PLoS Pathog 6: e1000804.
31. Malone JG, Jaeger T, Manfredi P, Dotsch A, Blanka A, Bos R et al. (2012). The YfiBNR signal transduction mechanism reveals novel targets for the evolution of persistent Pseudomonas aeruginosa in cystic fibrosis airways. PLoS Pathog 8: e1002760.
32. Mann EE, Wozniak DJ. (2012). Pseudomonas biofilm matrix composition and niche biology. FEMS Microbiol Rev 36: 893-916.
33. Manoil C. (2000). Tagging exported proteins using Escherichia coli alkaline phosphatase gene fusions. Methods Enzymol 326: 35-47.
34. Martin A, Orgogozo V. (2013). The Loci of repeated evolution: A catalog of genetic hotspots of phenotypic variation. Evolution 67: 1235-1250.
35. Martin M, Holscher T, Dragos A, Cooper VS, Kovacs AT. (2016). Laboratory evolution of microbial interactions in bacterial biofilms. J Bacteriol 198: 2564-2571.
36. Marvig RL, Sommer LM, Molin S, Johansen HK. (2015). Convergent evolution and adaptation of Pseudomonas aeruginosa within patients with cystic fibrosis. Nat Genet 47: 57-64.
37. McDonald MJ, Gehrig SM, Meintjes PL, Zhang XX, Rainey PB. (2009). Adaptive divergence in experimental populations of Pseudomonas fluorescens. IV. Genetic constraints guide evolutionary trajectories in a parallel adaptive radiation. Genetics 183: 1041-1053.
38. Moll A, Dorr T, Alvarez L, Chao MC, Davis BM, Cava F et al. (2014). Cell separation in Vibrio cholerae is mediated by a single amidase whose action is modulated by two nonredundant activators. J Bacteriol 196: 3937-3948.
39. Orgogozo V. (2015). Replaying the tape of life in the twenty-first century. Interface Focus 5: 20150057.
40. Rainey PB, Travisano M. (1998). Adaptive radiation in a heterogeneous environment. Nature 394: 69-72.
41. Rainey PB. (1999). Adaptation of Pseudomonas fluorescens to the plant rhizosphere. Environ Microbiol 1: 243-257.
42. Rainey PB, Cooper TF. (2004). Evolution of bacterial diversity and the origins of modularity. Res Microbiol 155: 370-375.
43. Rainey PB, Desprat N, Driscoll WW, Zhang XX. (2014). Microbes are not bound by sociobiology: response to Kummerli and Ross-Gillespie (2013). Evolution 68: 3344-3355.
44. Römling U, Rohde M, Olsen A, Normark S, Reinkoster J. (2000). AgfD, the checkpoint of multicellular and aggregative behaviour in Salmonella typhimurium regulates at least two independent pathways. Mol Microbiol 36: 10-23.
45. Römling U, Galperin MY, Gomelsky M. (2013). Cyclic di-GMP: the first 25 years of a universal bacterial second messenger. Microbiol Mol Biol Rev 77: 1-52.
46. Silby MW, Cerdeno-Tarraga AM, Vernikos GS, Giddens SR, Jackson RW, Preston GM et al. (2009). Genomic and genetic analyses of diversity and plant interactions of Pseudomonas fluorescens. Genome Biol 10: R51.
47. Smith EE, Buckley DG, Wu Z, Saenphimmachak C, Hoffman LR, D'Argenio DA et al. (2006). Genetic adaptation by Pseudomonas aeruginosa to the airways of cystic fibrosis patients. Proc Natl Acad Sci USA 103: 8487-8492.
48. Spiers AJ, Buckling A, Rainey PB. (2000). The causes of Pseudomonas diversity. Microbiology 146: 2345-2350.
49. Spiers AJ, Kahn SG, Bohannon J, Travisano M, Rainey PB. (2002). Adaptive divergence in experimental populations of Pseudomonas fluorescens. I. Genetic and phenotypic bases of wrinkly spreader fitness. Genetics 161: 33-46.
50. Spiers AJ, Bohannon J, Gehrig SM, Rainey PB. (2003). Biofilm formation at the air-liquid interface by the Pseudomonas fluorescens SBW25 wrinkly spreader requires an acetylated form of cellulose. Mol Microbiol 50: 15-27.
51. Srivastava D, Waters CM. (2012). A tangled web: regulatory connections between quorum sensing and cyclic di-GMP. J Bacteriol 194: 4485-4493.
52. Steiner S, Lori C, Boehm A, Jenal U. (2013). Allosteric activation of exopolysaccharide synthesis through cyclic di-GMP-stimulated protein-protein interaction. EMBO J 32: 354-368.
53. Stern DL. (2013). The genetic causes of convergent evolution. Nat Rev Genet 14: 751-764.
54. Tenaillon O, Rodriguez-Verdugo A, Gaut RL, McDonald P, Bennett AF, Long AD et al. (2012). The molecular diversity of adaptive convergence. Science 335: 457-461.
55. Tidhar A, Flashner Y, Cohen S, Levi Y, Zauberman A, Gur D et al. (2009). The NlpD lipoprotein is a novel Yersinia pestis virulence factor essential for the development of plague. Plos One 4: e7023.
56. Traverse CC, Mayo-Smith LM, Poltak SR, Cooper VS. (2013). Tangled bank of experimentally evolved Burkholderia biofilms reflects selection during chronic infections. Proc Natl Acad Sci USA 110: E250-E259.
57. Uehara T, Parzych KR, Dinh T, Bernhardt TG. (2010). Daughter cell separation is controlled by cytokinetic ring-activated cell wall hydrolysis. EMBO J 29: 1412-1422.
58. Wang X, Preston JF 3rd, Romeo T. (2004). The pgaABCD locus of Escherichia coli promotes the synthesis of a polysaccharide adhesin required for biofilm formation. J Bacteriol 186: 2724-2734.
59. Whiteside MD, Winsor GL, Laird MR, Brinkman FS. (2013). OrtholugeDB: A bacterial and archaeal orthology resource for improved comparative genomic analysis. Nucleic Acids Res 41: D366-D376.
60. Wichman HA, Badgett MR, Scott LA, Boulianne CM, Bull JJ. (1999). Different trajectories of parallel evolution during viral adaptation. Science 285: 422-424.
61. Winsor GL, Lam DK, Fleming L, Lo R, Whiteside MD, Yu NY et al. (2011). Pseudomonas Genome Database: improved comparative analysis and population genomics capability for Pseudomonas genomes. Nucleic Acids Res 39: D596-D600.
62. Zhen Y, Aardema ML, Medina EM, Schumer M, Andolfatto P. (2012). Parallel molecular evolution in an herbivore community. Science 337: 1634-1637.
63. Zogaj X, Nimtz M, Rohde M, Bokranz W, Romling U. (2001). The multicellular morphotypes of Salmonella typhimurium and Escherichia coli produce cellulose as the second component of the extracellular matrix. Mol Microbiol 39: 1452-1463.