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. 2002 May;161(1):33–46. doi: 10.1093/genetics/161.1.33

Adaptive divergence in experimental populations of Pseudomonas fluorescens. I. Genetic and phenotypic bases of wrinkly spreader fitness.

Andrew J Spiers 1, Sophie G Kahn 1, John Bohannon 1, Michael Travisano 1, Paul B Rainey 1
PMCID: PMC1462107  PMID: 12019221

Abstract

A central feature of all adaptive radiations is morphological divergence, but the phenotypic innovations that are responsible are rarely known. When selected in a spatially structured environment, populations of the bacterium Pseudomonas fluorescens rapidly diverge. Among the divergent morphs is a mutant type termed "wrinkly spreader" (WS) that colonizes a new niche through the formation of self-supporting biofilms. Loci contributing to the primary phenotypic innovation were sought by screening a WS transposon library for niche-defective (WS(-)) mutants. Detailed analysis of one group of mutants revealed an operon of 10 genes encoding enzymes necessary to produce a cellulose-like polymer (CLP). WS genotypes overproduce CLP and overproduction of the polymer is necessary for the distinctive morphology of WS colonies; it is also required for biofilm formation and to maximize fitness in spatially structured microcosms, but overproduction of CLP alone is not sufficient to cause WS. A working model predicts that modification of cell cycle control of CLP production is an important determinant of the phenotypic innovation. Analysis of >30 kb of DNA encoding traits required for expression of the WS phenotype, including a regulatory locus, has not revealed the mutational causes, indicating a complex genotype-phenotype map.

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Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Alfano J. R., Bauer D. W., Milos T. M., Collmer A. Analysis of the role of the Pseudomonas syringae pv. syringae HrpZ harpin in elicitation of the hypersensitive response in tobacco using functionally non-polar hrpZ deletion mutations, truncated HrpZ fragments, and hrmA mutations. Mol Microbiol. 1996 Feb;19(4):715–728. doi: 10.1046/j.1365-2958.1996.415946.x. [DOI] [PubMed] [Google Scholar]
  2. Ausmees N., Jonsson H., Höglund S., Ljunggren H., Lindberg M. Structural and putative regulatory genes involved in cellulose synthesis in Rhizobium leguminosarum bv. trifolii. Microbiology. 1999 May;145(Pt 5):1253–1262. doi: 10.1099/13500872-145-5-1253. [DOI] [PubMed] [Google Scholar]
  3. Blanton R. L., Fuller D., Iranfar N., Grimson M. J., Loomis W. F. The cellulose synthase gene of Dictyostelium. Proc Natl Acad Sci U S A. 2000 Feb 29;97(5):2391–2396. doi: 10.1073/pnas.040565697. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. 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., Mayhew G. F. The complete genome sequence of Escherichia coli K-12. Science. 1997 Sep 5;277(5331):1453–1462. doi: 10.1126/science.277.5331.1453. [DOI] [PubMed] [Google Scholar]
  5. Carroll S. B. Endless forms: the evolution of gene regulation and morphological diversity. Cell. 2000 Jun 9;101(6):577–580. doi: 10.1016/s0092-8674(00)80868-5. [DOI] [PubMed] [Google Scholar]
  6. Deckert G., Warren P. V., Gaasterland T., Young W. G., Lenox A. L., Graham D. E., Overbeek R., Snead M. A., Keller M., Aujay M. The complete genome of the hyperthermophilic bacterium Aquifex aeolicus. Nature. 1998 Mar 26;392(6674):353–358. doi: 10.1038/32831. [DOI] [PubMed] [Google Scholar]
  7. Ditta G., Stanfield S., Corbin D., Helinski D. R. Broad host range DNA cloning system for gram-negative bacteria: construction of a gene bank of Rhizobium meliloti. Proc Natl Acad Sci U S A. 1980 Dec;77(12):7347–7351. doi: 10.1073/pnas.77.12.7347. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Doi M., Wachi M., Ishino F., Tomioka S., Ito M., Sakagami Y., Suzuki A., Matsuhashi M. Determinations of the DNA sequence of the mreB gene and of the gene products of the mre region that function in formation of the rod shape of Escherichia coli cells. J Bacteriol. 1988 Oct;170(10):4619–4624. doi: 10.1128/jb.170.10.4619-4624.1988. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Erwin D. H. Macroevolution is more than repeated rounds of microevolution. Evol Dev. 2000 Mar-Apr;2(2):78–84. doi: 10.1046/j.1525-142x.2000.00045.x. [DOI] [PubMed] [Google Scholar]
  10. Fleischmann R. D., Adams M. D., White O., Clayton R. A., Kirkness E. F., Kerlavage A. R., Bult C. J., Tomb J. F., Dougherty B. A., Merrick J. M. Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science. 1995 Jul 28;269(5223):496–512. doi: 10.1126/science.7542800. [DOI] [PubMed] [Google Scholar]
  11. Franklin M. J., Ohman D. E. Identification of algI and algJ in the Pseudomonas aeruginosa alginate biosynthetic gene cluster which are required for alginate O acetylation. J Bacteriol. 1996 Apr;178(8):2186–2195. doi: 10.1128/jb.178.8.2186-2195.1996. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Gronewold T. M., Kaiser D. The act operon controls the level and time of C-signal production for Myxococcus xanthus development. Mol Microbiol. 2001 May;40(3):744–756. doi: 10.1046/j.1365-2958.2001.02428.x. [DOI] [PubMed] [Google Scholar]
  13. Herrero M., de Lorenzo V., Timmis K. N. Transposon vectors containing non-antibiotic resistance selection markers for cloning and stable chromosomal insertion of foreign genes in gram-negative bacteria. J Bacteriol. 1990 Nov;172(11):6557–6567. doi: 10.1128/jb.172.11.6557-6567.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Ishikawa J., Hotta K. FramePlot: a new implementation of the frame analysis for predicting protein-coding regions in bacterial DNA with a high G + C content. FEMS Microbiol Lett. 1999 May 15;174(2):251–253. doi: 10.1111/j.1574-6968.1999.tb13576.x. [DOI] [PubMed] [Google Scholar]
  15. Jenal U. Signal transduction mechanisms in Caulobacter crescentus development and cell cycle control. FEMS Microbiol Rev. 2000 Apr;24(2):177–191. doi: 10.1016/S0168-6445(99)00035-2. [DOI] [PubMed] [Google Scholar]
  16. Jones L. J., Carballido-López R., Errington J. Control of cell shape in bacteria: helical, actin-like filaments in Bacillus subtilis. Cell. 2001 Mar 23;104(6):913–922. doi: 10.1016/s0092-8674(01)00287-2. [DOI] [PubMed] [Google Scholar]
  17. Leigh EG., Jr The modern synthesis, Ronald Fisher and creationism. Trends Ecol Evol. 1999 Dec;14(12):495–498. doi: 10.1016/s0169-5347(99)01725-5. [DOI] [PubMed] [Google Scholar]
  18. Lenski R. E., Mongold J. A., Sniegowski P. D., Travisano M., Vasi F., Gerrish P. J., Schmidt T. M. Evolution of competitive fitness in experimental populations of E. coli: what makes one genotype a better competitor than another? Antonie Van Leeuwenhoek. 1998 Jan;73(1):35–47. doi: 10.1023/a:1000675521611. [DOI] [PubMed] [Google Scholar]
  19. Lowe T. M., Eddy S. R. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 1997 Mar 1;25(5):955–964. doi: 10.1093/nar/25.5.955. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Matthysse A. G., White S., Lightfoot R. Genes required for cellulose synthesis in Agrobacterium tumefaciens. J Bacteriol. 1995 Feb;177(4):1069–1075. doi: 10.1128/jb.177.4.1069-1075.1995. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Mortlock R. P. Metabolic acquisitions through laboratory selection. Annu Rev Microbiol. 1982;36:259–284. doi: 10.1146/annurev.mi.36.100182.001355. [DOI] [PubMed] [Google Scholar]
  22. Nielsen H., Engelbrecht J., Brunak S., von Heijne G. A neural network method for identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites. Int J Neural Syst. 1997 Oct-Dec;8(5-6):581–599. doi: 10.1142/s0129065797000537. [DOI] [PubMed] [Google Scholar]
  23. Nishijyo T., Park S. M., Lu C. D., Itoh Y., Abdelal A. T. Molecular characterization and regulation of an operon encoding a system for transport of arginine and ornithine and the ArgR regulatory protein in Pseudomonas aeruginosa. J Bacteriol. 1998 Nov;180(21):5559–5566. doi: 10.1128/jb.180.21.5559-5566.1998. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Okamoto K., Gotoh N., Tsujimoto H., Yamada H., Yoshihara E., Nakae T., Nishino T. Molecular cloning and characterization of the oprQ gene coding for outer membrane protein OprE3 of Pseudomonas aeruginosa. Microbiol Immunol. 1999;43(3):297–301. doi: 10.1111/j.1348-0421.1999.tb02407.x. [DOI] [PubMed] [Google Scholar]
  25. Pei J., Grishin N. V. GGDEF domain is homologous to adenylyl cyclase. Proteins. 2001 Feb 1;42(2):210–216. doi: 10.1002/1097-0134(20010201)42:2<210::aid-prot80>3.0.co;2-8. [DOI] [PubMed] [Google Scholar]
  26. Rainey P. B. Adaptation of Pseudomonas fluorescens to the plant rhizosphere. Environ Microbiol. 1999 Jun;1(3):243–257. doi: 10.1046/j.1462-2920.1999.00040.x. [DOI] [PubMed] [Google Scholar]
  27. Rainey P. B., Bailey M. J. Physical and genetic map of the Pseudomonas fluorescens SBW25 chromosome. Mol Microbiol. 1996 Feb;19(3):521–533. doi: 10.1046/j.1365-2958.1996.391926.x. [DOI] [PubMed] [Google Scholar]
  28. Rainey P. B., Travisano M. Adaptive radiation in a heterogeneous environment. Nature. 1998 Jul 2;394(6688):69–72. doi: 10.1038/27900. [DOI] [PubMed] [Google Scholar]
  29. Rainey PB, Buckling A, Kassen R, Travisano M. The emergence and maintenance of diversity: insights from experimental bacterial populations. Trends Ecol Evol. 2000 Jun;15(6):243–247. doi: 10.1016/s0169-5347(00)01871-1. [DOI] [PubMed] [Google Scholar]
  30. Rawlings M., Cronan J. E., Jr The gene encoding Escherichia coli acyl carrier protein lies within a cluster of fatty acid biosynthetic genes. J Biol Chem. 1992 Mar 25;267(9):5751–5754. [PubMed] [Google Scholar]
  31. Reynolds M. G. Compensatory evolution in rifampin-resistant Escherichia coli. Genetics. 2000 Dec;156(4):1471–1481. doi: 10.1093/genetics/156.4.1471. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. Römling U., Rohde M., Olsén A., Normark S., Reinköster J. AgfD, the checkpoint of multicellular and aggregative behaviour in Salmonella typhimurium regulates at least two independent pathways. Mol Microbiol. 2000 Apr;36(1):10–23. doi: 10.1046/j.1365-2958.2000.01822.x. [DOI] [PubMed] [Google Scholar]
  33. Saxena I. M., Brown R. M., Jr Identification of a second cellulose synthase gene (acsAII) in Acetobacter xylinum. J Bacteriol. 1995 Sep;177(18):5276–5283. doi: 10.1128/jb.177.18.5276-5283.1995. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. Saxena I. M., Kudlicka K., Okuda K., Brown R. M., Jr Characterization of genes in the cellulose-synthesizing operon (acs operon) of Acetobacter xylinum: implications for cellulose crystallization. J Bacteriol. 1994 Sep;176(18):5735–5752. doi: 10.1128/jb.176.18.5735-5752.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]
  35. Schrag S. J., Perrot V., Levin B. R. Adaptation to the fitness costs of antibiotic resistance in Escherichia coli. Proc Biol Sci. 1997 Sep 22;264(1386):1287–1291. doi: 10.1098/rspb.1997.0178. [DOI] [PMC free article] [PubMed] [Google Scholar]
  36. Shubin N., Tabin C., Carroll S. Fossils, genes and the evolution of animal limbs. Nature. 1997 Aug 14;388(6643):639–648. doi: 10.1038/41710. [DOI] [PubMed] [Google Scholar]
  37. Sofia H. J., Burland V., Daniels D. L., Plunkett G., 3rd, Blattner F. R. Analysis of the Escherichia coli genome. V. DNA sequence of the region from 76.0 to 81.5 minutes. Nucleic Acids Res. 1994 Jul 11;22(13):2576–2586. doi: 10.1093/nar/22.13.2576. [DOI] [PMC free article] [PubMed] [Google Scholar]
  38. Spiers A. J., Buckling A., Rainey P. B. The causes of Pseudomonas diversity. Microbiology. 2000 Oct;146(Pt 10):2345–2350. doi: 10.1099/00221287-146-10-2345. [DOI] [PubMed] [Google Scholar]
  39. Standal R., Iversen T. G., Coucheron D. H., Fjaervik E., Blatny J. M., Valla S. A new gene required for cellulose production and a gene encoding cellulolytic activity in Acetobacter xylinum are colocalized with the bcs operon. J Bacteriol. 1994 Feb;176(3):665–672. doi: 10.1128/jb.176.3.665-672.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]
  40. Stern D. L. Evolutionary developmental biology and the problem of variation. Evolution. 2000 Aug;54(4):1079–1091. doi: 10.1111/j.0014-3820.2000.tb00544.x. [DOI] [PubMed] [Google Scholar]
  41. Stover C. K., Pham X. Q., Erwin A. L., Mizoguchi S. D., Warrener P., Hickey M. J., Brinkman F. S., Hufnagle W. O., Kowalik D. J., Lagrou M. Complete genome sequence of Pseudomonas aeruginosa PAO1, an opportunistic pathogen. Nature. 2000 Aug 31;406(6799):959–964. doi: 10.1038/35023079. [DOI] [PubMed] [Google Scholar]
  42. Treves D. S., Manning S., Adams J. Repeated evolution of an acetate-crossfeeding polymorphism in long-term populations of Escherichia coli. Mol Biol Evol. 1998 Jul;15(7):789–797. doi: 10.1093/oxfordjournals.molbev.a025984. [DOI] [PubMed] [Google Scholar]
  43. Wachi M., Matsuhashi M. Negative control of cell division by mreB, a gene that functions in determining the rod shape of Escherichia coli cells. J Bacteriol. 1989 Jun;171(6):3123–3127. doi: 10.1128/jb.171.6.3123-3127.1989. [DOI] [PMC free article] [PubMed] [Google Scholar]
  44. Wong H. C., Fear A. L., Calhoon R. D., Eichinger G. H., Mayer R., Amikam D., Benziman M., Gelfand D. H., Meade J. H., Emerick A. W. Genetic organization of the cellulose synthase operon in Acetobacter xylinum. Proc Natl Acad Sci U S A. 1990 Oct;87(20):8130–8134. doi: 10.1073/pnas.87.20.8130. [DOI] [PMC free article] [PubMed] [Google Scholar]
  45. Zogaj X., Nimtz M., Rohde M., Bokranz W., Römling U. The multicellular morphotypes of Salmonella typhimurium and Escherichia coli produce cellulose as the second component of the extracellular matrix. Mol Microbiol. 2001 Mar;39(6):1452–1463. doi: 10.1046/j.1365-2958.2001.02337.x. [DOI] [PubMed] [Google Scholar]

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