A suppression subtractive hybridization approach reveals niche-specific genes that may be involved in predator avoidance in marine Synechococcus isolates

Applied and Environmental Microbiology

Volumn 72, Issue 4, 2006, Pages 2730-2737

  Jones, H ^a   Ostrowski, M ^a   Scanlan, D J ^a  

^a UNIVERSITY OF WARWICK   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

GENE ENCODING; PHOSPHATE EXPORT SYSTEM; PREDATOR AVOIDANCE;

BACTERIA; BACTERIOLOGY; GENETIC ENGINEERING; PHOSPHATES; PROTEINS;

GENES;

BACTERIAL POLYSACCHARIDE; GLYCOSYLTRANSFERASE; PERMEASE; POLYOL;

BACTERIOLOGY; BACTERIUM; BIODIVERSITY; GENE; GENOMICS; PREDATOR;

ARTICLE; BACTERIAL GENOME; BACTERIAL STRAIN; CLADISTICS; CYANOBACTERIUM; GENE IDENTIFICATION; GENETIC VARIABILITY; MARINE ENVIRONMENT; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PREDATOR AVOIDANCE; STRAIN IDENTIFICATION; SUPPRESSION SUBTRACTIVE HYBRIDIZATION; SYNECHOCOCCUS; UNINDEXED SEQUENCE;

BACTERIAL PROTEINS; ECOSYSTEM; FOOD CHAIN; MOLECULAR SEQUENCE DATA; NUCLEIC ACID HYBRIDIZATION; SEAWATER; SEQUENCE ANALYSIS, DNA; SYNECHOCOCCUS;

BACTERIA (MICROORGANISMS); SYNECHOCOCCUS; SYNECHOCOCCUS SP.;

EID: 33646109829     PISSN: 00992240     EISSN: None     Source Type: Journal    
DOI: 10.1128/AEM.72.4.2730-2737.2006     Document Type: Article

References (45)

1. Agron, P. G., M. Macht, L. Radnedge, E. W. Skowronski, W. Miller, and G. L. Andersen. 2002. Use of subtractive hybridisation for comprehensive surveys of prokaryotic genome differences. FEMS Microbiol. Lett. 211:175-182.
2. Akopyants, N. S., A. Fradkov, L. Diatchenko, J. E. Hill, P. D. Siebert, S. A. Lukyanov, E. D. Sverdlov, and D. E. Berg. 1998. PCR-based subtractive hybridization and differences in gene content among strains of Helicobacter pylon. Proc. Natl. Acad. Sci. USA 95:13108-13113.
3. Altschul, S. F., T. L. Madden, A. A. Schaffer, J. Zhang, Z. Zhang, W. Miller, and D. J. Lipman. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25:3389-3402.
4. Becker, H. D., and D. Kern. 1998. Thermus thermophilus: a link in evolution of the tRNA-dependent amino acid amidation pathways. Proc. Natl. Acad. Sci. USA 95:12832-12837.
5. Bird, C., and M. Wyman. 2003. Nitrate/nitrite assimilation system of the marine picoplanktonic cyanobacterium Synechococcus sp. strain WH 8103: effect of nitrogen source and availability on gene expression. Appl. Environ. Microbiol. 69:7009-7018.
6. Brahamsha, B. 1996. An abundant cell surface polypeptide is required for swimming by the nonflagellated marine cyanobacterium Synechococcus. Proc. Natl. Acad. Sci. USA 93:6504-6509.
7. Campbell, L., and E. J. Carpenter. 1987. Characterisation of phycoerythrin-containing Synechococcus spp. populations by immunofluorescence. J. Plankton Res. 9:1167-1181.
8. Campbell, L., and R. Iturriaga. 1988. Identification of Synechococcus spp. in the Sargasso Sea by immunofluorescence and fluorescence excitation spectroscopy performed on individual cells. Limnol. Oceanogr. 33:1196-1201.
9. Collier, J. L., B. Brahamsha, and B. Palenik. 1999. The marine cyanobacterium Synechococcus sp. WH 7805 requires urease (urea amidohydrolase, EC 3.5.1.5) to utilize urea as nitrogen source: molecular-genetic and biochemical analysis of the enzyme. Microbiology 145:447-459.
10. gln amidotransferase in Deinococcus radiodurans may be confined to asparagine biosynthesis. Proc. Natl. Acad. Sci. USA 95:12838-12843.
11. Diatchenko, L., Y. F. C. Lau, A. P. Campbell, A. Chenchik, F. Moqadam, B. Huang, S. Lukyanov, K. Lukyanov, N. Gurskaya, E. D. Sverdlov, and P. D. Siebert. 1996. Suppression subtractive hybridization: a method for generating differentially regulated or tissue-specific cDNA probes and libraries. Proc. Natl. Acad. Sci. USA 93:6025-6030.
12. Dufresne, A., M. Salanoubat, F. Partensky, F. Artiguenave, I. M. Axmann, V. Barbe, S. Duprat, M. Y. Galperin, E. V. Koonin, F. Le Gall, K. S. Makarova, M. Ostrowski, S. Oztas, C. Robert, I. B. Rogozin, D. J. Scanlan, N. Tandeau de Marsac, J. Weissenbach, P. Wincker, Y. I. Wolf, and W. R. Hess. 2003. Genome sequence of the cyanobacterium Prochlorococcus marinus SS120, a nearly minimal oxyphototrophic genome. Proc. Natl. Acad. Sci. USA 100:10020-10025.
13. Fuller, N. J., D. Marie, F. Partensky, D. Vaulot, A. F. Post, and D. J. Scanlan. 2003. Clade-specific 16S ribosomal DNA oligonucleotides reveal the predominance of a single marine Synechococcus clade throughout a stratified water column in the Red Sea. Appl. Environ. Microbiol. 69:2430-2443.
14. Fuller, N. J., N. J. West, D. Marie, M. Yallop, T. Rivlin, A. F. Post, and D. J. Scanlan. 2005. Dynamics of community structure and phosphate status of picocyanobacterial populations in the Gulf of Aqaba, Red Sea. Limnol. Oceanogr. 50:363-375.
15. Galbraith, E. A., D. A. Antonopoulos, and B. A. White. 2004. Suppressive subtractive hybridisation as a tool for identifying genetic diversity in an environmental metagenome: the rumen as a model. Environ. Microbiol. 6:928-937.
16. García-Fernández, J. M., and J. Diez. 2004. Adaptive mechanisms of nitrogen and carbon assimilatory pathways in the marine cyanobacteria Prochlorococcus. Res. Microbiol. 155:795-802.
17. Janke, B., U. Dobrindt, J. Hacker, and G. Blum-Oehler. 2001. A subtractive hybridisation analysis of genomic differences between the uropathogenic E. coli strain 536 and the E. coli K-12 strain MG1655. FEMS Microbiol. Lett. 199:61-66.
18. Li, W. K. W. 1994. Primary production of prochlorophytes, cyanobacteria, and eukaryotic ultraphytoplankton: measurements from flow cytometric sorting. Limnol. Oceanogr. 39:169-175.
19. Matz, C., and S. Kjelleberg. 2005. Off the hook-how bacteria survive protozoan grazing. Trends Microbiol. 13:302-307.
20. McCarren, J., and B. Brahamsha. 2005. Transposon mutagenesis in a marine Synechococcus strain: isolation of swimming motility mutants. J. Bacteriol. 187:4457-4462.
21. Min, B., J. T. Pelaschier, D. E. Graham, D. Tumbula-Hansen, and D. Soil. 2002. Transfer RNA-dependent amino acid biosynthesis: an essential route to asparagine formation. Proc. Natl. Acad. Sci. USA 99:2678-2683.
22. Monger, B. C., M. R. Landry, and S. L. Brown. 1999. Feeding selection of heterotrophic marine nanoflagellates based on the surface hydrophobicity of their picoplankton prey. Limnol. Oceanogr. 44:1917-1927.
23. Müller, H. 1996. Selective feeding of a freshwater chrysomonad, Paraphysomonas sp., on chroococcoid cyanobacteria and nanoflagellates. Arch. Hydrobiol. Spec. Issues Adv. Limnol. 48:63-71.
24. Omata, T. 1995. Structure, function and regulation of the nitrate transport system of the cyanobacterium Synechococcus sp. PCC7942. Plant Cell Physiol. 36:207-213.
25. Omata, T., X. And Hesse, and A. Hirano. 1993. Identification and characterization of a gene cluster involved in nitrate transport in the cyanobacterium Synechococcus sp. PCC7942. Mol. Gen. Genet. 236:193-202.
26. Otero, A., and M. Vincenzini. 2004. Nostoc (Cyanophyceae) goes nude: extracellular polysaccharides serve as a sink for reducing power under unbalanced C/N metabolism. J. Phycol. 40:74-81.
27. Palenik, B. 2001. Chromatic adaptation in marine Synechococcus strains. Appl. Environ. Microbiol. 67:991-994.
28. Palenik, B., B. Brahamsha, F. W. Larimer, M. Land, L. Hauser, P. Chain, J. Lamerdin, W. Regala, E. E. Allen, J. McCarren, I. Paulsen, A. Dufresne, F. Partensky, E. A. Webb, and J. Waterbury. 2003. The genome of a motile marine Synechococcus. Nature 424:1037-1042.
29. Parsons, Y. N., R. Banasko, M. G. Detsika, K. Duangsonk, L. Rainbow, C. A. Hart, and C. Winstanley. 2003. Suppression subtractive hybridisation reveals variations in gene distribution amongst the Burkholderia cepacia complex, including the presence in some strains of a genomic island containing putative polysaccharide production genes. Arch. Microbiol. 179:214-223.
30. Partensky, F., J. Blanchot, and D. Vaulot. 1999. Differential distribution and ecology of Prochlorococcus and Synechococcus in oceanic waters: a review. Bull. Inst. Oceanogr. (Monaco) 19:451-415.
31. +-dependent transporter associated with saxitoxin-producing strains of the cyanobacterium Anabaena circinalis. Appl. Environ. Microbiol. 70:4711-4719.
32. Rocap, G., D. L. Distel, J. B. Waterbury, and S. W. Chisholm. 2002. Resolution of Prochlorococcus and Synechococcus ecotypes by using 16S-23S ribosomal DNA internal transcribed spacer sequences. Appl. Environ. Microbiol. 68:1180-1191.
33. Rocap, G., F. W. Larimer, J. Lamerdin, S. Malfatti, P. Chain, N. A. Ahlgren, A. Arellano, M. Coleman, L. Hauser, W. R. Hess, Z. I. Johnson, M. Land, D. Lindell, A. F. Post, W. Regala, M. Shah, S. L. Shaw, C. Steglich, M. B. Sullivan, C. S. Ting, A. Tolonen, E. A. Webb, E. R. Zinser, and S. W. Chisholm. 2003. Genome divergence in two Prochlorococcus ecotypes reflects oceanic niche differentiation. Nature 424:1042-1047.
34. Roy, H., H. D. Becker, J. Reinbolt, and D. Kern. 2003. When contemporary aminoacyl-tRNA synthetases invent their cognate amino acid metabolism. Proc. Natl. Acad. Sci. USA 100:9837-9842.
35. Sakamoto, T., K. Inoue-Sakamoto, and D. A. Bryant. 1999. A novel nitrate/nitrite permease in the marine cyanobacterium Synechococcus sp. strain PCC7002. J. Bacteriol. 181:7363-7372.
36. Scanlan, D. J. 2003. Physiological diversity and niche adaptation in marine Synechococcus. Adv. Microb. Physiol. 47:1-64.
37. Smith, A. J., J. London, and R. Y. Stanier. 1967. Biochemical basis of obligate autotrophy in blue-green algae and thiobacilli. J. Bacteriol. 94:972-983.
38. Suttle, C. A., and A. M. Chan. 1994. Dynamics and distribution of cyanophages and their effect on marine Synechococcus spp. Appl. Environ. Microbiol. 60:3167-3174.
39. Toledo, G., and B. Palenik. 1997. Synechococcus diversity in the California current as seen by RNA polymerase (rpoC1) gene sequences of isolated strains. Appl. Environ. Microbiol. 63:4298-4303.
40. Toledo, G., and B. Palenik. 2003. A Synechococcus serotype is found preferentially in surface marine waters. Limnol. Oceanogr. 48:1744-1755.
41. Toledo, G., B. Palenik, and B. Brahamsha. 1999. Swimming marine Synechococcus strains with widely different photosynthetic pigment ratios form a monophyletic group. Appl. Environ. Microbiol. 65:5247-5251.
42. Valladares, A., M. L. Montesinos, A. Herrero, and E. Flores. 2002. An ABC-type, high-affinity urea permease identified in cyanobacteria. Mol. Microbiol. 43:703-715.
43. Wang, Q. F., and A. F. Post. 2000. Nitrate assimilation genes of the marine diazotrophic, filamentous cyanobacterium Trichodesmium sp strain WH9601. J. Bacteriol. 182:1764-1767.
44. Waterbury, J. B., S. W. Watson, F. W. Valois, and D. G. Franks. 1986. Biological and ecological characterisation of the marine unicellular cyanobacterium Synechococcus. Can. Bull. Fish. Aquat. Sci. 214:71-120.
45. Zhang, Y. L., C. T. Ong, and K. Y. Leung. 2000. Molecular analysis of genetic differences between virulent and avirulent strains of Aeromonas hydrophila isolated from diseased fish. Microbiology 146:999-1009.