Widespread known and novel phosphonate utilization pathways in marine bacteria revealed by functional screening and metagenomic analyses

Martinex, Asuncion, Tyson, Gene W. and DeLong, Edward F. (2009) Widespread known and novel phosphonate utilization pathways in marine bacteria revealed by functional screening and metagenomic analyses. Environmental Microbiology, 12 1: 222-238. doi:10.1111/j.1462-2920.2009.02062.x

Author Martinex, Asuncion
Tyson, Gene W.
DeLong, Edward F.
Title Widespread known and novel phosphonate utilization pathways in marine bacteria revealed by functional screening and metagenomic analyses
Journal name Environmental Microbiology   Check publisher's open access policy
ISSN 1462-2912
Publication date 2009
Year available 2009
Sub-type Article (original research)
DOI 10.1111/j.1462-2920.2009.02062.x
Volume 12
Issue 1
Start page 222
End page 238
Total pages 17
Editor David A Stahl
Kenneth N Timmis
Place of publication United Kingdom
Publisher Wiley-Blackwell Publishing Ltd
Collection year 2010
Language eng
Subject C1
Abstract Phosphonates (Pn), compounds with a direct C–P bond instead of the more common C–O–P ester bond, constitute a significant fraction of marine dissolved organic phosphorus and recent evidence suggests that they may be an alternative source of P for marine microorganisms. To further characterize the microorganisms and pathways involved in Pn utilization, we screened bacterioplankton genomic libraries for their ability to complement an Escherichia coli strain unable to use Pns as a P source. Using this approach we identified a phosphonatase pathway as well as a novel pair of genes that allowed utilization of 2-aminoethylphosphonate (2-AEPn) as the sole P source. These pathways are present in diverse bacteria common in marine plankton including representatives of Proteobacteria, Planctomycetes and Cyanobacteria. Analysis of metagenomic databases for Pn utilization genes revealed that they are widespread and abundant among marine bacteria, suggesting that Pn metabolism is likely to play an important role in P-depleted surface waters, as well as in the more P-rich deep-water column.
Keyword phosphonate unilization
metagenomic analyses
putative taxonomic
References Altschul, S.F., Madden, T.L., Schaeffer, A.A., Zhang, J., Zhang, Z., Miller, W., and Lipman, D.J. (1997) Gapped blast and psi-blast: a new generation of protein database search programs. Nucleic Acids Res 25: 3389–3402. Links Aravind, L., and Koonin, E.V. (1998) The HD domain defines a new superfamily of metal-dependent phosphohydrolases. Trends Biochem Sci 23: 469–472. Links Baba, T., Ara, T., Hasegawa, M., Takai, Y., Okumura, Y., Baba, M., et al. (2006) Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. Mol Syst Biol 2: 2006.0008. Links Benitez-Nelson, C.R., O'Neill, L., Kolowith, L.C., Pellecia, P., and Thunell, R. (2004) Phosphonates and particulate organic phosphorus cycling in an anoxic marine basin. Limnol Oceanogr 49: 1593–1604. Links Bjorkman, K.M., and Karl, D.M. (2003) Bioavailability of dissolved organic phosphorus in the euphotic zone at Station ALOHA, North Pacific Subtropical Gyre. Limnol Oceanogr 48: 1049–1057. Links Chen, C.C., Zhang, H., Kim, A.D., Howard, A., Sheldrick, G.M., Mariano-Dunaway, D., and Herzberg, O. (2002) Degradation pathway of the phosphonate ciliatine: crystal structure of 2-aminoethylphosphonate transaminase. Biochemistry 41: 13162–13169. Links Clark, L.L., Ingall, E.D., and Benner, R. (1999) Marine organic phosphorus cycling: novel insights from nuclear magnetic resonance. Am J Sci 2999: 724–737. Links Coleman, M.L., Sullivan, M.B., Martiny, A.C., Steglich, C., Barry, K., Delong, E.F., and Chisholm, S.W. (2006) Genomic islands and the ecology and evolution of Prochlorococcus. Science 311: 1768–1770. Links Datsenko, K.A., and Wanner, B.L. (2000) One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. Proc Natl Acad Sci USA 97: 6640–6645. Links DeLong, E.F. (2009) The microbial ocean from genomes to biomes. Nature 459: 200–206. Links DeLong, E.F., Preston, C.M., Mincer, T., Rich, V., Hallam, S.J., Frigaard, N.-U., et al. (2006) Community genomics among stratified microbial assemblages in the ocean's interior. Science 311: 496–503. Links Dumora, C., Lacoste, A.M., and Cassaigne, A. (1983) Purification and properties of 2-aminoethylphosphonate: pyruvate aminotransferase from Pseudomonas aeruginosa. Eur J Biochem 133: 119–125. Links Dumora, C., Marche, M., Doignon, F., Aigle, M., Cassaigne, A., and Crouzet, M. (1997) First characterization of the phosphonoacetaldehyde hydrolase gene of Pseudomonas aeruginosa. Gene 197: 405–412. Links Dyhrman, S.T., Chappell, P.D., Haley, S.T., Moffett, J.W., Orchard, E.D., Waterbury, J.B., and Webb, E.A. (2006) Phosphonate utilization by the globally important marine diazotroph. Trichodesmium 439: 68–71. Links Dyhrman, S.T., Ammerman, J.W., and Van Moy, B.A.S. (2007) Microbes and the marine phosphorus cycle. Oceanography 20: 110–116. Links Egli, T. (1988) (An)aerobic breakdown of chelating agents used in household detergents. Microbiol Sci 5: 36–41. Links Eichhorn, E., van der Ploeg, J.R., Kertesz, M.A., and Leisinger, T. (1997) Characterization of alpha-ketoglutarate-dependent taurine dioxygenase from Escherichia coli. J Biol Chem 272: 23031–23036. Links Frias-Lopez, J., Shi, Y., Tyson, G.W., Coleman, M.L., Schuster, S.C., Chisholm, S.W., and Delong, E.F. (2008) Microbial community gene expression in ocean surface waters. Proc Natl Acad Sci USA 105: 3805–3810. Links Gilbert, J.A., Thomas, S., Cooley, N.A., Kulakova, A., Field, D., Booth, T., et al. (2009) Potential for phosphonoacetate utilization by marine bacteria in temperate coastal waters. Environ Microbiol 11: 111–125. Links Gonzalez, J.M., Covert, J.S., Whitman, W.B., Henriksen, J.R., Mayer, F., Scharf, B., et al. (2003) Silicibacter pomeroyi sp. nov. and Roseovarius nubinhibens sp. nov., dimethylsulfoniopropionate-demethylating bacteria from marine environments. Int J Syst Evol Microbiol 53: 1261–1269. Links Hogan, D.A., Smith, S.R., Saari, E.A., McCracken, J., and Hausinger, R.P. (2000) Site-directed mutagenesis of 2,4-dichlorophenoxyacetic acid/alpha-ketoglutarate dioxygenase. Identification of residues involved in metallocenter formation and substrate binding. J Biol Chem 275: 12400–12409. Links Hopkinson, C.S., Jr, and Vallino, J.J. (2005) Efficient export of carbon to the deep ocean through dissolved organic matter. Nature 433: 142–145. Links Horiguchi, M. (1984) Occurence, identification and properties of phosphonic and phosphinic acids. In The Biochemistry of Natural C–P Compounds. Hoti, T., Horiguchi, M., and Hayshi, A. . Kyoto, Japan: Maruzen, pp. 24–52. Howard, E.C., Sun, S., Biers, E.J., and Moran, M.A. (2008) Abundant and diverse bacteria involved in DMSP degradation in marine surface waters. Environ Microbiol 10: 2397–2410. Links Huang, J., Su, Z., and Xu, Y. (2005) The evolution of microbial phosphonate degradative pathways. J Mol Evol 61: 682–690. Links Ishiyama, M., Tominaga, H., Shiga, M., Sasamoto, K., Ohkura, Y., and Ueno, K. (1996) A combined assay of cell viability and in vitro cytotoxicity with a highly water-soluble tetrazolium salt, neutral red and crystal violet. Biol Pharm Bull 19: 1518–1520. Links Jiang, W., Metcalf, W.W., Lee, K.S., and Wanner, B.L. (1995) Molecular cloning, mapping, and regulation of Pho regulon genes for phosphonate breakdown by the phosphonatase pathway of Salmonella typhimurium LT2. J Bacteriol 177: 6411–6421. Links Karl, D.M. (1999) A sea of change: biogeochemical variability in the North Pacific Subtropical Gyre. Ecosystems 2: 181–214. Links Karl, D.M., Beversdorf, L., Bjorman, K.M., Church, M.J., Martinez, A., and DeLong, E.F. (2008) Aerobic production of methane in the sea. Nat Geosci 1: 473–478. Links Kim, A.D., Baker, A.S., Dunaway-Mariano, D., Metcalf, W.W., Wanner, B.L., and Martin, B.M. (2002) The 2-aminoethylphosphonate-specific transaminase of the 2-aminoethylphosphonate degradation pathway. J Bacteriol 184: 4134–4140. Links Kolowith, L.C., Ingall, E.D., and Benner, R. (2001) Composition and cycling of marine organic phosphorus. Limnol Oceanogr 46: 309–320. Links Kostantinidis, K., Braff, J., Karl, D.M., and DeLong, E.F. (2009) Comparative metagenomic analysis of an abyssal microbial community from 4000 m deep at Station ALOHA in the North Pacific Ocean. Appl Environ Microbiol 75: 5345–5355. Links Krzysko-Lupicka, T., Strof, W., Kubs, K., Skorupa, M., Wieczorek, P., Lejczak, B., and Kafarski, P. (1997) The ability of soil-borne fungi to degrade organophosphonate carbon-to-phosphorus bonds. Appl Microbiol Biotechnol 48: 549–552. Links Lee, K.S., Metcalf, W.W., and Wanner, B.L. (1992) Evidence for two phosphonate degradative pathways in Enterobacter aerogenes. J Bacteriol 174: 2501–2510. Links Lindell, D., Sullivan, M.B., Johnson, Z.I., Tolonen, A.C., Rohwer, F., and Chisholm, S.W. (2004) Transfer of photosynthesis genes to and from Prochlorococcus viruses. Proc Natl Acad Sci USA 101: 11013–11018. Links Ludwig, W., Strunk, O., Westram, R., Richter, L., Meier, H., Yadhukumar, et al. (2004) ARB: a software environment for sequence data. Nucleic Acids Res 32: 1363–1371. Links McGrath, J.W., Ternan, N.G., and Quinn, J.P. (1997) Utilization of organophosphonates by environmental microorganisms. Lett Appl Microbiol 24: 69–73. Links McMullan, G., and Quinn, J.P. (1992) Detection of a novel carbon-phosphorus bond cleavage activity in cell-free extracts of an environmental Pseudomonas fluorescens isolate. Biochem Biophys Res Commun 184: 1022–1027. Links Marchler-Bauer, A., Anderson, J.B., Derbyshire, M.K., DeWeese-Scott, C., Gonzales, N.R., Gwadz, M., et al. (2007) CDD: a conserved domain database for interactive domain family analysis. Nucleic Acids Res 35: D237–D240. Links Marden, P., Tunlid, A., Malmcrona-Friberg, K., Odham, G., and Kjelleberg, S. (1985) Physioogical and morpholgical changes during short term starvation of marine bacterial isolates. Arch Microbiol 142: 326–332. Links Martinez, A., Bradley, A.S., Waldbauer, J.R., Summons, R.E., and DeLong, E.F. (2007) Proteorhodopsin photosystem gene expression enables photophosphorylation in a heterologous host. Proc Natl Acad Sci USA 104: 5590–5595. Links Martiny, A.C., Coleman, M.L., and Chisholm, S.W. (2006) Phosphate acquisition genes in Prochlorococcus ecotypes: evidence for genome-wide adaptation. Proc Natl Acad Sci USA 103: 12552–12557. Links Metcalf, W.W., and Wanner, B.L. (1991) Involvement of the Escherichia coli phn (psiD) gene cluster in assimilation of phosphorus in the form of phosphonates, phosphite, Pi esters, and Pi. J Bacteriol 173: 587–600. Links Metcalf, W.W., and Wanner, B.L. (1993a) Evidence for a fourteen-gene, phnC to phnP locus for phosphonate metabolism in Escherichia coli. Gene 129: 27–32. Links Metcalf, W.W., and Wanner, B.L. (1993b) Mutational analysis of an Escherichia coli fourteen-gene operon for phosphonate degradation, using TnphoA' elements. J Bacteriol 175: 3430–3442. Links Morais, M.C., Zhang, W., Baker, A.S., Zhang, G., Dunaway-Mariano, D., and Allen, K.N. (2000) The crystal structure of bacillus cereus phosphonoacetaldehyde hydrolase: insight into catalysis of phosphorus bond cleavage and catalytic diversification within the HAD enzyme superfamily. Biochemistry 39: 10385–10396. Links Morais, M.C., Zhang, G., Zhang, W., Olsen, D.B., Dunaway-Mariano, D., and Allen, K.N. (2004) X-ray crystallographic and site-directed mutagenesis analysis of the mechanism of Schiff-base formation in phosphonoacetaldehyde hydrolase catalysis. J Biol Chem 279: 9353–9361. Links O'Loughlin, S.N., Graham, R.L., McMullan, G., and Ternan, N.G. (2006) A role for carbon catabolite repression in the metabolism of phosphonoacetate by Agromyces fucosus Vs2. FEMS Microbiol Lett 261: 133–140. Links Quinn, J.P., Kulakova, A.N., Cooley, N.A., and McGrath, J.W. (2007) New ways to break an old bond: the bacterial carbon-phosphorus hydrolases and their role in biogeochemical phosphorus cycling. Environ Microbiol 9: 2392–2400. Links Raoult, D., Audic, S., Robert, C., Abergel, C., Renesto, P., Ogata, H., et al. (2004) The 1.2-megabase genome sequence of Mimivirus. Science 306: 1344–1350. Links Reisch, C.R., Moran, M.A., and Whitman, W.B. (2008) Dimethylsulfoniopropionate-dependent demethylase (DmdA) from Pelagibacter ubique and Silicibacter pomeroyi. J Bacteriol 190: 8018–8024. Links Rivkin, R.B., and Anderson, M.R. (1997) Inorganic nutrient limitation of oceanic bacterioplancton. Limnol Oceanogr 42: 730–740. Links Sambrook, J., Fritsch, E.F., and Maniatis, T. (1989) Molecular Cloning: A Laboratory Manual. Cold Spring Harbor, NY, USA: Cold Spring Harbor Laboratory Press. Schofield, C.J., and McDonough, M.A. (2007) Structural and mechanistic studies on the peroxisomal oxygenase phytanoyl-CoA 2-hydroxylase (PhyH). Biochem Soc Trans 35: 870–875. Links Sobecky, P.A., and Hazen, T.H. (2009) Horizontal gene transfer and mobile genetic elements in marine systems. Methods Mol Biol 532: 435–453. Links Sowell, S.M., Wilhelm, L.J., Norbeck, A.D., Lipton, M.S., Nicora, C.D., Barofsky, D.F., et al. (2009) Transport functions dominate the SAR11 metaproteome at low-nutrient extremes in the Sargasso Sea. ISME J 3: 93–105. Links Stingl, U., Tripp, H.J., and Giovannoni, S.J. (2007) Improvements of high-throughput culturing yielded novel SAR11 strains and other abundant marine bacteria from the Oregon coast and the Bermuda Atlantic Time Series study site. ISME J 1: 361–371. Links Ternan, N.G., and Quinn, J.P. (1998) Phosphate starvation-independent 2-aminoethylphosphonic acid biodegradation in a newly isolated strain of Pseudomonas putida, NG2. Syst Appl Microbiol 21: 346–352. Links Ternan, N.G., McGrath, J.W., McMullan, G., and Quinn, J.P. (1998) Review: organophosphonates: occurrence, synthesis and biodegradation. World J Microbiol Biotechnol 14: 635–647. Links Thompson, J.D., Higgins, D.G., and Gibson, T.J. (1994) clustal w: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22: 4673–4680. Links Todd, J.D., Curson, A.R., Dupont, C.L., Nicholson, P., and Johnston, A.W. (2009) The dddP gene, encoding a novel enzyme that converts dimethylsulfoniopropionate into dimethyl sulfide, is widespread in ocean metagenomes and marine bacteria and also occurs in some Ascomycete fungi. Environ Microbiol 11: 1376–1385. Links Venter, J.C., Remington, K., Heidelberg, J.F., Halpern, A.L., Rusch, D., Eisen, J.A., et al. (2004) Environmental genome shotgun sequencing of the Sargasso Sea. Science 304: 66–74. Links White, A.K., and Metcalf, W.W. (2002) Isolation and biochemical characterization of hypophosphite/2-oxoglutarate dioxygenase. A novel phosphorus-oxidizing enzyme from Psuedomonas stutzeri WM88. J Biol Chem 277: 38262–38271. Links White, A.K., and Metcalf, W.W. (2007) Microbial metabolism of reduced phosphorus compounds. Annu Rev Microbiol 61: 379–400. Links Wu, J., Sunda, W., Boyle, E.A., and Karl, D.M. (2000) Phosphate depletion in the western North Atlantic Ocean. Science 289: 759–762. Links Yakovleva, G.M., Kim, S.K., and Wanner, B.L. (1998) Phosphate-independent expression of the carbon-phosphorus lyase activity of Escherichia coli. Appl Microbiol Biotechnol 49: 573–578. Links Yooseph, S., Sutton, G., Rusch, D.B., Halpern, A.L., Williamson, S.J., Remington, K., et al. (2007) The Sorcerer II Global Ocean Sampling expedition: expanding the universe of protein families. PLoS Biol 5: e16. Links
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Additional Notes Published Online: 29 Sep 2009

Document type: Journal Article
Sub-type: Article (original research)
Collections: 2010 Higher Education Research Data Collection
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