Chapter 43
Novel Aromatic Degradation Pathway Genes and their Organization as Revealed by Metagenomic Analysis
Kentaro Miyazaki,
Kentaro Miyazaki
National Institute of Advanced Industrial Science and Technology (AIST), Ibaraki, Japan
The University of Tokyo, Ibaraki, Japan
Search for more papers by this authorKentaro Miyazaki,
Kentaro Miyazaki
National Institute of Advanced Industrial Science and Technology (AIST), Ibaraki, Japan
The University of Tokyo, Ibaraki, Japan
Search for more papers by this authorBook Editor(s):Frans J. de Bruijn,
Frans J. de Bruijn
Laboratory of Plant Micro-organism Interaction, CNRS-INRA, Castanet Tolosan, France
Search for more papers by this authorFirst published: 16 September 2011
Summary
This chapter contains sections titled:
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Introduction
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Materials and Methods
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Functional Screening of a Metagenomic Library for Genes Involved in the Microbial Degradation of Aromatic Compounds
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Novel Organization of Aromatic Degradative Pathway Genes in a Microbial Community as Revealed by Metagenomic Analysis
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Genes in the Fosmids Carrying I.2.G EDO Genes
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Concluding Remarks
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Computer Programs
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References
COMPUTER PROGRAMS
- Artemis (http://www.sanger.ac.uk/Software/Artemis/index.shtml)
- GenomeMatcher (http://www.ige.tohoku.ac.jp/joho/gmProject/gmhome.html)
- InterProScan (http://www.ebi.ac.uk/Tools/InterPro-Scan/)
- Pfam (http://PFAM.sanger.ac.uk/)
- tRNAscan-SE (http://lowelab.ucsc.edu/tRNAscan-SE/)
- REFERENCES
- Abe T, Kanaya S, Kinouchi M, Ichiba Y, Kozuki T, Ikemura T. 2003. Informatics for unveiling hidden genome signatures. Genome Res. 13: 693–702.
- Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. 1997. Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res. 25: 3389–3402.
- Amann RI, Ludwig W, Schleifer KH. 1995. Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol Rev. 59: 143–169.
- Asada K, Yoshikawa K, Takahashi M, Maeda Y, Enmanji K. 1975. Superoxide dismutases from a blue-green alga, Plectonema boryanum. J. Biol. Chem. 250: 2801–2807.
- Bartosik D, Putyrski M, Dziewit L, Malewska E, Szymanik M, Jagiello E, Lukasik J, Jadwiga J. 2008. Transposable modules generated by a single copy of insertion sequence ISPme1 and their influence on structure and evolution of natural plasmids of Paracoccus methylutens DM12. J. Bacteriol. 190: 3306–3313.
- Benndorf D, Loffhagen N, Babel W. 2001. Protein synthesis patterns in Acinetobacter calcoaceticus induced by phenol and catechol show specificities of responses to chemostress. FEMS Microbiol. Lett. 200: 247–252.
- Bloom JD, Labthavikul ST, Otey CR, Arnold FH. 2006. Protein stability promotes evolvability. Proc. Natl. Acad. Sci. USA 103: 5869–5874.
- Cerdan P, Rekik M, Harayama S. 1995. Substrate specificity differences between two catechol 2,3-dioxygenases encoded by the TOL and NAH plasmids from Pseudomonas putida. Eur. J. Biochem. 229: 113–118.
- Cevallos MA, Cervantes-Rivera R, Gutiérrez-Ríos RM. 2008. The repABC plasmid family. Plasmid 60: 19–37.
- Chang E-E, Hsing H-J, Chiang P-C, Chen M-Y, Shyng J-Y. 2008. The chemical and biological characteristics of coke-oven wastewater by ozonation. J. Hazard. Mater. 156: 560–567.
- Chao Y-M, Tseng I-C, Chang J-S. 2006. Mechanism for sludge acidification in aerobic treatment of coking wastewater. J. Hazard. Mater. 137: 1781–1787.
- Dennis JJ. 2005. The evolution of IncP catabolic plasmids. Curr. Opin. Biotechnol. 16: 291–298.
- Duffner FM, Kirchner U, Bauer MP, M üller R. 2000. Phenol/cresol degradation by the thermophilic Bacillus thermoglucosidasius A7: Cloning and sequence analysis of five genes involved in the pathway. Gene 256: 215–221.
- Dziewit L, Jazurek M, Drewniak L, Baj J, Bartosik D. 2007. The SXT conjugative element and linear prophage N15 encode toxin-antitoxin-stabilizing systems homologous to the tad-ata module of the Paracoccus aminophilus plasmid pAMI2. J. Bacteriol. 189: 1983–1997.
- Eltis LD, Bolin JT. 1996. Evolutionary relationships among extradiol dioxygenases. J. Bacteriol. 178: 5930–5937.
- Finn RD, Tate J, Mistry J, Coggill PC, Sammut JS, et al. 2008. The Pfam protein families database. Nucleic Acids Res. 36: D281–D288.
- Fortin, P. D., MacPherson, I., Neau, D. B., Bolin, J. T., Eltis, L. D. 2005. Directed evolution of a ring-cleaving dioxygenase for polychlorinated biphenyl degradation. J. Biol. Chem. 280: 42307–42314.
- Fukumori F, Saint CP. 2001. Complete nucleotide sequence of the catechol metabolic region of plasmid pTDN1. J. Gen. Appl. Microbiol. 47: 329–333.
- Furukawa K, Suenaga H, Goto M. 2004. Biphenyl dioxygenases: Functional versatilities and directed evolution. J. Bacteriol. 186: 5189–5196.
- Gibello A, Ferrer E, Martín M, Garrido-Pertierra A. 1994. 3,4-Dihydroxyphenylacetate 2,3-dioxygenase from Klebsiella pneumoniae, a Mg2+-containing dioxygenase involved in aromatic catabolism. Biochem. J. 301: 145–150.
- Gibson DT, Parales RE. 2000. Aromatic hydrocarbon dioxygenases in environmental biotechnology. Curr. Opin. Biotechnol. 11: 236–243.
- Gibson J, Harwood CS. 2002. Metabolic diversity in aromatic compound utilization by anaerobic microbes. Annu. Rev. Microbiol. 56: 345–369.
- Hatta T, Mukerjee-Dhar G, Damborsky J, Kiyohara H, Kimbara K. 2003. Characterization of a novel thermostable Mn(II)-dependent 2,3-dihydroxybiphenyl 1,2-dioxygenase from a polychlorinated biphenyl- and naphthalene-degrading Bacillus sp. JF8. J. Biol. Chem. 278: 21483–21492.
- Hirose J, Kimura N, Suyama A, Kobayashi A, Hayashida S, Furukawa K. 1994. Functional and structural relationship of various extradiol aromatic ring-cleavage dioxygenases of Pseudomonas origin. FEMS Microbiol. Lett. 118: 273–278.
- Joardar V, Lindeberg M, Jackson RW, Selengut J, Dodson R, et al. 2005. Whole-genome sequence analysis of Pseudomonas syringae pv. phaseolicola 1448A reveals divergence among pathovars in genes involved in virulence and transposition. J. Bacteriol. 187: 6488–6498.
- Junca H, Pieper DH. 2004. Functional gene diversity analysis in BTEX contaminated soils by means of PCR-SSCP DNA fingerprinting: Comparative diversity assessment against bacterial isolates and PCR-DNA clone libraries. Environ. Microbiol. 6: 95–110.
- Junca H, Plumeier I, Hecht HJ, Pieper DH. 2004. Difference in kinetic behaviour of catechol 2,3-dioxygenase variants from a polluted environment. Microbiology 150: 4181–4187.
- Kholodii GY, Mindlin SZ, Bass IA, Yurieva OV, Minakhina SV, Nikiforov VG. 1995. Four genes, two ends, and a res region are involved in transposition of Tn5053 : A paradigm for a novel family of transposons carrying either a mer operon or an integron. Mol. Microbiol. 17: 1189–1200.
- Kim IC, Oriel PJ. 1995. Characterization of the Bacillus stearothermophilus BR219 phenol hydroxylase gene. Appl. Environ. Microbiol. 61: 1252–1256.
- Lau SK, Wong GK, Li MW, Woo PC, Yuen KY. 2008. Distribution and molecular characterization of tetracycline resistance in Laribacter hongkongensis. J. Antimicrob. Chemother. 61: 488–497.
- Lowe TM, Eddy Sr. 1997. tRNAscan-SE: A program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 25: 955–964.
- Lumsden J, Cammack R, Hall DO. 1976. Purification and physico-chemical properties of superoxide dismutase from two photosynthetic microorganisms. Biochim. Biophys. Acta 438: 380–392.
- Mesarch MB, Nakatsu CH, Nies L. 2000. Development of catechol 2,3-dioxygenase-specific primers for monitoring bioremediation by competitive quantitative PCR. Appl. Environ. Microbiol. 66: 678–683.
- Minakhina S, Kholodii G, Mindlin S, Yurieva O, Nikiforov V. 1999. Tn5053 family transposons are res site hunters sensing plasmidal res sites occupied by cognate resolvases. Mol. Microbiol. 33: 1059–1068.
- Miyazawa D, Mukerjee-Dhar G, Shimura M, Hatta T, Kimbara K. 2004. Genes for Mn(II)-dependent NahC and Fe(II)-dependent NahH located in close proximity in the thermophilic naphthalene and PCB degrader, Bacillus sp. JF8: Cloning and characterization. Micro-biology 150: 993–1004.
- Nojiri H, Shintani M, Omori T. 2004. Divergence of mobile genetic elements involved in the distribution of xenobiotic-catabolic capacity. Appl. Microbiol. Biotechnol. 64: 154–174.
- Ohtsubo Y, Ikeda-Ohtsubo W, Nagata Y, Tsuda M. 2008. GenomeMatcher: A graphical user interface for DNA sequence comparison. BMC Bioinformatics 9: 376.
- Okuta A, Ohnishi K, Yagame S, Harayama S. 2003. Intersub-unit interaction and catalytic activity of catechol 2,3-dioxygenases. Biochem. J. 371: 557–564.
- Oppon JC, Sarnovsky RJ, Craig NL, Rawlings DE. 1998. A Tn7 like transposon is present in the glmUS region of the obligately chemoautolithotrophic bacterium Thiobacillus ferrooxidans. J. Bacteriol. 180: 3007–3012.
- Que L Jr, Widom J, Crawford RL. 1981. 3,4-Dihydroxyphenylacetate 2,3-dioxygenase. A manganese(II) dioxygenase from Bacillus brevis. J. Biol. Chem. 256: 10941–10944.
- Quevillon E, Silventoinen V, Pillai S, Harte N, Mulder N, Apweiler R, Lopez R. 2005. InterProScan: Protein domains identifier. Nucleic Acids Res. 33: W116–W120.
- Rutherford K, Parkhill J, Crook J, Horsnell T, Rice P, Rajan-dream MA, Barrell B. 2000. Artemis: Sequence visualization and annotation. Bioinformatics 16: 944–945.
- Schröder G, Lanka E. 2005. The mating pair formation system of conjugative plasmids—A versatile secretion machinery for transfer of proteins and DNA. Plasmid 54: 1–25.
- Shingler V, Powlowski J, Marklund U. 1992. Nucleotide sequence and functional analysis of the complete phenol/3,4-dimethyl phenol catabolic pathway of Pseudomonas sp. strain CF600. J. Bacteriol. 174: 711–724.
- Sota M, Yano H, Ono A, Miyazaki R, Ishii H, Genka H, Top EM, Tsuda M. 2006. Genomic and functional analysis of the IncP-9 naphthalene-catabolic plasmid NAH7 and its transposon Tn4655 suggests catabolic gene spread by a tyrosine recombinase. J. Bacteriol. 188: 4057–4067.
- Stamoudis VC, Luthy RG. 1980. Determination of biological removal of organic constituents in quench waters from high-BTU coal-gasification pilot plants. Water Res. 14: 1143–1156.
- Starkenburg SR, Larimer FW, Stein LY, Klotz MG, Chain PS, et al. 2008. Complete genome sequence of Nitrobacter hamburgensis X14 and comparative genomic analysis of species within the genus Nitrobacter. Appl. Environ. Microbiol. 74: 2852–2863.
- Suenaga H, Ohnuki T, Miyazaki K. 2007. Functional screening of a metagenomic library for genes involved in microbial degradation of aromatic compounds. Environ. Microbiol. 9: 2289–2297.
- Suenaga H, Mizuta S, Miyazaki K. 2009a. The molecular basis for adaptive evolution in novel extradiol dioxygenases retrieved from the metagenome. FEMS Microbiol. Ecol. 69: 472–480.
- Suenaga H, Koyama Y, Miyakoshi M, Miyazaki R, Yano H et al. 2009b. Novel organization of aromatic degradation pathway genes in a microbial community as revealed by metagenomic analysis. ISME J. 3: 1335–1348.
- Tennstedt T, Szczepanowski R, Krahn I, P ühler A, Schl üter A. 2005. Sequence of the 68,869bp IncP-1α plasmid pTB11 from a waste-water treatment plant reveals a highly conserved backbone, a Tn402 -like integron and other transposable elements. Plasmid 53: 218–238.
- Top EM, Springael D. 2003. The role of mobile genetic elements in bacterial adaptation to xenobiotic organic compounds. Curr. Opin. Biotechnol. 14: 262–269.
- Toussaint A, Merlin C, Monchy S, Benotmane MA, Leplae R, Mergeay M, Springael D. 2003. The biphenyl- and 4-chlorobiphenyl-catabolic transposon Tn4371 , a member of a new family of genomic islands related to IncP and Ti plasmids. Appl. Environ. Microbiol. 69: 4837–4845.
- Tsuda M, Tan HM, Nishi A, Furukawa K. 1999. Mobile catabolic genes in bacteria. J. Biosci. Bioeng. 87: 401–410.
-
Vaillancourt FH, Bolin JT, Eltis LD. 2004. Ring-cleavage dioxygenases. InRamos JL, ed. Pseudomonas, Vol. 3. New York: Kluwer Academic/Plenum Publishers, pp. 359–395.
10.1007/978-1-4419-9088-4_13 Google Scholar
- van der Meer JR, de Vos WM, Harayama S, Zehnder AJB. 1992. Molecular mechanisms of genetic adaptation to xenobiotic compounds. Microbiol. Rev. 56: 677–694.
- Viggiani A, Siani L, Notomista E, Birolo L, Pucci P, Donato AD. 2004. The role of the conserved residues His-246, His-199, and Tyr-255 in the catalysis of catechol 2,3-dioxygenase from Pseudomonas stutzeri OX1. J. Biol. Chem. 279: 48630–48639.
- Whiting AK, Boldt YR, Hendrich MP, Wackett LP, Que L Jr. 1996. Manganese(II)-dependent extradiol-cleaving catechol dioxygenase from Arthrobacter globiformis CM-2. Biochemistry 35: 160–170.
- Wittich R-M. 1998. Degradation of dioxin-like compounds by microorganisms. Appl. Microbiol. Biotechnol. 49: 489–499.
- Williams PA, Sayers Jr. 1994. The evolution of pathways for aromatic hydrocarbon oxidation in Pseudomonas. Biodegradation 5: 195–217.
- Zhou N-Y, Fuenmayor SL, Williams PA. 2001. nag genes of Ralstonia (formerly Pseudomonas) sp. strain U2 encoding enzymes for gentisate catabolism. J. Bacteriol. 183: 700–708.
