Genomic organization and genomic structural rearrangements of Sphingobium japonicum UT26, an archetypal γ-hexachlorocyclohexane-degrading bacterium

Enzyme and Microbial Technology

Volumn 49, Issue 6-7, 2011, Pages 499-508

  Nagata, Yuji ^a   Natsui, Shunsuke ^a   Endo, Ryo ^a   Ohtsubo, Yoshiyuki ^a   Ichikawa, Natsuko ^b   Ankai, Akiho ^b   Oguchi, Akio ^b   Fukui, Shigehiro ^b   Fujita, Nobuyuki ^b   Tsuda, Masataka ^a  

^a TOHOKU UNIVERSITY   (Japan)

^b NATIONAL INSTITUTE OF TECHNOLOGY AND EVALUATION   (Japan)

Author keywords

Hexachlorocyclohexane; Biodegradation; Environmental pollutant; Genome; Insertion sequence; Sphingomonads

Indexed keywords

ABC TRANSPORTER; COMPLETE GENOMES; CORE FUNCTIONS; ENVIRONMENTAL POLLUTANTS; GENOME REARRANGEMENTS; GENOMIC ORGANIZATION; HEXACHLOROCYCLOHEXANES; HORIZONTAL TRANSFER; INSERTION SEQUENCES; LARGE PLASMIDS; SPHINGOMONADS; STRUCTURAL REARRANGEMENT;

BIODEGRADATION;

GENES;

ABC TRANSPORTER; LINDANE;

ARTICLE; BACTERIUM; CHROMOSOME 1; CHROMOSOME 1Q; CHROMOSOME 2; GENE DELETION; GENE REARRANGEMENT; GENE SEQUENCE; NONHUMAN; NUCLEOTIDE SEQUENCE; SPHINGOBIUM JAPONICUM;

ADIPIC ACIDS; ATP-BINDING CASSETTE TRANSPORTERS; BACTERIAL PROTEINS; BIODEGRADATION, ENVIRONMENTAL; GENE DELETION; GENE REARRANGEMENT; GENE TRANSFER, HORIZONTAL; GENES, BACTERIAL; GENOME, BACTERIAL; LINDANE; METABOLIC NETWORKS AND PATHWAYS; MODELS, GENETIC; PHYLOGENY; REPLICATION ORIGIN; REPLICON; SPECIES SPECIFICITY; SPHINGOMONADACEAE;

EID: 82955240671     PISSN: 01410229     EISSN: 18790909     Source Type: Journal    
DOI: 10.1016/j.enzmictec.2011.10.005     Document Type: Article

References (58)

1. Lal R., Pandey G., Sharma P., Kumari K., Malhotra S., Pandey R., et al. Biochemistry of microbial degradation of hexachlorocyclohexane and prospects for bioremediation. Microbiol Mol Biol Rev 2010, 74:58-80.
2. Vijgen J., Abhilash P.C., Li Y.F., Lal R., Forter M., Torres J., et al. Hexachlorocyclohexane (HCH) as new Stockholm Convention POPs-a global perspective on the management of Lindane and its waste isomers. Environ Sci Pollut Res Int 2011, 18:152-162.
3. Li Y.F., Scholtz M.T., Van Heyst B.J. Global gridded emission inventories of β-hexachlorocyclohexane. Environ Sci Technol 2003, 37:3493-3498.
4. Walker K., Vallero D.A., Lewins R.G. Factors influencing the distribution of lindane and other hexachlorocyclohexanes in the environment. Environ Sci Technol 1999, 33:4373-4378.
5. Imai R., Nagata Y., Senoo K., Wada H., Fukuda M., Takagi M., et al. Dehydrochlorination of γ-hexachlorocyclohexane (γ-BHC) by γ-BHC-assimilating Pseudomonas paucimobilis. Agric Biol Chem 1989, 53:2015-2017.
6. Senoo K., Wada H. Isolation and identification of an aerobic γ-HCH-decomposing bacterium from soil. Soil Sci Plant Nutr 1989, 35:79-87.
7. Nagata Y., Endo R., Ito M., Ohtsubo Y., Tsuda M. Aerobic degradation of lindane (γ-hexachlorocyclohexane) in bacteria and its biochemical and molecular basis. Appl Microbiol Biotechnol 2007, 76:741-752.
8. Miyauchi K., Lee H.S., Fukuda M., Takagi M., Nagata Y. Cloning and characterization of linR, involved in regulation of the downstream pathway for γ-hexachlorocyclohexane degradation in Sphingomonas paucimobilis UT26. Appl Environ Microbiol 2002, 68:1803-1807.
9. Harwood C.S., Parales R.E. The β-ketoadipate pathway and the biology of self-identity. Annu Rev Microbiol 1996, 50:553-590.
10. Endo R., Ohtsubo Y., Tsuda M., Nagata Y. Identification and characterization of genes encoding a putative ABC-type transporter essential for utilization of γ-hexachlorocyclohexane in Sphingobium japonicum UT26. J Bacteriol 2007, 189:3712-3720.
11. Endo R., Kamakura M., Miyauchi K., Fukuda M., Ohtsubo Y., Tsuda M., et al. Identification and characterization of genes involved in the downstream degradation pathway of γ-hexachlorocyclohexane in Sphingomonas paucimobilis UT26. J Bacteriol 2005, 187:847-853.
12. Nagata Y., Futamura A., Miyauchi K., Takagi M. Two different types of dehalogenases, LinA and LinB, involved in γ-hexachlorocyclohexane degradation in Sphingomonas paucimobilis UT26 are localized in the periplasmic space without molecular processing. J Bacteriol 1999, 181:5409-5413.
13. Nagata Y., Ohtomo R., Miyauchi K., Fukuda M., Yano K., Takagi M. Cloning and sequencing of a 2,5-dichloro-2,5-cyclohexadiene-1,4-diol dehydrogenase gene involved in the degradation of γ-hexachlorocyclohexane in Pseudomonas paucimobilis. J Bacteriol 1994, 176:3117-3125.
14. Miyauchi K., Fukuda M., Tsuda M., Takagi M., Nagata Y. Identification of insertion sequence from a γ-hexachlorocyclohexane degrading bacterium, Sphingomonas paucimobilis UT26. Biosci Biotechnol Biochem 2005, 69:216-219.
15. Nagata Y., Imai R., Sakai A., Fukuda M., Yano K., Takagi M. Isolation and characterization of Tn5-induced mutants of Pseudomonas paucimobilis UT26 defective in γ-hexachlorocyclohexane dehydrochlorinase (LinA). Biosci Biotechnol Biochem 1993, 57:703-709.
16. Sekine M., Tanikawa S., Omata S., Saito M., Fujisawa T., Tsukatani N., et al. Sequence analysis of three plasmids harboured in Rhodococcus erythropolis strain PR4. Environ Microbiol 2006, 8:334-346.
17. Takarada H., Sekine M., Kosugi H., Matsuo Y., Fujisawa T., Omata S., et al. Complete genome sequence of the soil actinomycete Kocuria rhizophila. J Bacteriol 2008, 190:4139-4146.
18. Ewing B., Hillier L., Wendl M.C., Green P. Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res 1998, 8:175-185.
19. Ewing B., Green P. Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res 1998, 8:186-194.
20. Gordon D., Abajian C., Green P. Consed: a graphical tool for sequence finishing. Genome Res 1998, 8:195-202.
21. Delcher A.L., Bratke K.A., Powers E.C., Salzberg S.L. Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics 2007, 23:673-679.
22. The UniProt Consortium Ongoing and future developments at the Universal Protein Resource. Nucleic Acids Res 2011, 39:D214-D219.
23. Hunter S., Apweiler R., Attwood T.K., Bairoch A., Bateman A., Binns D., et al. InterPro: the integrative protein signature database. Nucleic Acids Res 2009, 37:D211-D215.
24. Lima T., Auchincloss A.H., Coudert E., Keller G., Michoud K., Rivoire C., et al. HAMAP: a database of completely sequenced microbial proteome sets and manually curated microbial protein families in UniProtKB/Swiss-Prot. Nucleic Acids Res 2009, 37:D471-D478.
25. Laslett D., Canback B. ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences. Nucleic Acids Res 2004, 32:11-16.
26. Worning P., Jensen L.J., Hallin P.F., Staerfeldt H.H., Ussery D.W. Origin of replication in circular prokaryotic chromosomes. Environ Microbiol 2006, 8:353-361.
27. Ohtsubo Y., Ikeda-Ohtsubo W., Nagata Y., Tsuda M. GenomeMatcher: a graphical user interface for DNA sequence comparison. BMC Bioinform 2008, 9:376.
28. Nagata Y., Ohtsubo Y., Endo R., Ichikawa N., Ankai A., Oguchi A., et al. Complete genome sequence of the representative γ-hexachlorocyclohexane-degrading bacterium Sphingobium japonicum UT26. J Bacteriol 2010, 192:5852-5853.
29. Gil R., Silva F.J., Pereto J., Moya A. Determination of the core of a minimal bacterial gene set. Microbiol Mol Biol Rev 2004, 68:518-537.
30. Brassinga A.K., Marczynski G.T. Replication intermediate analysis confirms that chromosomal replication origin initiates from an unusual intergenic region in Caulobacter crescentus. Nucleic Acids Res 2001, 29:4441-4451.
31. Sibley C.D., MacLellan S.R., Finan T. The Sinorhizobium meliloti chromosomal origin of replication. Microbiology 2006, 152:443-455.
32. Schaper S., Messer W. Interaction of the initiator protein DnaA of Escherichia coli with its DNA target. J Biol Chem 1995, 270:17622-17626.
33. Cevallos M.A., Cervantes-Rivera R., Gutierrez-Rios R.M. The repABC plasmid family. Plasmid 2008, 60:19-37.
34. Chattoraj D.K. Control of plasmid DNA replication by iterons: no longer paradoxical. Mol Microbiol 2000, 37:467-476.
35. Krasowiak R., Sevastsyanovich Y., Konieczny I., Bingle L.E., Thomas C.M. IncP-9 replication initiator protein binds to multiple DNA sequences in oriV and recruits host DnaA protein. Plasmid 2006, 56:187-201.
36. Ferguson A.D., Deisenhofer J. TonB-dependent receptors-structural perspectives. Biochim Biophys Acta 2002, 1565:318-332.
37. Cheng Q., Yu M.C., Reeves A.R., Salyers A.A. Identification and characterization of a Bacteroides gene, csuF, which encodes an outer membrane protein that is essential for growth on chondroitin sulfate. J Bacteriol 1995, 177:3721-3727.
38. Reeves A.R., D'Elia J.N., Frias J., Salyers A.A. A Bacteroides thetaiotaomicron outer membrane protein that is essential for utilization of maltooligosaccharides and starch. J Bacteriol 1996, 178:823-830.
39. Tani A., Charoenpanich J., Mori T., Takeichi M., Kimbara K., Kawai F. Structure and conservation of a polyethylene glycol-degradative operon in sphingomonads. Microbiology 2007, 153:338-346.
40. Kahnert A., Mirleau P., Wait R., Kertesz M.A. The LysR-type regulator SftR is involved in soil survival and sulphate ester metabolism in Pseudomonas putida. Environ Microbiol 2002, 4:225-237.
41. Hashimoto W., He J., Wada Y., Nankai H., Mikami B., Murata K. Proteomics-based identification of outer-membrane proteins responsible for import of macromolecules in Sphingomonas sp. A1: alginate-binding flagellin on the cell surface. Biochemistry 2005, 44:13783-13794.
42. Miller T.R., Delcher A.L., Salzberg S.L., Saunders E., Detter J.C., Halden R.U. Genome sequence of the dioxin-mineralizing bacterium Sphingomonas wittichii RW1. J Bacteriol 2010, 192:6101-6102.
43. Davison J. Genetic exchange between bacteria in the environment. Plasmid 1999, 42:73-91.
44. Maeda K., Nojiri H., Shintani M., Yoshida T., Habe H., Omori T. Complete nucleotide sequence of carbazole/dioxin-degrading plasmid pCAR1 in Pseudomonas resinovorans strain CA10 indicates its mosaicity and the presence of large catabolic transposon Tn4676. J Mol Biol 2003, 326:21-33.
45. Sota M., Yano H., Ono A., Miyazaki R., Ishii H., Genka H., et al. 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 2006, 188:4057-4067.
46. Yano H., Miyakoshi M., Ohshima K., Tabata M., Nagata Y., Hattori M., et al. Complete nucleotide sequence of TOL plasmid pDK1 provides evidence for evolutionary history of IncP-7 catabolic plasmids. J Bacteriol 2010, 192:4337-4347.
47. Stanier R.Y., Palleroni N.J., Doudoroff M. The aerobic pseudomonads: a taxonomic study. J Gen Microbiol 1966, 43:159-271.
48. Yuhara S., Komatsu H., Goto H., Ohtsubo Y., Nagata Y., Tsuda M. Pleiotropic roles of iron-responsive transcriptional regulator Fur in Burkholderia multivorans. Microbiology 2008, 154:1763-1774.
49. Stolz A. Molecular characteristics of xenobiotic-degrading sphingomonads. Appl Microbiol Biotechnol 2009, 81:793-811.
50. Nagata Y., Kamakura M., Endo R., Miyazaki R., Ohtsubo Y., Tsuda M. Distribution of γ-hexachlorocyclohexane-degrading genes on three replicons in Sphingobium japonicum UT26. FEMS Microbiol Lett 2006, 256:112-118.
51. Mahillon J., Chandler M. Insertion sequences. Microbiol Mol Biol Rev 1998, 62:725-774.
52. Boltner D., Moreno-Morillas S., Ramos J.L. 16S rDNA phylogeny and distribution of lin genes in novel hexachlorocyclohexane-degrading Sphingomonas strains. Environ Microbiol 2005, 7:1329-1338.
53. Fuchu G., Ohtsubo Y., Ito M., Miyazaki R., Ono A., Nagata Y., et al. Insertion sequence-based cassette PCR: cultivation-independent isolation of γ-hexachlorocyclohexane-degrading genes from soil DNA. Appl Microbiol Biotechnol 2008, 79:627-632.
54. Tabata M., Endo R., Ito M., Ohtsubo Y., Kumar A., Tsuda M., et al. The lin genes for γ-hexachlorocyclohexane degradation in Sphingomonas sp. MM-1 proved to be dispersed across multiple plasmids. Biosci Biotechnol Biochem 2011, 75:466-472.
55. Miyazaki R., Sato Y., Ito M., Ohtsubo Y., Nagata Y., Tsuda M. Complete nucleotide sequence of an exogenously isolated plasmid, pLB1, involved in γ-hexachlorocyclohexane degradation. Appl Environ Microbiol 2006, 72:6923-6933.
56. Shintani M., Urata M., Inoue K., Eto K., Habe H., Omori T., et al. The Sphingomonas plasmid pCAR3 is involved in complete mineralization of carbazole. J Bacteriol 2007, 189:2007-2020.
57. Masai E., Katayama Y., Fukuda M. Genetic and biochemical investigations on bacterial catabolic pathways for lignin-derived aromatic compounds. Biosci Biotechnol Biochem 2007, 71:1-15.
58. Lauro F.M., McDougald D., Thomas T., Williams T.J., Egan S., Rice S., et al. The genomic basis of trophic strategy in marine bacteria. Proc Natl Acad Sci U S A 2009, 106:15527-15533.