Degradative plasmids from sphingomonads

FEMS Microbiology Letters

Volumn 350, Issue 1, 2014, Pages 9-19

  Stolz, Andreas ^a  

^a UNIVERSITY OF STUTTGART   (Germany)

Author keywords

Biodegradation; Conjugation; Incompatibility groups; Replication initiation (Rep) proteins

Indexed keywords

CARBAZOLE DERIVATIVE; DIBENZO 4 DIOXIN; DIBENZODIOXIN DERIVATIVE; LINDANE; POLYCYCLIC AROMATIC HYDROCARBON DERIVATIVE; UNCLASSIFIED DRUG; XENOBIOTIC AGENT;

BACTERIUM CONJUGATION; CATABOLISM; CONTROLLED STUDY; GENETIC CODE; GENETIC STRAIN; INTERMETHOD COMPARISON; MICROBIAL DEGRADATION; NONHUMAN; NUCLEOTIDE SEQUENCE; PHASE PARTITIONING; PLASMID; PRIORITY JOURNAL; PROTEIN FAMILY; REVIEW; SPHINGOMONADACEAE; TRANSCRIPTION INITIATION;

SPHINGOMONADACEAE; VIR;

BIODEGRADATION; CONJUGATION; INCOMPATIBILITY GROUPS; REPLICATION INITIATION (REP) PROTEINS;

BACTERIAL PROTEINS; CONJUGATION, GENETIC; DNA HELICASES; DNA REPLICATION; DNA, BACTERIAL; GENOME, BACTERIAL; PHYLOGENY; PLASMIDS; SEQUENCE ANALYSIS, DNA; SPECIES SPECIFICITY; SPHINGOMONADACEAE; TRANS-ACTIVATORS;

EID: 84891831734     PISSN: 03781097     EISSN: 15746968     Source Type: Journal    
DOI: 10.1111/1574-6968.12283     Document Type: Review

References (40)

1. Aylward FO, McDonald BR, Adams SM, Valenzuela A, Schmidt RA, Goodwin LA, Woyke T, Currie CR, Suene G & Poulsen M (2013) Comparison of 26 sphingomonad genomes reveals diverse environmental adptations and biodegradative capabilities. Appl Environ Microbiol 79: 3724-3733.
2. Basta T, Keck A, Klein J & Stolz A (2004) Detection and characterization of conjugative degradative plasmids in xenobiotics degrading Sphingomonas strains. J Bacteriol 186: 3862-3872.
3. Basta T, Bürger S & Stolz A (2005) Structural and replicative diversity of large plasmids from polycyclic aromatic compounds and xenobiotics degrading Sphingomonas strains. Microbiology 151: 2025-2037.
4. Cevallos MA, Cervantes-Rivera R & Gutiérrez-Rios RM (2008) The repABC plasmid family. Plasmid 60: 19-37.
5. Cho J-C & Kim S-J (2001) Detection of mega plasmid from polycyclic aromatic hydrocarbon degrading Sphingomonas sp. strain KS14. J Mol Microbiol Biotechnol 3: 503-506.
6. Colquhoun DR, Hartmann EM & Halden RU (2012) Proteomic profiling of the dioxin-degrading bacterium Spingomonas wittichii RW1. J Biomed Biotechnol, doi:10.1155/2012/408690.
7. Copley SD, Rokicki J, Turner P, Daligault H, Nolan M & Lund M (2012) The whole genome sequence of Sphingobium chlorophenolicum L-1: insights into the evolution of the pentachlorophenol degradation pathway. Genome Biol Evol 4: 184-198.
8. D'Argenio V, Petrillo M, Cantiello P, Naso B, Cozzuto L, Notomista E, Paolella G, Di Donato A & Salvatore F (2011) De novo sequencing and assembly of the whole genome of Novosphingobium sp. strain PP1Y. J Bacteriol 193: 4296.
9. Feng X, Ou L-T & Ogram A (1997a) Plasmid-mediated mineralization of carbofuran by Sphingomonas sp. CF-06. Appl Environ Microbiol 63: 1332-1337.
10. Feng X, Ou L-T & Ogram A (1997b) Cloning and sequence analysis of a novel insertion element from plasmids harbored by the carbofuran-degrading bacterium, Sphingomonas sp. CF-06. Plasmid 37: 169-179.
11. Fernández-Lopez R, Garcillán-Barcia MP, Revilla C, LázaroM Vielva L & de la Cruz F (2006) Dynamics of the IncW genetic backbone imply general trends in conjugative plasmid evolution. FEMS Microbiol Rev 30: 942-966.
12. Fredrickson JK, Balkwill DL, Romine MF & Shi T (1999) Ecology, physiology, and phylogeny of deep subsurface Sphingomonas sp. J Ind Microbiol Biotechnol 23: 273-283.
13. Funnell BE & Slavcev RA (2004) Partition systems of bacterial plasmids. Plasmid Biology (Funnell BE & Phillips GJ, eds), pp. 81-103. ASM Press, Washington, DC.
14. Hu X, Mamoto R, Jujioka Y, Tani A, Kimbara K & Kawai F (2008) The pva operon is located on the megaplasmid of Sphingopyxis sp. strain 113P and is constitutively expressed, although expression is enhanced by PVA. Appl Microbiol Biotechnol 78: 685-693.
15. Jogler M, Chen H, Simon J, Rohde M, Busse HJ, Klenk HP, Tindall BJ & Overmann J (2013) Description of Sphingorhabdus planktonica gen. nov., sp. nov. and reclassification of three related members of the genus Sphingopyxis in the genus Sphingorhabdus gen. nov. Int J Syst Evol Microbiol 63: 1342-1349.
16. Kalnin K, Stegalkina S & Yarmolinsky M (2000) pTAR-encoded proteins in plasmid partitioning. J Bacteriol 182: 1889-1894.
17. Kämpfer P, Arun AB, Young CC, Busse HJ, Kassmannhuber J, Rosselló-Móra R, Geueke B, Rekha PD & Chen WM (2012) Sphingomicrobium lutaoense gen. nov., sp. nov., isolated from a coastal hot spring. Int J Syst Evol Microbiol 62: 1326-1330.
18. Lawley T, Wilkins BM & Frost LS (2004) Bacterial conjugation in Gram-negative bacteria. Plasmid Biology (Funnell BE & Phillips GJ, eds), pp. 81-103. ASM Press, Washington, DC.
19. Luo YR, Kang SG, Kim S-J, Li N, Lee J-H & Kwon KK (2012) Genome sequence of benzo[a]pyrene-degrading bacterium Novosphingobium pentaaromativorans US6-1. J Bacteriol 194: 907.
20. Masai E, Kamimura N, Kasai D et al. (2012) Complete genome sequence of Sphingobium sp. strain SYK-6, a degrader of lignin-derived biaryls and monoaryls. J Bacteriol 194: 534-535.
21. Miller TD, Delcher AL, Salzberg SL, Saunders E, Detter JC & Halden RU (2010) Genome sequence of the dioxin-mineralizing bacterium Sphingomonas wittichii RW1. J Bacteriol 192: 6101-6102.
22. Nagata Y, Kamakura M, Endo R, Miyazaki R, Ohtsubo Y & Tsuda M (2006) Distribution of γ-hexachlorocyclohexane-degrading genes on three replicons in Sphingobium japonicum UT26. FEMS Microbiol Lett 256: 112-118.
23. Nagata Y, Ohtsubo Y, Endo R, Ichikawa N, Ankai A, Oguchi A, Fukui S, Fujita N & Tsuda M (2010) Complete genome sequence of the representative γ-hexachlorocyclohexane-degrading bacterium Sphingobium japonicum UT26. J Bacteriol 192: 5852-5853.
24. Nagata Y, Natsui S, Endo R, Ohtsubo Y, Ichiwaka N, Ankai A, Oguchi A, Fukui S, Fujita N & Tsuda M (2011) Genomic organization and genomic structural rearrangements of Sphingobium japonicum UT26, an archetypal γ-hexachlorocyclohexane-degrading bacterium. Enzyme Microb Technol 49: 499-508.
25. Ochou M, Saito M & Kurusu Y (2008) Characterization of two compatible small plasmids from Sphingobium yanoikuyae. Biosci Biotechnol Biochem 72: 1130-1133.
26. Ogram A, Duan Y-P, Trabue SL, Feng X, Castro H & Ou L-T (2000) Carbofuran degradation mediated by three related plasmid systems. FEMS Microbiol Ecol 32: 197-203.
27. Pandeeti EV, Longkumer T, Chakka D et al. (2012) Multiple mechanisms contribute to lateral transfer of an organophosphate degradation (opd) island in Spingobium fuliginis ATCC 27551. G3 (Bethesda) 2: 1541-1554.
28. Petersen J (2011) Phylogeny and compatibility: plasmid classification in the genomics era. Arch Microbiol 193: 313-321.
29. Romine MF, Stillwell LC, Wong K-K, Thurston SJ, Sisk EC, Sensen C, Gaasterland T, Fredrickson JK & Saffer JD (1999) Complete sequence of a 184-kilobase catabolic plasmid from Sphingomonas aromaticivorans F199. J Bacteriol 181: 1585-1602.
30. Sentchilo V, Mayer AP, Guy L, Miyazaki R, Tringe SG, Barry K, Malfatti S, Goessmann A, Robinson-Rechavi M & van der Meer JR (2013) Community-wide plasmid gene mobilization and selection. ISME J 7: 1173-1186.
31. Shintani M, Urata M, Inoue K, Eto K, Habe H, Omori T, Yamane H & Nojiri H (2007) The Sphingomonas plasmid pCAR3 is involved in complete mineralization of carbazole. J Bacteriol 189: 2007-2020.
32. Shuttleworth KL, Sung J, Kim E & Cerniglia CE (2000) Physiological and genetic comparison of two aromatic hydrocarbon-degrading Sphingomonas strains. Mol Cells 10: 199-205.
33. Stolz A (2009) Molecular characteristics of xenobiotics-degrading sphingomonads. Appl Microbiol Biotechnol 81: 793-810.
34. Tabata M, Endo R, Ohtsubo Y, Kumar A, Tsuda M & Nagata Y (2011) The lin genes for γ-hexachlorocyclohexane degradation in Sphingomonas sp. strain MM-1 proved to be dispersed across multiple plasmids. Biosci Biotechnol Biochem 15: 466-472.
35. Tabata M, Ohtsubo Y, Ohhata S, Tsuda M & Nagata Y (2013) Complete genome sequence of the γ-hexachlorocyclohexane-degrading bacterium Sphingomonas sp. strain MM-1. Genome Announc 1: e00247-13. doi:10.1128/genomeA.00247-13.
36. Tani A, Charoenpanich J, Mori T, Takeichi M, Kimbara K & Kawai F (2007) Structure and conservation of a polyethylene glycol-degradative operon in sphingomonads. Microbiology 153: 338-346.
37. Tani A, Tanaka A, Minami T, Kimbara K & Kawai F (2011) Characterization of a cryptic plasmid, pSM103mini, from polyethylene-glycol degrading Sphingopyxis macrogoltabida strain 103. Biosci Biotechnol Biochem 75: 295-298.
38. Uchida H, Hamana K, Miyazaki M, Yoshida T & Nogi Y (2012) Parasphingopyxis lamellibrachiae gen. nov., sp. nov., isolated from a marine annelid worm. Int J Syst Evol Microbiol 62: 2224-2228.
39. Venkova-Canoca T, Soberón NE, Ramirez-Romero MA & Cevallos MA (2004) Two discrete elements are required for the replication of a repABC plasmid: an antisense RNA and a stem-loop structure. Mol Microbiol 54: 1431-1444.
40. Yeon SM & Kim YC (2011) Complete sequence and organization of the Sphingobium chungbukense DJ77 pSY2 plasmid. J Microbiol 49: 684-688.