title: Role of IncP-1β plasmids pWDL7::rfp and pNB8c in chloroaniline catabolism as determined by genomic and functional analyses.
abstract: Broad-host-range catabolic plasmids play an important role in bacterial degradation of man-made compounds. To gain insight into the role of these plasmids in chloroaniline degradation, we determined the first complete nucleotide sequences of an IncP-1 chloroaniline degradation plasmid, pWDL7::rfp and its close relative pNB8c, as well as the expression pattern, function, and bioaugmentation potential of the putative 3-chloroaniline (3-CA) oxidation genes. Based on phylogenetic analysis of backbone proteins, both plasmids are members of a distinct clade within the IncP-1β subgroup. The plasmids are almost identical, but whereas pWDL7::rfp carries a duplicate inverted catabolic transposon, Tn6063, containing a putative 3-CA oxidation gene cluster, dcaQTA1A2BR, pNB8c contains only a single copy of the transposon. No genes for an aromatic ring cleavage pathway were detected on either plasmid, suggesting that only the upper 3-CA degradation pathway was present. The dcaA1A2B gene products expressed from a high-copy-number vector were shown to convert 3-CA to 4-chlorocatechol in Escherichia coli. Slight differences in the dca promoter region between the plasmids and lack of induction of transcription of the pNB8c dca genes by 3-CA may explain previous findings that pNB8C does not confer 3-CA transformation. Bioaugmentation of activated sludge with pWDL7::rfp accelerated removal of 3-CA, but only in the presence of an additional carbon source. Successful bioaugmentation requires complementation of the upper pathway genes with chlorocatechol cleavage genes in indigenous bacteria. The genome sequences of these plasmids thus help explain the molecular basis of their catabolic activities.
authors.affiliation: Department of Biological Sciences, Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, Idaho, USA.
authors.forename: J E
authors.initials: JE
authors.lastname: Król
authors.forename: J T
authors.initials: JT
authors.lastname: Penrod
authors.forename: H
authors.initials: H
authors.lastname: McCaslin
authors.forename: L M
authors.initials: LM
authors.lastname: Rogers
authors.forename: H
authors.initials: H
authors.lastname: Yano
authors.forename: A D
authors.initials: AD
authors.lastname: Stancik
authors.forename: W
authors.initials: W
authors.lastname: Dejonghe
authors.forename: C J
authors.initials: CJ
authors.lastname: Brown
authors.forename: R E
authors.initials: RE
authors.lastname: Parales
authors.forename: S
authors.initials: S
authors.lastname: Wuertz
authors.forename: E M
authors.initials: EM
authors.lastname: Top
mesh_terms: D000814:Aniline Compounds / Q000378:metabolism*; D002244:Carbon / Q000378:metabolism; D002396:Catechols / Q000378:metabolism; D016000:Cluster Analysis; D004251:DNA Transposable Elements; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics; D004926:Escherichia coli / Q000235:genetics / Q000378:metabolism; D020869:Gene Expression Profiling; D015964:Gene Expression Regulation, Bacterial; D053858:Metabolic Networks and Pathways / Q000235:genetics*; D008969:Molecular Sequence Data; D005810:Multigene Family; D010084:Oxidation-Reduction; D010802:Phylogeny; D011401:Promoter Regions, Genetic; D017422:Sequence Analysis, DNA; D014158:Transcription, Genetic
chemical_list: D000814:Aniline Compounds; D002396:Catechols; D004251:DNA Transposable Elements; D004269:DNA, Bacterial; C031392:3-chloroaniline; D002244:Carbon; C038861:4-chlorocatechol
references.citation: Nat Commun. 2011;2:268
references.pmid: 21468020
references.citation: Appl Environ Microbiol. 2011 Nov;77(22):7975-83
references.pmid: 21948829
references.citation: Microbiology (Reading). 2005 Oct;151(Pt 10):3435-3446
references.pmid: 16207925
references.citation: J Agric Food Chem. 2007 Jun 13;55(12):4722-7
references.pmid: 17497880
references.citation: Appl Microbiol Biotechnol. 2002 Apr;58(5):679-82
references.pmid: 11956754
references.citation: Appl Environ Microbiol. 1992 Apr;58(4):1292-300
references.pmid: 1599248
references.citation: Appl Environ Microbiol. 1995 May;61(5):1691-8
references.pmid: 7646006
references.citation: Appl Environ Microbiol. 2003 Mar;69(3):1532-41
references.pmid: 12620840
references.citation: Appl Environ Microbiol. 2011 Aug;77(15):5079-88
references.pmid: 21642400
references.citation: Appl Environ Microbiol. 1996 Jul;62(7):2470-6
references.pmid: 8779586
references.citation: Appl Environ Microbiol. 2006 Jan;72(1):291-7
references.pmid: 16391056
references.citation: J Environ Sci Health B. 2003 Mar;38(2):121-32
references.pmid: 12617551
references.citation: J Bacteriol. 1990 Nov;172(11):6557-67
references.pmid: 2172216
references.citation: Res Microbiol. 2010 Apr;161(3):208-18
references.pmid: 20146937
references.citation: FEMS Microbiol Ecol. 2002 Nov 1;42(2):315-25
references.pmid: 19709291
references.citation: Appl Environ Microbiol. 2007 Oct;73(20):6345-50
references.pmid: 17675426
references.citation: Plasmid. 2006 Jul;56(1):11-23
references.pmid: 16445980
references.citation: Appl Environ Microbiol. 2007 Jul;73(14):4477-83
references.pmid: 17526790
references.citation: J Bacteriol. 1980 May;142(2):668-82
references.pmid: 6247328
references.citation: Bioresour Technol. 2009 Jun;100(12):2902-9
references.pmid: 19268574
references.citation: FEMS Microbiol Lett. 1992 Oct 15;76(3):261-6
references.pmid: 1427016
references.citation: J Bacteriol. 2001 Oct;183(19):5684-97
references.pmid: 11544232
references.citation: Curr Opin Biotechnol. 2003 Jun;14(3):262-9
references.pmid: 12849778
references.citation: J Bacteriol. 1998 Jan;180(2):296-302
references.pmid: 9440519
references.citation: J Bacteriol. 1983 Sep;155(3):1015-26
references.pmid: 6411681
references.citation: Appl Environ Microbiol. 1994 Sep;60(9):3323-8
references.pmid: 7944365
references.citation: Res Microbiol. 2008 Mar;159(2):118-27
references.pmid: 18249097
references.citation: J Bacteriol. 1997 Jan;179(2):399-408
references.pmid: 8990291
references.citation: Appl Microbiol Biotechnol. 1994 Nov;42(2-3):415-20
references.pmid: 7765781
references.citation: Appl Environ Microbiol. 1984 Oct;48(4):868-9
references.pmid: 16346652
references.citation: Plasmid. 2008 May;59(3):193-201
references.pmid: 18295880
references.citation: Genome Res. 2004 Jul;14(7):1394-403
references.pmid: 15231754
references.citation: Int J Syst Bacteriol. 1999 Apr;49 Pt 2:567-76
references.pmid: 10319477
references.citation: Nucleic Acids Res. 1997 Sep 1;25(17):3389-402
references.pmid: 9254694
references.citation: J Bacteriol. 2004 Nov;186(21):7161-74
references.pmid: 15489427
references.citation: J Mol Biol. 1998 Oct 9;282(5):969-90
references.pmid: 9753548
references.citation: Appl Environ Microbiol. 2000 Jul;66(7):2906-13
references.pmid: 10877785
references.citation: Bioinformatics. 2006 Nov 1;22(21):2688-90
references.pmid: 16928733
references.citation: Gene. 1995 Dec 1;166(1):175-6
references.pmid: 8529885
references.citation: Appl Environ Microbiol. 2001 Mar;67(3):1107-15
references.pmid: 11229899
references.citation: J Gen Microbiol. 1990 Apr;136(4):615-25
references.pmid: 2168927
references.citation: Appl Environ Microbiol. 2011 Dec;77(24):8754-64
references.pmid: 22003008
references.citation: Water Res. 2010 Sep;44(17):5109-15
references.pmid: 20864141
references.citation: FEMS Microbiol Ecol. 2002 Nov 1;42(2):199-208
references.pmid: 19709279
references.citation: Microbiology (Reading). 1997 Jan;143 ( Pt 1):93-99
references.pmid: 9025282
references.citation: Environ Microbiol. 2004 Jul;6(7):655-68
references.pmid: 15186344
references.citation: J Bacteriol. 2000 Nov;182(22):6482-9
references.pmid: 11053394
references.citation: Annu Rev Microbiol. 1998;52:287-331
references.pmid: 9891800
references.citation: Nucleic Acids Res. 2004 Mar 19;32(5):1792-7
references.pmid: 15034147
references.citation: J Gen Microbiol. 1966 May;43(2):159-271
references.pmid: 5963505
references.citation: Mol Genet Genomics. 2003 Feb;268(5):570-84
references.pmid: 12589432
references.citation: Biosci Biotechnol Biochem. 2003 Nov;67(11):2351-8
references.pmid: 14646193
references.citation: Biosci Biotechnol Biochem. 2004 Dec;68(12):2457-65
references.pmid: 15618615
references.citation: J Bacteriol. 2003 Nov;185(22):6741-5
references.pmid: 14594853
references.citation: Lett Appl Microbiol. 2004;38(6):527-31
references.pmid: 15130151