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Complete genome sequence of Pseudomonas alcaliphila JAB1 (=DSM 26533), a versatile degrader of organic pollutants
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SYSNO ASEP 0501882 Document Type J - Journal Article R&D Document Type Journal Article Subsidiary J Článek ve WOS Title Complete genome sequence of Pseudomonas alcaliphila JAB1 (=DSM 26533), a versatile degrader of organic pollutants Author(s) Rídl, Jakub (UMG-J) ORCID
Šuman, J. (CZ)
Fraraccio, S. (CZ)
Hradilová, Miluše (UMG-J)
Strejček, M. (CZ)
Cajthaml, Tomáš (MBU-M) RID, ORCID
Zubrova, A. (CZ)
Macek, Tomáš (MBU-M) ORCID
Strnad, Hynek (UMG-J) RID
Uhlík, O. (CZ)Number of authors 10 Article number 3 Source Title Standards in Genomic Sciences. - : BioMed Central - ISSN 1944-3277
Roč. 13, February (2018)Number of pages 10 s. Language eng - English Country GB - United Kingdom Keywords Pseudomonas alcaliphila JAB1 ; Pseudomonadaceae ; Genome ; Dioxygenase ; Monooxygenase ; Biodegradation ; Aromatic compounds ; Biphenyl ; Polychlorinated biphenyls (PCBs) ; Chlorobenzoic acids (CBAs) ; cis-1,2-dichloroethylene (cDCE) ; Phenol ; bph genes ; ben genes ; phe genes ; maldi-tof ms Subject RIV EB - Genetics ; Molecular Biology OECD category Biochemistry and molecular biology Subject RIV - cooperation Institute of Microbiology - Microbiology, Virology R&D Projects GA13-28283S GA ČR - Czech Science Foundation (CSF) Institutional support UMG-J - RVO:68378050 ; MBU-M - RVO:61388971 UT WOS 000424476300001 DOI 10.1186/s40793-017-0306-7 Annotation In this study, following its isolation from contaminated soil, the genomic sequence of Pseudomonas alcaliphila strain JAB1 (=DSM 26533), a biphenyl-degrading bacterium, is reported and analyzed in relation to its extensive degradative capabilities. The P. alcaliphila JAB1 genome (GenBank accession no. CP016162) consists of a single 5.34 Mbp-long chromosome with a GC content of 62.5%. Gene function was assigned to 3816 of the 4908 predicted genes. The genome harbors a bph gene cluster, permitting degradation of biphenyl and many congeners of polychlorinated biphenyls (PCBs), a ben gene cluster, enabling benzoate and its derivatives to be degraded, and phe gene cluster, which permits phenol degradation. In addition, P. alcaliphila JAB1 is capable of cometabolically degrading cis-1,2-dichloroethylene (cDCE) when grown on phenol. The strain carries both catechol and protocatechuate branches of the beta-ketoadipate pathway, which is used to funnel the pollutants to the central metabolism. Furthermore, we propose that clustering of MALDI-TOF MS spectra with closest phylogenetic relatives should be used when taxonomically classifying the isolated bacterium, this, together with 16S rRNA gene sequence and chemotaxonomic data analyses, enables more precise identification of the culture at the species level. Workplace Institute of Molecular Genetics Contact Nikol Škňouřilová, nikol.sknourilova@img.cas.cz, Tel.: 241 063 217 Year of Publishing 2019
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