Insights into Mobile Genetic Elements of the Biocide-Degrading Bacterium <i>Pseudomonas nitroreducens </i>HBP-1

• Main Authors: Nicolas Carraro, Vladimir Sentchilo, Lenka Polák, Claire Bertelli, Jan Roelof van der Meer
• Format: Article
• Language: English
• Published: MDPI AG 2020-08-01
• Series: Genes
• Subjects: <i>Pseudomonas</i> <i>azelaica</i>; integrative and conjugative elements; ICE<i>clc</i>; aromatic compounds; heavy metal; adaptation
• Online Access: https://www.mdpi.com/2073-4425/11/8/930

The sewage sludge isolate <i>Pseudomonas nitroreducens</i> HBP-1 was the first bacterium known to completely degrade the fungicide 2-hydroxybiphenyl. PacBio and Illumina whole-genome sequencing revealed three circular DNA replicons: a chromosome and two plasmids. Plasmids were shown to code for putative adaptive functions such as heavy metal resistance, but with unclarified ability for self-transfer. About one-tenth of strain HBP-1′s chromosomal genes are likely of recent horizontal influx, being part of genomic islands, prophages and integrative and conjugative elements (ICEs). <i>P.</i><i>nitroreducens</i> carries two large ICEs with different functional specialization, but with homologous core structures to the well-known ICE<i>clc</i> of <i>Pseudomonas knackmussii </i>B13. The variable regions of ICE<i>Pni</i>1 (96 kb) code for, among others, heavy metal resistances and formaldehyde detoxification, whereas those of ICE<i>Pni</i>2 (171 kb) encodes complete <i>meta</i>-cleavage pathways for catabolism of 2-hydroxybiphenyl and salicylate, a protocatechuate pathway and peripheral enzymes for 4-hydroxybenzoate, ferulate, vanillin and vanillate transformation. Both ICEs transferred at frequencies of 10⁻⁶–10⁻⁸ per <i>P. nitroreducens </i>HBP-1 donor into <i>Pseudomonas putida</i>, where they integrated site specifically into <i>tRNA^Gly</i>-gene targets, as expected. Our study highlights the underlying determinants and mechanisms driving dissemination of adaptive properties allowing bacterial strains to cope with polluted environments.