Insights into the genomic plasticity of Pseudomonas putida KF715, a strain with unique biphenyl‐utilizing activity and genome instability properties

Abstract

Pseudomonas putida KF715 exhibits unique properties in both catabolic activity and genome plasticity. Our previous studies revealed that the DNA region containing biphenyl and salycilate metabolism gene clusters (termed the bph-sal element) was frequently deleted and transferred by conjugation to closely related P. putida strains. In this study, we first determined the complete nucleotide sequence of the KF715 genome. Next, to determine the underlying cause of genome plasticity in KF715, we compared the KF715 genome with the genomes of one KF715 defective mutant, two transconjugants, and several P. putida strains available from public databases. The gapless KF715 genome sequence revealed five replicons: one circular chromosome, and four plasmids. Southern blot analysis indicated that most of the KF715 cell population carries the bph-sal element on the chromosome whereas a small number carry it on a huge plasmid, pKF715A. Moreover, the bph-sal element is present stably on the plasmid and did not integrate into the chromosome of its transconjugants. Comparative genome analysis and experiments showed that a number of diverse putative genetic elements are present in KF715 and are likely involved in genome rearrangement. These data provide insights into the genetic plasticity and adaptability of microorganisms for survival in various ecological niches.

Biphenyl/PCB Degrading bph Genes of Ten Bacterial Strains Isolated from Biphenyl-Contaminated Soil in Kitakyushu, Japan: Comparative and Dynamic Features as Integrative Conjugative Elements (ICEs)

“…KF707 possessed one circular chromosome of 6,242,949 bp and one plasmid (pKF707) of 59,819 bp. On the other hand, P. putida KF715 possessed one circular chromosome of 6,583,376 bp and four plasmids as previously reported in Reference [16]. The total length of the contigs (total number of contigs, >500 bp) of the remaining strains were as follows: P. abietaniphila KF701, 6,886,250 bp (140) [17]; P. aeruginosa KF702, 7,167,540 bp (91) [24]; P. putida KF703, 6,434,897 bp (135) [18]; C. basilensis KF708, 7,826,077 bp (62) [20]; C. pauculus KF709, 6,826,799 bp (227) [24]; P. toyotomiensis KF710, 5,596,721 bp (29) [27]; C. testosteroni KF712, 5,890,323 bp (97) [21]; and P. stutzeri KF716, 4,188,013 bp (30) [29].…”

“…The bph-sal cluster was localized on the chromosome in KF707. The same cluster was located on the chromosome in the majority of the KF715 cells and also existed as an extrachromosomal circular form (483,376 bp) as well in the minor part of the cells in the stationary phase culture [16]. Based on the features of the bph genes, we classified the ten strains into four groups.…”

“…Previously, we isolated more than ten biphenyl-utilizing bacterial strains (KF strains) from biphenyl-contaminated soil in Kitakyushu, Japan [15]. Among these KF strains, we determined the complete nucleotide sequence of the P. putida KF715 genome [16], which revealed five replicons: one circular chromosome and four plasmids. Southern blot analysis indicated that the majority of the KF715 cell population carried the bph-sal cluster on its chromosome.…”

The Integrative Conjugative Element clc (ICEclc) of Pseudomonas aeruginosa JB2

“…ICEs have been most extensively studied with respect to their roles in conferring virulence factors and/or resistance to antimicrobial compounds ( Chowdhury et al, 2016 ; Clawson et al, 2016 ; Leon-Sampedro et al, 2016 ; Olaitan et al, 2016 ; Bie et al, 2017 ; Chuzeville et al, 2017 ; Ryan et al, 2017 ; Sugimoto et al, 2017 ; Vanneste, 2017 ; Zhou et al, 2017 ). But, the spectrum of ICE-encoded adaptation functions is broad and also includes resistance to heavy metals ( Colombi et al, 2017 ; Harmer et al, 2017 ), rhizobial nodulation functions ( Ling et al, 2016 ), biofilm formation characteristics ( Wang et al, 2017 ) and components of metabolic pathways ( Gaillard et al, 2006 ; Zamarro et al, 2016 ; Suenaga et al, 2017 ).…”

“…Biodegradation of xenobiotic compounds is a key environmental service of bacterial communities, and MGE are well-established as playing a central role in the evolution of metabolic capacity essential for these activities ( Top et al, 2002 ; Top and Springael, 2003 ; Diaz, 2004 ; Shintani et al, 2010 ). While initial work exploring MGE centered largely on plasmids, the advent of genome sequencing has revealed the role of ICE and other types of genomic islands ( van der Meer and Sentchilo, 2003 ; Gaillard et al, 2006 ; Hickey et al, 2012 ; Chong et al, 2014 ; Pathak et al, 2016 ; Zamarro et al, 2016 ; Suenaga et al, 2017 ).…”