Architecture and functions of a multipartite genome of the methylotrophic bacterium Paracoccus aminophilus JCM 7686, containing primary and secondary chromids

Abstract

BackgroundParacoccus aminophilus JCM 7686 is a methylotrophic α-Proteobacterium capable of utilizing reduced one-carbon compounds as sole carbon and energy source for growth, including toxic N,N-dimethylformamide, formamide, methanol, and methylamines, which are widely used in the industry. P. aminophilus JCM 7686, as many other Paracoccus spp., possesses a genome representing a multipartite structure, in which the genomic information is split between various replicons, including chromids, essential plasmid-like replicons, with properties of both chromosomes and plasmids. In this study, whole-genome sequencing and functional genomics approaches were applied to investigate P. aminophilus genome information.ResultsThe P. aminophilus JCM 7686 genome has a multipartite structure, composed of a single circular chromosome and eight additional replicons ranging in size between 5.6 and 438.1 kb. Functional analyses revealed that two of the replicons, pAMI5 and pAMI6, are essential for host viability, therefore they should be considered as chromids. Both replicons carry housekeeping genes, e.g. responsible for de novo NAD biosynthesis and ammonium transport. Other mobile genetic elements have also been identified, including 20 insertion sequences, 4 transposons and 10 prophage regions, one of which represents a novel, functional serine recombinase-encoding bacteriophage, ϕPam-6. Moreover, in silico analyses allowed us to predict the transcription regulatory network of the JCM 7686 strain, as well as components of the stress response, recombination, repair and methylation machineries. Finally, comparative genomic analyses revealed that P. aminophilus JCM 7686 has a relatively distant relationship to other representatives of the genus Paracoccus.ConclusionsP. aminophilus genome exploration provided insights into the overall structure and functions of the genome, with a special focus on the chromids. Based on the obtained results we propose the classification of bacterial chromids into two types: “primary” chromids, which are indispensable for host viability and “secondary” chromids, which are essential, but only under some environmental conditions and which were probably formed quite recently in the course of evolution. Detailed genome investigation and its functional analysis, makes P. aminophilus JCM 7686 a suitable reference strain for the genus Paracoccus. Moreover, this study has increased knowledge on overall genome structure and composition of members within the class Alphaproteobacteria.

Molecular Characterization of a Novel Temperate Sinorhizobium Bacteriophage, ФLM21, Encoding DNA Methyltransferase with CcrM-Like Specificity

“…We have identified the first example of an MTase in an Alphaproteobacteria phage that could methylate the GANTC sequence in a temperate phage, ⌽Pam-6, of P. aminophilus JCM 7686. We have also demonstrated that two other putative prophages in the P. aminophilus JCM 7686 genome encoded MTases with the same specificity as the host CcrM (65). Here, we report another example of this interesting phenomenon.…”

“…We have shown previously that the three m 6 A MTases (JCM7 686_1231, JCM7686_2255, and JCM7686_2934) identified in the prophage regions of the genome of Paracoccus aminophilus JCM 7686 methylated the GANTC sequence (65). It is noteworthy that all of the genes coding for phage MTases (⌽LM21 as well as ⌽Pam-2, ⌽Pam-4, and ⌽Pam-6 of P. aminophilus) are localized within the predicted replication module.…”

Two novel temperate bacteriophages co-existing in Aeromonas sp. ARM81 – characterization of their genomes, proteomes and DNA methyltransferases

“…Genome analyses of many genera, such as Bacillus, Enterococcus, Listeria, Mannheimia, Paracoccus, Staphylococcus and Streptococcus revealed that polylysogeny is a common phenomenon (Dziewit et al, 2014a;Goerke et al, 2009;Niu et al, 2015). Recently, we have also identified a polylysogenic Sinorhizobium sp.…”

The effect of light intensity and shear stress on microbial biostabilization and the community composition of natural biofilms

“…However, besides other bacterial species, R. gelatinosus might play an essential role in conditioning the sediment surface, facilitating subsequent diatom settlement and development, as described for other heterotrophic bacteria. 65 Moreover, the fast growth and potential for high EPS production of R. capsulatus and P. aminophilus [95][96][97] may lead to a solid biofilm fundament tightly attached to the sediment grains, especially in crucial early developmental stages. This could be of major structural importance for the overall biofilm system and lead to higher biofilm stability.…”