Comparative structural and functional genomics of Paracoccus aminovorans JCM 7685 and Paracoccus aminophilus JCM 7686 – methylotrophic bacteria utilizing toxic compounds

This project involves the analysis of two methylotrophic strains: Paracoccus aminovorans JCM 7685 and Paracoccus aminophilus JCM 7686, which are of significant biotechnological importance due to their ability to degrade various toxic compounds, including N,N-dimethylformamide and mono-, di-, and trimethylamines. As part of a project funded by the Iuventus Plus 2010 program, comprehensive studies were initiated, during which the complete nucleotide sequence of the P. aminophilus JCM 7686 genome (4.6 Mb) was determined. The proposed project aims to continue and expand these studies. A genomic analysis of the P. aminovorans JCM 7685 strain is planned, along with comprehensive comparative analyses of the obtained sequences with the genome of the phylogenetically related P. aminophilus JCM 7686.

Comparative genomics of the closely related P. aminophilus and P. aminovorans will allow for the definition of the conserved chromosomal backbone of both strains while highlighting similarities and differences with other members of the Paracoccus genus. It will also enable the identification of the shared portion of the Paracoccus pangenome and provide insights into the evolution of this group of microorganisms.

In-depth bioinformatics analyses of the JCM 7685 genome sequence will facilitate in silico identification of metabolic pathway components responsible for the physiological properties of the studied strain. The genome will be analyzed to identify:

(i) the conserved backbone (specific to Paracoccus spp.), composed of genes involved in core metabolism,

(ii) the mobilome, which includes mobile genetic elements, and

(iii) a set of adaptive genetic determinants that enable bacterial growth in contaminated environments. These analyses will also help identify genes and genetic modules encoding enzymes with potential applications.

Bioinformatics analyses of the JCM 7685 and JCM 7686 genomes will be correlated with physiological study results, enabling verification of the functionality of the in silico-identified genes and genetic modules and the creation of a reliable metabolic profile of the studied strains.

Selected genetic modules will undergo more detailed analyses. The identified genes (either individually or in clusters) will be cloned into functional cassettes carrying complete genetic information required for toxic compound degradation or other genetic information of biotechnological significance. In accordance with synthetic biology principles, these “standardized” components can be combined in various configurations to achieve desired biological properties. The prepared genetic cassettes will form a bank of functional genetic modules, which can be used for constructing various types of plasmids (including shuttle vectors for E. coli–Alphaproteobacteria) and biological systems with potential applications in biotechnology and bioremediation.