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Genome Structure of the Opportunistic Pathogen Paracoccus yeei (Alphaproteobacteria) and Identification of Putative

Robert Lasek¹, Magdalena Szuplewska¹, Monika Mitura¹

¹Department of Bacterial Genetics, Faculty of Biology, University of Warsaw, Warsaw, Poland.

Frontiers in Microbiology

|November 10, 2018

Abstract:

Bacteria of the genus Paracoccus are common components of the microbiomes of many naturally- and anthropogenically shaped environments. One species, Paracoccus yeei, is unique within the genus because it is associated with opportunistic human infections. Therefore, strains of P. yeei may serve as an interesting model to study the transition from a saprophytic to a pathogenic lifestyle in environmental bacteria. Unfortunately, knowledge concerning the biology, genetics and genomic content of P. yeei is fragmentary; also the mechanisms of pathogenicity of this bacterium remain unclear. In this study we provide the first insight into the genome composition and metabolic potential of a clinical isolate, P. yeei CCUG 32053. This strain has a multipartite genome (4,632,079 bp) composed of a circular chromosome plus eight extrachromosomal replicons pYEE1-8: 3 chromids and 5 plasmids, with a total size of 1,247,173 bp. The genome has been significantly shaped by the acquisition of genomic islands, prophages (Myoviridae and Siphoviridae phage families) and numerous insertion sequences (ISs) representing seven IS families. Detailed comparative analysis with other complete genomic sequences of Paracoccus spp. (including P. yeei FDAARGOS_252 and TT13, as well as non-pathogenic strains of other species in this genus) enabled us to identify P. yeei species-specific genes and to predict putative determinants of virulence. This is the first attempt to identify pathoadaptive genetic information of P. yeei and to estimate the role of the mobilome in the evolution of pathogenicity in this species.

Insights

Paracoccus yeei, an opportunistic pathogen, has a complex genome with plasmids and mobile genetic elements. This study reveals its unique genetic makeup, offering insights into how environmental bacteria evolve pathogenicity.

Area of Science:

Microbiology
Genomics
Evolutionary Biology

Background:

Bacteria of the genus Paracoccus are widespread in various environments.
Paracoccus yeei is unique for causing opportunistic human infections, making it a model for studying the saprophytic-to-pathogenic transition.
Current knowledge on P. yeei biology, genetics, and pathogenicity mechanisms is limited.

Purpose of the Study:

To provide the first comprehensive analysis of the genome composition and metabolic potential of a clinical P. yeei isolate (CCUG 32053).
To identify species-specific genes and predict potential virulence factors.
To investigate the role of the mobilome in the evolution of pathogenicity in P. yeei.

Main Methods:

Whole-genome sequencing of the clinical isolate P. yeei CCUG 32053.
Analysis of the multipartite genome structure, including chromosome and extrachromosomal replicons (chromids and plasmids).
Comparative genomic analysis with other Paracoccus species to identify unique genetic features and mobile elements (genomic islands, prophages, insertion sequences).

Main Results:

The P. yeei CCUG 32053 strain possesses a large, multipartite genome (4,632,079 bp) comprising a chromosome and eight extrachromosomal replicons (3 chromids, 5 plasmids).
The genome is rich in mobile genetic elements, including genomic islands, prophages (Myoviridae, Siphoviridae), and insertion sequences from seven families.
Comparative genomics identified P. yeei-specific genes and potential virulence determinants, highlighting the mobilome's contribution to pathogenicity.

Conclusions:

This study presents the first detailed genomic insights into P. yeei, revealing a complex genome shaped by horizontal gene transfer.
The identified species-specific genes and mobile elements provide a foundation for understanding P. yeei pathogenicity.
This work offers a starting point for investigating the pathoadaptive evolution of P. yeei and its transition to an opportunistic pathogen.

Read full analysis

Keywords:

Paracoccus yeei chromids evolution of pathogenic bacteria genomic islands mobilome opportunistic pathogen plasmids virulence factors

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