Analysis of the core genome and pangenome of Pseudomonas putida

Abstract

Pseudomonas putida are strict aerobes that proliferate in a range of temperate niches and are of interest for environmental applications due to their capacity to degrade pollutants and ability to promote plant growth. Furthermore solvent-tolerant strains are useful for biosynthesis of added-value chemicals. We present a comprehensive comparative analysis of nine strains and the first characterization of the Pseudomonas putida pangenome. The core genome of P. putida comprises approximately 3386 genes. The most abundant genes within the core genome are those that encode nutrient transporters. Other conserved genes include those for central carbon metabolism through the Entner-Doudoroff pathway, the pentose phosphate cycle, arginine and proline metabolism, and pathways for degradation of aromatic chemicals. Genes that encode transporters, enzymes and regulators for amino acid metabolism (synthesis and degradation) are all part of the core genome, as well as various electron transporters, which enable aerobic metabolism under different oxygen regimes. Within the core genome are 30 genes for flagella biosynthesis and 12 key genes for biofilm formation. Pseudomonas putida strains share 85% of the coding regions with Pseudomonas aeruginosa; however, in P. putida, virulence factors such as exotoxins and type III secretion systems are absent.

Iron Uptake Analysis in a Set of Clinical Isolates of Pseudomonas putida

“…Interestingly, in P. aeruginosa the pyoverdine genes have been described as having a “core-accessory” character; they are present in all the strains that make up the species, but their codon usage, especially of the fpvA and the non-ribosomal peptide synthetase module genes, is different from the rest of the genes of the genome (Smith et al, 2005). This latter characteristic is specific to accessory genes, and is an indication of a differential evolution rate (Udaondo et al, 2016). This different codon usage is not consequence of direct acquisition from other microorganisms, but rather of the accumulation of polymorphisms and positive selection of these genes, which contribute to niche adaptation (Yang et al, 2012).…”

“…Bacterial survival under these conditions implies the acquisition of new capacities or the evolution of existing ones (Sharma et al, 2016). P. putida has an open-pangenome (Udaondo et al, 2016) and the acquisition of accessory genes and the evolution of those already existing in the core may help to colonize new environments. Gene acquisition from these niches has been demonstrated to be involved the capacity of some of P. putida strains to resist multiple antibiotics and the degradation of toxic compounds used in medicine, industry, and agriculture (Molina et al, 2013, 2014, 2016; Udaondo et al, 2016).…”

“…P. putida has an open-pangenome (Udaondo et al, 2016) and the acquisition of accessory genes and the evolution of those already existing in the core may help to colonize new environments. Gene acquisition from these niches has been demonstrated to be involved the capacity of some of P. putida strains to resist multiple antibiotics and the degradation of toxic compounds used in medicine, industry, and agriculture (Molina et al, 2013, 2014, 2016; Udaondo et al, 2016). However, the average total protein identity amongst the three strains is >95%, significantly higher than the identity with other strains of Clade I, thus reinforcing the idea of a common ancestor for the three strains.…”

“…Recently, a few P. putida strains have been isolated from hospital environments (von Graevenitz and Weinstein, 1971; Galli et al, 1992; Yoshino et al, 2011; Molina et al, 2013, 2014, 2016). The ubiquitous character of this microorganism has been linked to its broad metabolic potential, its ability to produce a large variety of secondary metabolites that may enable colonization of different environments and a complex array of sigma factors and two-component regulatory systems that allow a fast adaptation to environmental changes (Matilla et al, 2011; Udaondo et al, 2012, 2013, 2016; Planchamp et al, 2015). …”

Characterization and Genome Analysis of a Nicotine and Nicotinic Acid-Degrading Strain Pseudomonas putida JQ581 Isolated from Marine

“…The genome size (6.56 Mb) was slightly larger than the reported Pseudomonas putida genomes (an average of 6.08 Mb) [35]. It contained 93 contigs, with an average contig length of 49.93 kb, a median coverage depth of 75-fold, and an average GC content of 63.00%.…”