The pangenome of (Antarctic) Pseudoalteromonas bacteria: evolutionary and functional insights

Bosi, Emanuele; Fondi, Marco; Orlandini, Valerio; Perrin, Elena; Maida, Isabel; Pascale, Donatella de; Tutino, Maria Luisa; Parrilli, Ermenegilda; Giudice, Angelina Lo; Filloux, Alain; Fani, Renato

doi:10.1186/s12864-016-3382-y

Cited by 56 publications

(59 citation statements)

References 70 publications

(85 reference statements)

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…2b ) and that could be the result of high genomic plasticity within this species [ 1 ]. This finding is in agreement with the level of openness of the pan-genome for other representatives of Gammaproteobacteria as it was reported before [ 35 – 38 ]. In contrast to P. parmentieri pan-genome, closely related and very homogenous D. solani species have a closed pan-genome [ 39 ].…”

Section: Resultssupporting

confidence: 93%

High genomic variability in the plant pathogenic bacterium Pectobacterium parmentieri deciphered from de novo assembled complete genomes

et al. 2018

View full text Add to dashboard Cite

BackgroundPectobacterium parmentieri is a newly established species within the plant pathogenic family Pectobacteriaceae. Bacteria belonging to this species are causative agents of diseases in economically important crops (e.g. potato) in a wide range of different environmental conditions, encountered in Europe, North America, Africa, and New Zealand. Severe disease symptoms result from the activity of P. parmentieri virulence factors, such as plant cell wall degrading enzymes. Interestingly, we observe significant phenotypic differences among P. parmentieri isolates regarding virulence factors production and the abilities to macerate plants. To establish the possible genomic basis of these differences, we sequenced 12 genomes of P. parmentieri strains (10 isolated in Poland, 2 in Belgium) with the combined use of Illumina and PacBio approaches. De novo genome assembly was performed with the use of SPAdes software, while annotation was conducted by NCBI Prokaryotic Genome Annotation Pipeline.ResultsThe pan-genome study was performed on 15 genomes (12 de novo assembled and three reference strains: P. parmentieri CFBP 8475T, P. parmentieri SCC3193, P. parmentieri WPP163). The pan-genome includes 3706 core genes, a high number of accessory (1468) genes, and numerous unique (1847) genes. We identified the presence of well-known genes encoding virulence factors in the core genome fraction, but some of them were located in the dispensable genome. A significant fraction of horizontally transferred genes, virulence-related gene duplications, as well as different CRISPR arrays were found, which can explain the observed phenotypic differences. Finally, we found also, for the first time, the presence of a plasmid in one of the tested P. parmentieri strains isolated in Poland.ConclusionsWe can hypothesize that a large number of the genes in the dispensable genome and significant genomic variation among P. parmentieri strains could be the basis of the potential wide host range and widespread diffusion of P. parmentieri. The obtained data on the structure and gene content of P. parmentieri strains enabled us to speculate on the importance of high genomic plasticity for P. parmentieri adaptation to different environments.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-5140-9) contains supplementary material, which is available to authorized users.

show abstract

Section: Resultssupporting

confidence: 93%

High genomic variability in the plant pathogenic bacterium Pectobacterium parmentieri deciphered from de novo assembled complete genomes

et al. 2018

View full text Add to dashboard Cite

show abstract

“…2013 ). Recently, based on genome data, bacteriocins were also predicted to be produced by members of the obligate marine genus Pseudoalteromonas ( Bosi et al. 2017 ).…”

Section: Resultsmentioning

confidence: 99%

Comparative Genomics Highlights Symbiotic Capacities and High Metabolic Flexibility of the Marine Genus Pseudovibrio

Versluis

Nijsse

Mohamad

et al. 2018

Genome Biology and Evolution

View full text Add to dashboard Cite

Pseudovibrio is a marine bacterial genus members of which are predominantly isolated from sessile marine animals, and particularly sponges. It has been hypothesized that Pseudovibrio spp. form mutualistic relationships with their hosts. Here, we studied Pseudovibrio phylogeny and genetic adaptations that may play a role in host colonization by comparative genomics of 31 Pseudovibrio strains, including 25 sponge isolates. All genomes were highly similar in terms of encoded core metabolic pathways, albeit with substantial differences in overall gene content. Based on gene composition, Pseudovibrio spp. clustered by geographic region, indicating geographic speciation. Furthermore, the fact that isolates from the Mediterranean Sea clustered by sponge species suggested host-specific adaptation or colonization. Genome analyses suggest that Pseudovibrio hongkongensis UST20140214-015BT is only distantly related to other Pseudovibrio spp., thereby challenging its status as typical Pseudovibrio member. All Pseudovibrio genomes were found to encode numerous proteins with SEL1 and tetratricopeptide repeats, which have been suggested to play a role in host colonization. For evasion of the host immune system, Pseudovibrio spp. may depend on type III, IV, and VI secretion systems that can inject effector molecules into eukaryotic cells. Furthermore, Pseudovibrio genomes carry on average seven secondary metabolite biosynthesis clusters, reinforcing the role of Pseudovibrio spp. as potential producers of novel bioactive compounds. Tropodithietic acid, bacteriocin, and terpene biosynthesis clusters were highly conserved within the genus, suggesting an essential role in survival, for example through growth inhibition of bacterial competitors. Taken together, these results support the hypothesis that Pseudovibrio spp. have mutualistic relations with sponges.

show abstract

“…In addition, representatives of the genus Pseudoalteromonas have also been shown to produce a broad array of bioactive molecules such as antibiotics, antitumor agents, and toxins/antitoxins [11,42,43,44,45]. …”

Section: Resultsmentioning

confidence: 99%

Biotechnological Potential of Cold Adapted Pseudoalteromonas spp. Isolated from ‘Deep Sea’ Sponges

et al. 2017

View full text Add to dashboard Cite

The marine genus Pseudoalteromonas is known for its versatile biotechnological potential with respect to the production of antimicrobials and enzymes of industrial interest. We have sequenced the genomes of three Pseudoalteromonas sp. strains isolated from different deep sea sponges on the Illumina MiSeq platform. The isolates have been screened for various industrially important enzymes and comparative genomics has been applied to investigate potential relationships between the isolates and their host organisms, while comparing them to free-living Pseudoalteromonas spp. from shallow and deep sea environments. The genomes of the sponge associated Pseudoalteromonas strains contained much lower levels of potential eukaryotic-like proteins which are known to be enriched in symbiotic sponge associated microorganisms, than might be expected for true sponge symbionts. While all the Pseudoalteromonas shared a large distinct subset of genes, nonetheless the number of unique and accessory genes is quite large and defines the pan-genome as open. Enzymatic screens indicate that a vast array of enzyme activities is expressed by the isolates, including β-galactosidase, β-glucosidase, and protease activities. A β-glucosidase gene from one of the Pseudoalteromonas isolates, strain EB27 was heterologously expressed in Escherichia coli and, following biochemical characterization, the recombinant enzyme was found to be cold-adapted, thermolabile, halotolerant, and alkaline active.

show abstract

The pangenome of (Antarctic) Pseudoalteromonas bacteria: evolutionary and functional insights

Cited by 56 publications

References 70 publications

High genomic variability in the plant pathogenic bacterium Pectobacterium parmentieri deciphered from de novo assembled complete genomes

High genomic variability in the plant pathogenic bacterium Pectobacterium parmentieri deciphered from de novo assembled complete genomes

Comparative Genomics Highlights Symbiotic Capacities and High Metabolic Flexibility of the Marine Genus Pseudovibrio

Biotechnological Potential of Cold Adapted Pseudoalteromonas spp. Isolated from ‘Deep Sea’ Sponges

Contact Info

Product

Resources

About