The pangenome of (Antarctic) Pseudoalteromonas bacteria: Evolutionary and functional insights
Background: Pseudoalteromonas is a genus of ubiquitous marine bacteria used as model organisms to study the biological mechanisms involved in the adaptation to cold conditions. A remarkable feature shared by these bacteria is their ability to produce secondary metabolites with a strong antimicrobial...
Published in: | BMC Genomics |
---|---|
Main Authors: | , , , , , , , , , , |
Other Authors: | , , , , , , , , , , |
Format: | Article in Journal/Newspaper |
Language: | English |
Published: |
BioMed Central Ltd.
2017
|
Subjects: | |
Online Access: | https://hdl.handle.net/11567/1072784 https://doi.org/10.1186/s12864-016-3382-y |
id |
ftunivgenova:oai:iris.unige.it:11567/1072784 |
---|---|
record_format |
openpolar |
spelling |
ftunivgenova:oai:iris.unige.it:11567/1072784 2024-04-14T08:04:22+00:00 The pangenome of (Antarctic) Pseudoalteromonas bacteria: Evolutionary and functional insights Bosi E. Fondi M. Orlandini V. Perrin E. Maida I. de Pascale D. Tutino M. L. Parrilli E. Lo Giudice A. Filloux A. Fani R. Bosi, E. Fondi, M. Orlandini, V. Perrin, E. Maida, I. de Pascale, D. Tutino, M. L. Parrilli, E. Lo Giudice, A. Filloux, A. Fani, R. 2017 ELETTRONICO https://hdl.handle.net/11567/1072784 https://doi.org/10.1186/s12864-016-3382-y eng eng BioMed Central Ltd. place:236 GRAYS INN RD, FLOOR 6, LONDON WC1X 8HL, ENGLAND info:eu-repo/semantics/altIdentifier/wos/WOS:000394379700005 volume:18 firstpage:1 lastpage:18 numberofpages:18 journal:BMC GENOMICS https://hdl.handle.net/11567/1072784 doi:10.1186/s12864-016-3382-y info:eu-repo/semantics/altIdentifier/scopus/2-s2.0-85011409912 Antarctic bacteria Antibiotic Comparative genomic Horizontal gene transfer Marine bacteria Microbial evolution Pangenome Pseudoalteromonas info:eu-repo/semantics/article 2017 ftunivgenova https://doi.org/10.1186/s12864-016-3382-y 2024-03-21T02:37:55Z Background: Pseudoalteromonas is a genus of ubiquitous marine bacteria used as model organisms to study the biological mechanisms involved in the adaptation to cold conditions. A remarkable feature shared by these bacteria is their ability to produce secondary metabolites with a strong antimicrobial and antitumor activity. Despite their biotechnological relevance, representatives of this genus are still lacking (with few exceptions) an extensive genomic characterization, including features involved in the evolution of secondary metabolites production. Indeed, biotechnological applications would greatly benefit from such analysis. Results: Here, we analyzed the genomes of 38 strains belonging to different Pseudoalteromonas species and isolated from diverse ecological niches, including extreme ones (i.e. Antarctica). These sequences were used to reconstruct the largest Pseudoalteromonas pangenome computed so far, including also the two main groups of Pseudoalteromonas strains (pigmented and not pigmented strains). The downstream analyses were conducted to describe the genomic diversity, both at genus and group levels. This allowed highlighting a remarkable genomic heterogeneity, even for closely related strains. We drafted all the main evolutionary steps that led to the current structure and gene content of Pseudoalteromonas representatives. These, most likely, included an extensive genome reduction and a strong contribution of Horizontal Gene Transfer (HGT), which affected biotechnologically relevant gene sets and occurred in a strain-specific fashion. Furthermore, this study also identified the genomic determinants related to some of the most interesting features of the Pseudoalteromonas representatives, such as the production of secondary metabolites, the adaptation to cold temperatures and the resistance to abiotic compounds. Conclusions: This study poses the bases for a comprehensive understanding of the evolutionary trajectories followed in time by this peculiar bacterial genus and for a focused exploitation ... Article in Journal/Newspaper Antarc* Antarctic Antarctica Università degli Studi di Genova: CINECA IRIS Antarctic BMC Genomics 18 1 |
institution |
Open Polar |
collection |
Università degli Studi di Genova: CINECA IRIS |
op_collection_id |
ftunivgenova |
language |
English |
topic |
Antarctic bacteria Antibiotic Comparative genomic Horizontal gene transfer Marine bacteria Microbial evolution Pangenome Pseudoalteromonas |
spellingShingle |
Antarctic bacteria Antibiotic Comparative genomic Horizontal gene transfer Marine bacteria Microbial evolution Pangenome Pseudoalteromonas Bosi E. Fondi M. Orlandini V. Perrin E. Maida I. de Pascale D. Tutino M. L. Parrilli E. Lo Giudice A. Filloux A. Fani R. The pangenome of (Antarctic) Pseudoalteromonas bacteria: Evolutionary and functional insights |
topic_facet |
Antarctic bacteria Antibiotic Comparative genomic Horizontal gene transfer Marine bacteria Microbial evolution Pangenome Pseudoalteromonas |
description |
Background: Pseudoalteromonas is a genus of ubiquitous marine bacteria used as model organisms to study the biological mechanisms involved in the adaptation to cold conditions. A remarkable feature shared by these bacteria is their ability to produce secondary metabolites with a strong antimicrobial and antitumor activity. Despite their biotechnological relevance, representatives of this genus are still lacking (with few exceptions) an extensive genomic characterization, including features involved in the evolution of secondary metabolites production. Indeed, biotechnological applications would greatly benefit from such analysis. Results: Here, we analyzed the genomes of 38 strains belonging to different Pseudoalteromonas species and isolated from diverse ecological niches, including extreme ones (i.e. Antarctica). These sequences were used to reconstruct the largest Pseudoalteromonas pangenome computed so far, including also the two main groups of Pseudoalteromonas strains (pigmented and not pigmented strains). The downstream analyses were conducted to describe the genomic diversity, both at genus and group levels. This allowed highlighting a remarkable genomic heterogeneity, even for closely related strains. We drafted all the main evolutionary steps that led to the current structure and gene content of Pseudoalteromonas representatives. These, most likely, included an extensive genome reduction and a strong contribution of Horizontal Gene Transfer (HGT), which affected biotechnologically relevant gene sets and occurred in a strain-specific fashion. Furthermore, this study also identified the genomic determinants related to some of the most interesting features of the Pseudoalteromonas representatives, such as the production of secondary metabolites, the adaptation to cold temperatures and the resistance to abiotic compounds. Conclusions: This study poses the bases for a comprehensive understanding of the evolutionary trajectories followed in time by this peculiar bacterial genus and for a focused exploitation ... |
author2 |
Bosi, E. Fondi, M. Orlandini, V. Perrin, E. Maida, I. de Pascale, D. Tutino, M. L. Parrilli, E. Lo Giudice, A. Filloux, A. Fani, R. |
format |
Article in Journal/Newspaper |
author |
Bosi E. Fondi M. Orlandini V. Perrin E. Maida I. de Pascale D. Tutino M. L. Parrilli E. Lo Giudice A. Filloux A. Fani R. |
author_facet |
Bosi E. Fondi M. Orlandini V. Perrin E. Maida I. de Pascale D. Tutino M. L. Parrilli E. Lo Giudice A. Filloux A. Fani R. |
author_sort |
Bosi E. |
title |
The pangenome of (Antarctic) Pseudoalteromonas bacteria: Evolutionary and functional insights |
title_short |
The pangenome of (Antarctic) Pseudoalteromonas bacteria: Evolutionary and functional insights |
title_full |
The pangenome of (Antarctic) Pseudoalteromonas bacteria: Evolutionary and functional insights |
title_fullStr |
The pangenome of (Antarctic) Pseudoalteromonas bacteria: Evolutionary and functional insights |
title_full_unstemmed |
The pangenome of (Antarctic) Pseudoalteromonas bacteria: Evolutionary and functional insights |
title_sort |
pangenome of (antarctic) pseudoalteromonas bacteria: evolutionary and functional insights |
publisher |
BioMed Central Ltd. |
publishDate |
2017 |
url |
https://hdl.handle.net/11567/1072784 https://doi.org/10.1186/s12864-016-3382-y |
geographic |
Antarctic |
geographic_facet |
Antarctic |
genre |
Antarc* Antarctic Antarctica |
genre_facet |
Antarc* Antarctic Antarctica |
op_relation |
info:eu-repo/semantics/altIdentifier/wos/WOS:000394379700005 volume:18 firstpage:1 lastpage:18 numberofpages:18 journal:BMC GENOMICS https://hdl.handle.net/11567/1072784 doi:10.1186/s12864-016-3382-y info:eu-repo/semantics/altIdentifier/scopus/2-s2.0-85011409912 |
op_doi |
https://doi.org/10.1186/s12864-016-3382-y |
container_title |
BMC Genomics |
container_volume |
18 |
container_issue |
1 |
_version_ |
1796300859066286080 |