Tags

Type your tag names separated by a space and hit enter

Genome-wide analyses of chitin synthases identify horizontal gene transfers towards bacteria and allow a robust and unifying classification into fungi.
BMC Evol Biol. 2016 11 24; 16(1):252.BE

Abstract

BACKGROUND

Chitin, the second most abundant biopolymer on earth after cellulose, is found in probably all fungi, many animals (mainly invertebrates), several protists and a few algae, playing an essential role in the development of many of them. This polysaccharide is produced by type 2 glycosyltransferases, called chitin synthases (CHS). There are several contradictory classifications of CHS isoenzymes and, as regards their evolutionary history, their origin and diversity is still a matter of debate.

RESULTS

A genome-wide analysis resulted in the detection of more than eight hundred putative chitin synthases in proteomes associated with about 130 genomes. Phylogenetic analyses were performed with special care to avoid any pitfalls associated with the peculiarities of these sequences (e.g. highly variable regions, truncated or recombined sequences, long-branch attraction). This allowed us to revise and unify the fungal CHS classification and to study the evolutionary history of the CHS multigenic family. This update has the advantage of being user-friendly due to the development of a dedicated website (http://wwwabi.snv.jussieu.fr/public/CHSdb), and it includes any correspondences with previously published classifications and mutants. Concerning the evolutionary history of CHS, this family has mainly evolved via duplications and losses. However, it is likely that several horizontal gene transfers (HGT) also occurred in eukaryotic microorganisms and, even more surprisingly, in bacteria.

CONCLUSIONS

This comprehensive multi-species analysis contributes to the classification of fungal CHS, in particular by optimizing its robustness, consensuality and accessibility. It also highlights the importance of HGT in the evolutionary history of CHS and describes bacterial chs genes for the first time. Many of the bacteria that have acquired a chitin synthase are plant pathogens (e.g. Dickeya spp; Pectobacterium spp; Brenneria spp; Agrobacterium vitis and Pseudomonas cichorii). Whether they are able to produce a chitin exopolysaccharide or secrete chitooligosaccharides requires further investigation.

Authors+Show Affiliations

Univ Lyon, Université Claude Bernard Lyon 1, CNRS UMR5240, Microbiologie Adaptation et Pathogénie, Bâtiment André Lwoff, 10 rue Raphaël Dubois, F-69622, Villeurbanne, France. isabelle.goncalves@univ-lyon1.fr. BAYER S.A.S., Centre de Recherche de la Dargoire, F-69263, Lyon, France. isabelle.goncalves@univ-lyon1.fr.Sorbonne Universités, UPMC Univ Paris 06, UMR 7205 (MNHN, UPMC, CNRS, EPHE), Atelier de Bioinformatique, F-75231, Paris, Cedex 05, France.Sorbonne Universités, UPMC Univ Paris 06, INRA-AgroParisTech UMR1318, F-78026, Versailles, France.Institut Pasteur, Unité Biologie Moléculaire du Gène chez les Extrêmophiles, Département de Microbiologie, 25 rue du Docteur Roux, F-75015, Paris, France.BAYER S.A.S., Centre de Recherche de la Dargoire, F-69263, Lyon, France.BAYER S.A.S., Centre de Recherche de la Dargoire, F-69263, Lyon, France.Sorbonne Universités, UPMC Univ Paris 06, UMR 7205 (MNHN, UPMC, CNRS, EPHE), Atelier de Bioinformatique, F-75231, Paris, Cedex 05, France.Univ Lyon, Université Claude Bernard Lyon 1, CNRS UMR5240, Microbiologie Adaptation et Pathogénie, Bâtiment André Lwoff, 10 rue Raphaël Dubois, F-69622, Villeurbanne, France. BAYER S.A.S., Centre de Recherche de la Dargoire, F-69263, Lyon, France.

Pub Type(s)

Journal Article

Language

eng

PubMed ID

27881071

Citation

Gonçalves, Isabelle R., et al. "Genome-wide Analyses of Chitin Synthases Identify Horizontal Gene Transfers Towards Bacteria and Allow a Robust and Unifying Classification Into Fungi." BMC Evolutionary Biology, vol. 16, no. 1, 2016, p. 252.
Gonçalves IR, Brouillet S, Soulié MC, et al. Genome-wide analyses of chitin synthases identify horizontal gene transfers towards bacteria and allow a robust and unifying classification into fungi. BMC Evol Biol. 2016;16(1):252.
Gonçalves, I. R., Brouillet, S., Soulié, M. C., Gribaldo, S., Sirven, C., Charron, N., Boccara, M., & Choquer, M. (2016). Genome-wide analyses of chitin synthases identify horizontal gene transfers towards bacteria and allow a robust and unifying classification into fungi. BMC Evolutionary Biology, 16(1), 252.
Gonçalves IR, et al. Genome-wide Analyses of Chitin Synthases Identify Horizontal Gene Transfers Towards Bacteria and Allow a Robust and Unifying Classification Into Fungi. BMC Evol Biol. 2016 11 24;16(1):252. PubMed PMID: 27881071.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Genome-wide analyses of chitin synthases identify horizontal gene transfers towards bacteria and allow a robust and unifying classification into fungi. AU - Gonçalves,Isabelle R, AU - Brouillet,Sophie, AU - Soulié,Marie-Christine, AU - Gribaldo,Simonetta, AU - Sirven,Catherine, AU - Charron,Noémie, AU - Boccara,Martine, AU - Choquer,Mathias, Y1 - 2016/11/24/ PY - 2016/07/18/received PY - 2016/10/28/accepted PY - 2016/11/25/entrez PY - 2016/11/25/pubmed PY - 2017/8/10/medline KW - Bacteria KW - Chitin synthase KW - Classification KW - Evolution KW - Fungi KW - Horizontal gene transfer SP - 252 EP - 252 JF - BMC evolutionary biology JO - BMC Evol. Biol. VL - 16 IS - 1 N2 - BACKGROUND: Chitin, the second most abundant biopolymer on earth after cellulose, is found in probably all fungi, many animals (mainly invertebrates), several protists and a few algae, playing an essential role in the development of many of them. This polysaccharide is produced by type 2 glycosyltransferases, called chitin synthases (CHS). There are several contradictory classifications of CHS isoenzymes and, as regards their evolutionary history, their origin and diversity is still a matter of debate. RESULTS: A genome-wide analysis resulted in the detection of more than eight hundred putative chitin synthases in proteomes associated with about 130 genomes. Phylogenetic analyses were performed with special care to avoid any pitfalls associated with the peculiarities of these sequences (e.g. highly variable regions, truncated or recombined sequences, long-branch attraction). This allowed us to revise and unify the fungal CHS classification and to study the evolutionary history of the CHS multigenic family. This update has the advantage of being user-friendly due to the development of a dedicated website (http://wwwabi.snv.jussieu.fr/public/CHSdb), and it includes any correspondences with previously published classifications and mutants. Concerning the evolutionary history of CHS, this family has mainly evolved via duplications and losses. However, it is likely that several horizontal gene transfers (HGT) also occurred in eukaryotic microorganisms and, even more surprisingly, in bacteria. CONCLUSIONS: This comprehensive multi-species analysis contributes to the classification of fungal CHS, in particular by optimizing its robustness, consensuality and accessibility. It also highlights the importance of HGT in the evolutionary history of CHS and describes bacterial chs genes for the first time. Many of the bacteria that have acquired a chitin synthase are plant pathogens (e.g. Dickeya spp; Pectobacterium spp; Brenneria spp; Agrobacterium vitis and Pseudomonas cichorii). Whether they are able to produce a chitin exopolysaccharide or secrete chitooligosaccharides requires further investigation. SN - 1471-2148 UR - https://www.unboundmedicine.com/medline/citation/27881071/Genome_wide_analyses_of_chitin_synthases_identify_horizontal_gene_transfers_towards_bacteria_and_allow_a_robust_and_unifying_classification_into_fungi_ L2 - https://bmcevolbiol.biomedcentral.com/articles/10.1186/s12862-016-0815-9 DB - PRIME DP - Unbound Medicine ER -