Cargando…

Phylogenetic Distribution of Polysaccharide-Degrading Enzymes in Marine Bacteria

Deconstruction is an essential step of conversion of polysaccharides, and polysaccharide-degrading enzymes play a key role in this process. Although there is recent progress in the identification of these enzymes, the diversity and phylogenetic distribution of these enzymes in marine microorganisms...

Descripción completa

Detalles Bibliográficos
Autores principales: Sun, Zhong-Zhi, Ji, Bo-Wen, Zheng, Ning, Wang, Meng, Cao, Ye, Wan, Lu, Li, Yi-Song, Rong, Jin-Cheng, He, Hai-Lun, Chen, Xiu-Lan, Zhang, Yu-Zhong, Xie, Bin-Bin
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8012555/
https://www.ncbi.nlm.nih.gov/pubmed/33815349
http://dx.doi.org/10.3389/fmicb.2021.658620
_version_ 1783673387605819392
author Sun, Zhong-Zhi
Ji, Bo-Wen
Zheng, Ning
Wang, Meng
Cao, Ye
Wan, Lu
Li, Yi-Song
Rong, Jin-Cheng
He, Hai-Lun
Chen, Xiu-Lan
Zhang, Yu-Zhong
Xie, Bin-Bin
author_facet Sun, Zhong-Zhi
Ji, Bo-Wen
Zheng, Ning
Wang, Meng
Cao, Ye
Wan, Lu
Li, Yi-Song
Rong, Jin-Cheng
He, Hai-Lun
Chen, Xiu-Lan
Zhang, Yu-Zhong
Xie, Bin-Bin
author_sort Sun, Zhong-Zhi
collection PubMed
description Deconstruction is an essential step of conversion of polysaccharides, and polysaccharide-degrading enzymes play a key role in this process. Although there is recent progress in the identification of these enzymes, the diversity and phylogenetic distribution of these enzymes in marine microorganisms remain largely unknown, hindering our understanding of the ecological roles of marine microorganisms in the ocean carbon cycle. Here, we studied the phylogenetic distribution of nine types of polysaccharide-degrading enzymes in marine bacterial genomes. First, we manually compiled a reference sequence database containing 961 experimentally verified enzymes. With this reference database, we annotated 9,335 enzyme sequences from 2,182 high-quality marine bacterial genomes, revealing extended distribution for six enzymes at the phylum level and for all nine enzymes at lower taxonomic levels. Next, phylogenetic analyses revealed intra-clade diversity in the encoding potentials and phylogenetic conservation of a few enzymes at the genus level. Lastly, our analyses revealed correlations between enzymes, with alginate lyases demonstrating the most extensive correlations with others. Intriguingly, chitinases showed negative correlations with cellulases, alginate lyases, and agarases in a few genera. This result suggested that intra-genus lifestyle differentiation occurred many times in marine bacteria and that the utilization of polysaccharides may act as an important driver in the recent ecological differentiation of a few lineages. This study expanded our knowledge of the phylogenetic distribution of polysaccharide enzymes and provided insights into the ecological differentiation of marine bacteria.
format Online
Article
Text
id pubmed-8012555
institution National Center for Biotechnology Information
language English
publishDate 2021
publisher Frontiers Media S.A.
record_format MEDLINE/PubMed
spelling pubmed-80125552021-04-02 Phylogenetic Distribution of Polysaccharide-Degrading Enzymes in Marine Bacteria Sun, Zhong-Zhi Ji, Bo-Wen Zheng, Ning Wang, Meng Cao, Ye Wan, Lu Li, Yi-Song Rong, Jin-Cheng He, Hai-Lun Chen, Xiu-Lan Zhang, Yu-Zhong Xie, Bin-Bin Front Microbiol Microbiology Deconstruction is an essential step of conversion of polysaccharides, and polysaccharide-degrading enzymes play a key role in this process. Although there is recent progress in the identification of these enzymes, the diversity and phylogenetic distribution of these enzymes in marine microorganisms remain largely unknown, hindering our understanding of the ecological roles of marine microorganisms in the ocean carbon cycle. Here, we studied the phylogenetic distribution of nine types of polysaccharide-degrading enzymes in marine bacterial genomes. First, we manually compiled a reference sequence database containing 961 experimentally verified enzymes. With this reference database, we annotated 9,335 enzyme sequences from 2,182 high-quality marine bacterial genomes, revealing extended distribution for six enzymes at the phylum level and for all nine enzymes at lower taxonomic levels. Next, phylogenetic analyses revealed intra-clade diversity in the encoding potentials and phylogenetic conservation of a few enzymes at the genus level. Lastly, our analyses revealed correlations between enzymes, with alginate lyases demonstrating the most extensive correlations with others. Intriguingly, chitinases showed negative correlations with cellulases, alginate lyases, and agarases in a few genera. This result suggested that intra-genus lifestyle differentiation occurred many times in marine bacteria and that the utilization of polysaccharides may act as an important driver in the recent ecological differentiation of a few lineages. This study expanded our knowledge of the phylogenetic distribution of polysaccharide enzymes and provided insights into the ecological differentiation of marine bacteria. Frontiers Media S.A. 2021-03-18 /pmc/articles/PMC8012555/ /pubmed/33815349 http://dx.doi.org/10.3389/fmicb.2021.658620 Text en Copyright © 2021 Sun, Ji, Zheng, Wang, Cao, Wan, Li, Rong, He, Chen, Zhang and Xie. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Microbiology
Sun, Zhong-Zhi
Ji, Bo-Wen
Zheng, Ning
Wang, Meng
Cao, Ye
Wan, Lu
Li, Yi-Song
Rong, Jin-Cheng
He, Hai-Lun
Chen, Xiu-Lan
Zhang, Yu-Zhong
Xie, Bin-Bin
Phylogenetic Distribution of Polysaccharide-Degrading Enzymes in Marine Bacteria
title Phylogenetic Distribution of Polysaccharide-Degrading Enzymes in Marine Bacteria
title_full Phylogenetic Distribution of Polysaccharide-Degrading Enzymes in Marine Bacteria
title_fullStr Phylogenetic Distribution of Polysaccharide-Degrading Enzymes in Marine Bacteria
title_full_unstemmed Phylogenetic Distribution of Polysaccharide-Degrading Enzymes in Marine Bacteria
title_short Phylogenetic Distribution of Polysaccharide-Degrading Enzymes in Marine Bacteria
title_sort phylogenetic distribution of polysaccharide-degrading enzymes in marine bacteria
topic Microbiology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8012555/
https://www.ncbi.nlm.nih.gov/pubmed/33815349
http://dx.doi.org/10.3389/fmicb.2021.658620
work_keys_str_mv AT sunzhongzhi phylogeneticdistributionofpolysaccharidedegradingenzymesinmarinebacteria
AT jibowen phylogeneticdistributionofpolysaccharidedegradingenzymesinmarinebacteria
AT zhengning phylogeneticdistributionofpolysaccharidedegradingenzymesinmarinebacteria
AT wangmeng phylogeneticdistributionofpolysaccharidedegradingenzymesinmarinebacteria
AT caoye phylogeneticdistributionofpolysaccharidedegradingenzymesinmarinebacteria
AT wanlu phylogeneticdistributionofpolysaccharidedegradingenzymesinmarinebacteria
AT liyisong phylogeneticdistributionofpolysaccharidedegradingenzymesinmarinebacteria
AT rongjincheng phylogeneticdistributionofpolysaccharidedegradingenzymesinmarinebacteria
AT hehailun phylogeneticdistributionofpolysaccharidedegradingenzymesinmarinebacteria
AT chenxiulan phylogeneticdistributionofpolysaccharidedegradingenzymesinmarinebacteria
AT zhangyuzhong phylogeneticdistributionofpolysaccharidedegradingenzymesinmarinebacteria
AT xiebinbin phylogeneticdistributionofpolysaccharidedegradingenzymesinmarinebacteria