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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...
Autores principales: | , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Frontiers Media S.A.
2021
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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 |
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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 |
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