Genetic Determinants of Xylan Utilization in Humisphaera borealis M1803T, a Planctomycete of the Class Phycisphaerae
— Planctomycetes of the class Phycisphaerae are aerobic and anaerobic heterotrophic bacteria that colonize a wide range of marine and terrestrial habitats. Their functional roles in the environment, however, are still poorly understood. Humisphaera borealis M1803 T is one of the very few characteriz...
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| Published in: | Microbiology (New York) Vol. 91; no. 3; pp. 249 - 258 |
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| Main Authors: | , , |
| Format: | Journal Article |
| Language: | English |
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Pleiades Publishing
2022
Springer Nature B.V |
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| Abstract | —
Planctomycetes of the class
Phycisphaerae
are aerobic and anaerobic heterotrophic bacteria that colonize a wide range of marine and terrestrial habitats. Their functional roles in the environment, however, are still poorly understood.
Humisphaera borealis
M1803
T
is one of the very few characterized planctomycetes of this class. It is also the first described representative of the previously uncultured group WD2101, which is commonly detected in soils and peatlands. This work analyzed the genetic determinants that define the ability of
Humisphaera borealis
M1803
T
to grow on xylan, one of the plant cell wall polymers. The whole genome sequence analysis of this planctomycete resulted in identification of five genes encoding the proteins homologous to previously described endo-β-xylanases. For two of these proteins, evolutionarily closer experimentally characterized homologs with other substrate specificities were found. In a member of the GH10 family of glycoside hydrolases, the active center of the enzyme was destroyed. We consider two proteins from GH62 and GH141 families as the most likely candidates for the role of β-xylanase responsible for xylan utilization. Phylogenetic analysis of proteins of GH10, GH62, and GH141 families was carried out. The role of lateral transfers in the evolution of the genes for glycoside hydrolases and their close homologs is discussed. |
|---|---|
| AbstractList | —
Planctomycetes of the class
Phycisphaerae
are aerobic and anaerobic heterotrophic bacteria that colonize a wide range of marine and terrestrial habitats. Their functional roles in the environment, however, are still poorly understood.
Humisphaera borealis
M1803
T
is one of the very few characterized planctomycetes of this class. It is also the first described representative of the previously uncultured group WD2101, which is commonly detected in soils and peatlands. This work analyzed the genetic determinants that define the ability of
Humisphaera borealis
M1803
T
to grow on xylan, one of the plant cell wall polymers. The whole genome sequence analysis of this planctomycete resulted in identification of five genes encoding the proteins homologous to previously described endo-β-xylanases. For two of these proteins, evolutionarily closer experimentally characterized homologs with other substrate specificities were found. In a member of the GH10 family of glycoside hydrolases, the active center of the enzyme was destroyed. We consider two proteins from GH62 and GH141 families as the most likely candidates for the role of β-xylanase responsible for xylan utilization. Phylogenetic analysis of proteins of GH10, GH62, and GH141 families was carried out. The role of lateral transfers in the evolution of the genes for glycoside hydrolases and their close homologs is discussed. Abstract—Planctomycetes of the class Phycisphaerae are aerobic and anaerobic heterotrophic bacteria that colonize a wide range of marine and terrestrial habitats. Their functional roles in the environment, however, are still poorly understood. Humisphaera borealis M1803T is one of the very few characterized planctomycetes of this class. It is also the first described representative of the previously uncultured group WD2101, which is commonly detected in soils and peatlands. This work analyzed the genetic determinants that define the ability of Humisphaera borealis M1803T to grow on xylan, one of the plant cell wall polymers. The whole genome sequence analysis of this planctomycete resulted in identification of five genes encoding the proteins homologous to previously described endo-β-xylanases. For two of these proteins, evolutionarily closer experimentally characterized homologs with other substrate specificities were found. In a member of the GH10 family of glycoside hydrolases, the active center of the enzyme was destroyed. We consider two proteins from GH62 and GH141 families as the most likely candidates for the role of β-xylanase responsible for xylan utilization. Phylogenetic analysis of proteins of GH10, GH62, and GH141 families was carried out. The role of lateral transfers in the evolution of the genes for glycoside hydrolases and their close homologs is discussed. |
| Author | Kulichevskaya, I. S. Dedysh, S. N. Naumoff, D. G. |
| Author_xml | – sequence: 1 givenname: D. G. surname: Naumoff fullname: Naumoff, D. G. email: daniil_naumoff@yahoo.com organization: Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences – sequence: 2 givenname: I. S. surname: Kulichevskaya fullname: Kulichevskaya, I. S. organization: Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences – sequence: 3 givenname: S. N. surname: Dedysh fullname: Dedysh, S. N. organization: Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences |
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| Copyright | The Author(s), 2022. ISSN 0026-2617, Microbiology, 2022, Vol. 91, No. 3, pp. 249–258. © The Author(s), 2022. This article is an open access publication. Russian Text © The Author(s), 2022, published in Mikrobiologiya, 2022, Vol. 91, No. 3, pp. 300–311. The Author(s), 2022. ISSN 0026-2617, Microbiology, 2022, Vol. 91, No. 3, pp. 249–258. © The Author(s), 2022. This article is an open access publication. Russian Text © The Author(s), 2022, published in Mikrobiologiya, 2022, Vol. 91, No. 3, pp. 300–311. This work is published under http://creativecommons.org/licenses/by/4.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License. |
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| Keywords | glycoside hydrolase GH141 family protein evolution xylan degradation β-xylanase GH62 family protein phylogenetic tree search for homologs gene annotation lateral gene transfer |
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Planctomycetes of the class
Phycisphaerae
are aerobic and anaerobic heterotrophic bacteria that colonize a wide range of marine and terrestrial habitats.... Abstract—Planctomycetes of the class Phycisphaerae are aerobic and anaerobic heterotrophic bacteria that colonize a wide range of marine and terrestrial... |
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| SubjectTerms | Biomedical and Life Sciences Cell walls Evolutionary genetics Experimental Articles Genomes Glycoside hydrolase Heterotrophic bacteria Life Sciences Medical Microbiology Microbiology Nucleotide sequence Peatlands Phylogeny Proteins Sequence analysis Xylan |
| Title | Genetic Determinants of Xylan Utilization in Humisphaera borealis M1803T, a Planctomycete of the Class Phycisphaerae |
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