Identification of Novel Putative Bacterial Feruloyl Esterases From Anaerobic Ecosystems by Use of Whole-Genome Shotgun Metagenomics and Genome Binning
Feruloyl esterases (FAEs) can reduce the recalcitrance of lignocellulosic biomass to enzymatic hydrolysis, thereby enhancing biorefinery potentials or animal feeding values of the biomass. In addition, ferulic acid, a product of FAE activity, has applications in pharmaceutical and food/beverage indu...
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Language: | English |
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Frontiers Media S.A.
2019-11-01
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Series: | Frontiers in Microbiology |
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Online Access: | https://www.frontiersin.org/article/10.3389/fmicb.2019.02673/full |
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author | Kamyar Mogodiniyai Kasmaei John Sundh |
author_facet | Kamyar Mogodiniyai Kasmaei John Sundh |
author_sort | Kamyar Mogodiniyai Kasmaei |
collection | DOAJ |
description | Feruloyl esterases (FAEs) can reduce the recalcitrance of lignocellulosic biomass to enzymatic hydrolysis, thereby enhancing biorefinery potentials or animal feeding values of the biomass. In addition, ferulic acid, a product of FAE activity, has applications in pharmaceutical and food/beverage industries. It is therefore of great interest to identify new FAEs to enhance understanding about this enzyme family. For this purpose, we used whole-genome shotgun metagenomics and genome binning to explore rumens of dairy cows, large intestines of horses, sediments of freshwater and forest topsoils to identify novel prokaryotic FAEs and trace the responsible microorganisms. A number of prokaryotic genomes were recovered of which, genomes of Clostridiales order and Candidatus Rhabdochlamydia genus showed FAE coding capacities. In total, five sequences were deemed as putative FAE. The BLASTP search against non-redundant protein database of NCBI indicated that these putative FAEs represented novel sequences within this enzyme family. The phylogenetic analysis showed that at least three putative sequences shared evolutionary lineage with FAEs of type A and thus could possess specific activities similar to this type of FAEs, something that is not previously found outside fungal kingdom. We nominate Candidatus Rhabdochlamydia genus as a novel FAE producing taxonomic unit. |
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format | Article |
id | doaj.art-deb3fe113c354e17b20c9c54378dcb40 |
institution | Directory Open Access Journal |
issn | 1664-302X |
language | English |
last_indexed | 2024-12-24T03:41:33Z |
publishDate | 2019-11-01 |
publisher | Frontiers Media S.A. |
record_format | Article |
series | Frontiers in Microbiology |
spelling | doaj.art-deb3fe113c354e17b20c9c54378dcb402022-12-21T17:16:53ZengFrontiers Media S.A.Frontiers in Microbiology1664-302X2019-11-011010.3389/fmicb.2019.02673480422Identification of Novel Putative Bacterial Feruloyl Esterases From Anaerobic Ecosystems by Use of Whole-Genome Shotgun Metagenomics and Genome BinningKamyar Mogodiniyai Kasmaei0John Sundh1Department of Animal Nutrition and Management, Swedish University of Agricultural Sciences, Uppsala, SwedenScience for Life Laboratory, Department of Biochemistry and Biophysics, National Bioinformatics Infrastructure Sweden, Stockholm University, Solna, SwedenFeruloyl esterases (FAEs) can reduce the recalcitrance of lignocellulosic biomass to enzymatic hydrolysis, thereby enhancing biorefinery potentials or animal feeding values of the biomass. In addition, ferulic acid, a product of FAE activity, has applications in pharmaceutical and food/beverage industries. It is therefore of great interest to identify new FAEs to enhance understanding about this enzyme family. For this purpose, we used whole-genome shotgun metagenomics and genome binning to explore rumens of dairy cows, large intestines of horses, sediments of freshwater and forest topsoils to identify novel prokaryotic FAEs and trace the responsible microorganisms. A number of prokaryotic genomes were recovered of which, genomes of Clostridiales order and Candidatus Rhabdochlamydia genus showed FAE coding capacities. In total, five sequences were deemed as putative FAE. The BLASTP search against non-redundant protein database of NCBI indicated that these putative FAEs represented novel sequences within this enzyme family. The phylogenetic analysis showed that at least three putative sequences shared evolutionary lineage with FAEs of type A and thus could possess specific activities similar to this type of FAEs, something that is not previously found outside fungal kingdom. We nominate Candidatus Rhabdochlamydia genus as a novel FAE producing taxonomic unit.https://www.frontiersin.org/article/10.3389/fmicb.2019.02673/fullbiorefineryde novo assemblylignocellulosic biomassphylogenetic analysissequence motiftaxonomic classification |
spellingShingle | Kamyar Mogodiniyai Kasmaei John Sundh Identification of Novel Putative Bacterial Feruloyl Esterases From Anaerobic Ecosystems by Use of Whole-Genome Shotgun Metagenomics and Genome Binning Frontiers in Microbiology biorefinery de novo assembly lignocellulosic biomass phylogenetic analysis sequence motif taxonomic classification |
title | Identification of Novel Putative Bacterial Feruloyl Esterases From Anaerobic Ecosystems by Use of Whole-Genome Shotgun Metagenomics and Genome Binning |
title_full | Identification of Novel Putative Bacterial Feruloyl Esterases From Anaerobic Ecosystems by Use of Whole-Genome Shotgun Metagenomics and Genome Binning |
title_fullStr | Identification of Novel Putative Bacterial Feruloyl Esterases From Anaerobic Ecosystems by Use of Whole-Genome Shotgun Metagenomics and Genome Binning |
title_full_unstemmed | Identification of Novel Putative Bacterial Feruloyl Esterases From Anaerobic Ecosystems by Use of Whole-Genome Shotgun Metagenomics and Genome Binning |
title_short | Identification of Novel Putative Bacterial Feruloyl Esterases From Anaerobic Ecosystems by Use of Whole-Genome Shotgun Metagenomics and Genome Binning |
title_sort | identification of novel putative bacterial feruloyl esterases from anaerobic ecosystems by use of whole genome shotgun metagenomics and genome binning |
topic | biorefinery de novo assembly lignocellulosic biomass phylogenetic analysis sequence motif taxonomic classification |
url | https://www.frontiersin.org/article/10.3389/fmicb.2019.02673/full |
work_keys_str_mv | AT kamyarmogodiniyaikasmaei identificationofnovelputativebacterialferuloylesterasesfromanaerobicecosystemsbyuseofwholegenomeshotgunmetagenomicsandgenomebinning AT johnsundh identificationofnovelputativebacterialferuloylesterasesfromanaerobicecosystemsbyuseofwholegenomeshotgunmetagenomicsandgenomebinning |