Identification and distribution of cellobiose 2-epimerase genes by a PCR-based metagenomic approach
Cellobiose 2-epimerase (CE) catalyzes the reversible epimerization of cellobiose to 4-O-β-D-glucopyranosyl-D-mannose. By using a PCR-based metagenomic approach, 71 ce-like gene fragments were obtained from wide-ranging environmental samples such as sheep rumen, soils, sugar beet extracts, and anaero...
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| Veröffentlicht in: | Applied microbiology and biotechnology 2015-05, Vol.99 (10), p.4287-4295 |
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| creator | Wasaki, Jun Taguchi, Hidenori Senoura, Takeshi Akasaka, Hiroshi Watanabe, Jun Kawaguchi, Kazuki Komata, Yosuke Hanashiro, Kiyotoshi Ito, Susumu |
| description | Cellobiose 2-epimerase (CE) catalyzes the reversible epimerization of cellobiose to 4-O-β-D-glucopyranosyl-D-mannose. By using a PCR-based metagenomic approach, 71 ce-like gene fragments were obtained from wide-ranging environmental samples such as sheep rumen, soils, sugar beet extracts, and anaerobic sewage sludge. The frequency of isolation of the fragments similar to known sequences varied depending on the nature of the samples used. The ce-like genes appeared to be widely distributed in environmental bacteria belonging to the phyla Bacteroidetes, Chloroflexi, Dictyoglomi, Firmicutes, Proteobacteria, Spirochaetes, and Verrucomicrobia. The phylogenetic analysis suggested that the cluster of CE and CE-like proteins was functionally and evolutionarily separated from that of N-acetyl-D-glucosamine 2-epimerase (AGE) and AGE-like proteins. Two ce-like genes containing full-length ORFs, designated md1 and md2, were obtained by PCR and expressed in Escherichia coli. The recombinant mD1 and mD2 exhibited low Kₘvalues and high catalytic efficiencies (kcₐₜ/Kₘ) for mannobiose compared with cellobiose, suggesting that they should be named mannobiose 2-epimerase, which is involved in a new mannan catabolic pathway we proposed. |
| doi_str_mv | 10.1007/s00253-014-6265-7 |
| format | Article |
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By using a PCR-based metagenomic approach, 71 ce-like gene fragments were obtained from wide-ranging environmental samples such as sheep rumen, soils, sugar beet extracts, and anaerobic sewage sludge. The frequency of isolation of the fragments similar to known sequences varied depending on the nature of the samples used. The ce-like genes appeared to be widely distributed in environmental bacteria belonging to the phyla Bacteroidetes, Chloroflexi, Dictyoglomi, Firmicutes, Proteobacteria, Spirochaetes, and Verrucomicrobia. The phylogenetic analysis suggested that the cluster of CE and CE-like proteins was functionally and evolutionarily separated from that of N-acetyl-D-glucosamine 2-epimerase (AGE) and AGE-like proteins. Two ce-like genes containing full-length ORFs, designated md1 and md2, were obtained by PCR and expressed in Escherichia coli. The recombinant mD1 and mD2 exhibited low Kₘvalues and high catalytic efficiencies (kcₐₜ/Kₘ) for mannobiose compared with cellobiose, suggesting that they should be named mannobiose 2-epimerase, which is involved in a new mannan catabolic pathway we proposed.</description><identifier>ISSN: 0175-7598</identifier><identifier>EISSN: 1432-0614</identifier><identifier>DOI: 10.1007/s00253-014-6265-7</identifier><identifier>PMID: 25487892</identifier><language>eng</language><publisher>Berlin/Heidelberg: Springer-Verlag</publisher><subject>Amino Acid Sequence ; Amino acids ; Analysis ; Animals ; Bacteria ; Bacteria - classification ; Bacteria - enzymology ; Bacteria - genetics ; Bacteria - isolation & purification ; Bacterial Proteins - chemistry ; Bacterial Proteins - genetics ; Bacterial Proteins - metabolism ; Biomedical and Life Sciences ; Biotechnologically Relevant Enzymes and Proteins ; Biotechnology ; cellobiose ; Cellobiose - metabolism ; Deoxyribonucleic acid ; Design ; DNA ; E coli ; Enzymes ; Escherichia coli ; Firmicutes ; Genes ; Genetic aspects ; Genetic recombination ; Identification and classification ; Isomerases ; Kinetics ; Life Sciences ; Metagenomics ; Methods ; Microbial Genetics and Genomics ; Microbiology ; Molecular Sequence Data ; Phylogeny ; Physiology ; Polymerase Chain Reaction ; Proteins ; Proteobacteria ; Racemases and Epimerases - chemistry ; Racemases and Epimerases - genetics ; Racemases and Epimerases - metabolism ; rumen ; Rumen - microbiology ; Sequence Alignment ; Sewage sludge ; Sheep ; soil ; Soil Microbiology ; Soil sciences ; Spirochaetales ; Studies ; Substrate Specificity ; sugar beet ; Verrucomicrobia ; Verrucomicrobium</subject><ispartof>Applied microbiology and biotechnology, 2015-05, Vol.99 (10), p.4287-4295</ispartof><rights>Springer-Verlag Berlin Heidelberg 2014</rights><rights>COPYRIGHT 2015 Springer</rights><rights>Springer-Verlag Berlin Heidelberg 2015</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c703t-b896c5e868388849253c6c7c51ed6d797e65c2dcbacc856b70e657b0357020273</citedby><cites>FETCH-LOGICAL-c703t-b896c5e868388849253c6c7c51ed6d797e65c2dcbacc856b70e657b0357020273</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://link.springer.com/content/pdf/10.1007/s00253-014-6265-7$$EPDF$$P50$$Gspringer$$H</linktopdf><linktohtml>$$Uhttps://link.springer.com/10.1007/s00253-014-6265-7$$EHTML$$P50$$Gspringer$$H</linktohtml><link.rule.ids>314,780,784,27923,27924,41487,42556,51318</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/25487892$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Wasaki, Jun</creatorcontrib><creatorcontrib>Taguchi, Hidenori</creatorcontrib><creatorcontrib>Senoura, Takeshi</creatorcontrib><creatorcontrib>Akasaka, Hiroshi</creatorcontrib><creatorcontrib>Watanabe, Jun</creatorcontrib><creatorcontrib>Kawaguchi, Kazuki</creatorcontrib><creatorcontrib>Komata, Yosuke</creatorcontrib><creatorcontrib>Hanashiro, Kiyotoshi</creatorcontrib><creatorcontrib>Ito, Susumu</creatorcontrib><title>Identification and distribution of cellobiose 2-epimerase genes by a PCR-based metagenomic approach</title><title>Applied microbiology and biotechnology</title><addtitle>Appl Microbiol Biotechnol</addtitle><addtitle>Appl Microbiol Biotechnol</addtitle><description>Cellobiose 2-epimerase (CE) catalyzes the reversible epimerization of cellobiose to 4-O-β-D-glucopyranosyl-D-mannose. By using a PCR-based metagenomic approach, 71 ce-like gene fragments were obtained from wide-ranging environmental samples such as sheep rumen, soils, sugar beet extracts, and anaerobic sewage sludge. The frequency of isolation of the fragments similar to known sequences varied depending on the nature of the samples used. The ce-like genes appeared to be widely distributed in environmental bacteria belonging to the phyla Bacteroidetes, Chloroflexi, Dictyoglomi, Firmicutes, Proteobacteria, Spirochaetes, and Verrucomicrobia. The phylogenetic analysis suggested that the cluster of CE and CE-like proteins was functionally and evolutionarily separated from that of N-acetyl-D-glucosamine 2-epimerase (AGE) and AGE-like proteins. Two ce-like genes containing full-length ORFs, designated md1 and md2, were obtained by PCR and expressed in Escherichia coli. The recombinant mD1 and mD2 exhibited low Kₘvalues and high catalytic efficiencies (kcₐₜ/Kₘ) for mannobiose compared with cellobiose, suggesting that they should be named mannobiose 2-epimerase, which is involved in a new mannan catabolic pathway we proposed.</description><subject>Amino Acid Sequence</subject><subject>Amino acids</subject><subject>Analysis</subject><subject>Animals</subject><subject>Bacteria</subject><subject>Bacteria - classification</subject><subject>Bacteria - enzymology</subject><subject>Bacteria - genetics</subject><subject>Bacteria - isolation & purification</subject><subject>Bacterial Proteins - chemistry</subject><subject>Bacterial Proteins - genetics</subject><subject>Bacterial Proteins - metabolism</subject><subject>Biomedical and Life Sciences</subject><subject>Biotechnologically Relevant Enzymes and Proteins</subject><subject>Biotechnology</subject><subject>cellobiose</subject><subject>Cellobiose - metabolism</subject><subject>Deoxyribonucleic acid</subject><subject>Design</subject><subject>DNA</subject><subject>E coli</subject><subject>Enzymes</subject><subject>Escherichia coli</subject><subject>Firmicutes</subject><subject>Genes</subject><subject>Genetic aspects</subject><subject>Genetic recombination</subject><subject>Identification and classification</subject><subject>Isomerases</subject><subject>Kinetics</subject><subject>Life Sciences</subject><subject>Metagenomics</subject><subject>Methods</subject><subject>Microbial Genetics and Genomics</subject><subject>Microbiology</subject><subject>Molecular Sequence Data</subject><subject>Phylogeny</subject><subject>Physiology</subject><subject>Polymerase Chain Reaction</subject><subject>Proteins</subject><subject>Proteobacteria</subject><subject>Racemases and Epimerases - 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classification</topic><topic>Bacteria - enzymology</topic><topic>Bacteria - genetics</topic><topic>Bacteria - isolation & purification</topic><topic>Bacterial Proteins - chemistry</topic><topic>Bacterial Proteins - genetics</topic><topic>Bacterial Proteins - metabolism</topic><topic>Biomedical and Life Sciences</topic><topic>Biotechnologically Relevant Enzymes and Proteins</topic><topic>Biotechnology</topic><topic>cellobiose</topic><topic>Cellobiose - metabolism</topic><topic>Deoxyribonucleic acid</topic><topic>Design</topic><topic>DNA</topic><topic>E coli</topic><topic>Enzymes</topic><topic>Escherichia coli</topic><topic>Firmicutes</topic><topic>Genes</topic><topic>Genetic aspects</topic><topic>Genetic recombination</topic><topic>Identification and classification</topic><topic>Isomerases</topic><topic>Kinetics</topic><topic>Life Sciences</topic><topic>Metagenomics</topic><topic>Methods</topic><topic>Microbial Genetics and Genomics</topic><topic>Microbiology</topic><topic>Molecular Sequence Data</topic><topic>Phylogeny</topic><topic>Physiology</topic><topic>Polymerase Chain Reaction</topic><topic>Proteins</topic><topic>Proteobacteria</topic><topic>Racemases and Epimerases - chemistry</topic><topic>Racemases and Epimerases - genetics</topic><topic>Racemases and Epimerases - metabolism</topic><topic>rumen</topic><topic>Rumen - microbiology</topic><topic>Sequence Alignment</topic><topic>Sewage sludge</topic><topic>Sheep</topic><topic>soil</topic><topic>Soil Microbiology</topic><topic>Soil sciences</topic><topic>Spirochaetales</topic><topic>Studies</topic><topic>Substrate Specificity</topic><topic>sugar beet</topic><topic>Verrucomicrobia</topic><topic>Verrucomicrobium</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Wasaki, Jun</creatorcontrib><creatorcontrib>Taguchi, Hidenori</creatorcontrib><creatorcontrib>Senoura, Takeshi</creatorcontrib><creatorcontrib>Akasaka, Hiroshi</creatorcontrib><creatorcontrib>Watanabe, Jun</creatorcontrib><creatorcontrib>Kawaguchi, Kazuki</creatorcontrib><creatorcontrib>Komata, Yosuke</creatorcontrib><creatorcontrib>Hanashiro, Kiyotoshi</creatorcontrib><creatorcontrib>Ito, Susumu</creatorcontrib><collection>AGRIS</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Gale In Context: Science</collection><collection>ProQuest Central (Corporate)</collection><collection>Bacteriology Abstracts (Microbiology B)</collection><collection>Industrial and Applied Microbiology Abstracts (Microbiology A)</collection><collection>ABI/INFORM Collection</collection><collection>ABI/INFORM Global (PDF only)</collection><collection>Health & Medical Collection</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>ABI/INFORM Global (Alumni Edition)</collection><collection>Biology Database (Alumni Edition)</collection><collection>Medical Database (Alumni Edition)</collection><collection>Science Database (Alumni Edition)</collection><collection>ProQuest Pharma Collection</collection><collection>Technology Research Database</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>Hospital Premium Collection</collection><collection>Hospital Premium Collection (Alumni Edition)</collection><collection>ProQuest Central (Alumni) (purchase pre-March 2016)</collection><collection>ABI/INFORM Collection (Alumni Edition)</collection><collection>ProQuest Central (Alumni Edition)</collection><collection>ProQuest One Sustainability</collection><collection>ProQuest Central UK/Ireland</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>ProQuest Central</collection><collection>Business Premium Collection</collection><collection>Natural Science Collection</collection><collection>Environmental Sciences and Pollution Management</collection><collection>ProQuest One Community College</collection><collection>ProQuest Central Korea</collection><collection>Engineering Research Database</collection><collection>Business Premium Collection (Alumni)</collection><collection>Health Research Premium Collection</collection><collection>ABI/INFORM Global (Corporate)</collection><collection>Health Research Premium Collection (Alumni)</collection><collection>ProQuest Central Student</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Business Collection (Alumni Edition)</collection><collection>ProQuest Business Collection</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>ABI/INFORM Professional Advanced</collection><collection>ProQuest Biological Science Collection</collection><collection>ABI/INFORM Global</collection><collection>Health & Medical Collection (Alumni Edition)</collection><collection>Medical Database</collection><collection>Science Database</collection><collection>Algology Mycology and Protozoology Abstracts (Microbiology C)</collection><collection>Biological Science Database</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>ProQuest One Business</collection><collection>ProQuest One Business (Alumni)</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>ProQuest Central Basic</collection><collection>MEDLINE - 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By using a PCR-based metagenomic approach, 71 ce-like gene fragments were obtained from wide-ranging environmental samples such as sheep rumen, soils, sugar beet extracts, and anaerobic sewage sludge. The frequency of isolation of the fragments similar to known sequences varied depending on the nature of the samples used. The ce-like genes appeared to be widely distributed in environmental bacteria belonging to the phyla Bacteroidetes, Chloroflexi, Dictyoglomi, Firmicutes, Proteobacteria, Spirochaetes, and Verrucomicrobia. The phylogenetic analysis suggested that the cluster of CE and CE-like proteins was functionally and evolutionarily separated from that of N-acetyl-D-glucosamine 2-epimerase (AGE) and AGE-like proteins. Two ce-like genes containing full-length ORFs, designated md1 and md2, were obtained by PCR and expressed in Escherichia coli. The recombinant mD1 and mD2 exhibited low Kₘvalues and high catalytic efficiencies (kcₐₜ/Kₘ) for mannobiose compared with cellobiose, suggesting that they should be named mannobiose 2-epimerase, which is involved in a new mannan catabolic pathway we proposed.</abstract><cop>Berlin/Heidelberg</cop><pub>Springer-Verlag</pub><pmid>25487892</pmid><doi>10.1007/s00253-014-6265-7</doi><tpages>9</tpages></addata></record> |
| fulltext | fulltext |
| identifier | ISSN: 0175-7598 |
| ispartof | Applied microbiology and biotechnology, 2015-05, Vol.99 (10), p.4287-4295 |
| issn | 0175-7598 1432-0614 |
| language | eng |
| recordid | cdi_proquest_miscellaneous_1683348157 |
| source | MEDLINE; SpringerLink Journals - AutoHoldings |
| subjects | Amino Acid Sequence Amino acids Analysis Animals Bacteria Bacteria - classification Bacteria - enzymology Bacteria - genetics Bacteria - isolation & purification Bacterial Proteins - chemistry Bacterial Proteins - genetics Bacterial Proteins - metabolism Biomedical and Life Sciences Biotechnologically Relevant Enzymes and Proteins Biotechnology cellobiose Cellobiose - metabolism Deoxyribonucleic acid Design DNA E coli Enzymes Escherichia coli Firmicutes Genes Genetic aspects Genetic recombination Identification and classification Isomerases Kinetics Life Sciences Metagenomics Methods Microbial Genetics and Genomics Microbiology Molecular Sequence Data Phylogeny Physiology Polymerase Chain Reaction Proteins Proteobacteria Racemases and Epimerases - chemistry Racemases and Epimerases - genetics Racemases and Epimerases - metabolism rumen Rumen - microbiology Sequence Alignment Sewage sludge Sheep soil Soil Microbiology Soil sciences Spirochaetales Studies Substrate Specificity sugar beet Verrucomicrobia Verrucomicrobium |
| title | Identification and distribution of cellobiose 2-epimerase genes by a PCR-based metagenomic approach |
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