Transcriptomic analysis of xylan utilization systems in Paenibacillus sp. strain JDR-2
Xylans, including methylglucuronoxylans (MeGX(n)) and methylglucuronoarabinoxylans (MeGAXn), are the predominant polysaccharidesin hemicellulose fractions of dicots and monocots available for conversion to biofuels and chemicals. Paenibacillus sp. strain JDR-2 (Pjdr2) efficiently depolymerizes MeGX(...
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| Veröffentlicht in: | Applied and Environmental Microbiology 2015-02, Vol.81 (4), p.1490-1501 |
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| creator | Sawhney, Neha Crooks, Casey St John, Franz Preston, James F |
| description | Xylans, including methylglucuronoxylans (MeGX(n)) and methylglucuronoarabinoxylans (MeGAXn), are the predominant polysaccharidesin hemicellulose fractions of dicots and monocots available for conversion to biofuels and chemicals. Paenibacillus sp. strain JDR-2 (Pjdr2) efficiently depolymerizes MeGX(n) and MeGAX(n) and assimilates the generated oligosaccharides, resulting in efficient saccharification and subsequent metabolism of these polysaccharides. A xylan utilization regulon encoding a cellassociated GH10 (glycoside hydrolase family 10) endoxylanase, transcriptional regulators, ABC (ATP binding cassette) transporters, an intracellular GH67 -glucuronidase, and other glycoside hydrolases contributes to complete metabolism. This GH10/GH67 system has been proposed to account for preferential utilization of xylans compared to free oligo- and monosaccharides. To identify additional genes contributing to MeGX(n) and MeGAXn utilization, the transcriptome of Pjdr2 has been sequenced following growth on each of these substrates as well as xylose and arabinose. Increased expression of genes with different substrates identified pathways common or unique to the utilization of MeGX(n) or MeGAX(n). Coordinate upregulation of genes comprising the GH10/GH67 xylan utilization regulon is accompanied with upregulation of genes encoding a GH11 endoxylanase and a GH115 -glucuronidase, providing evidence for a novel complementary pathway for processing xylans. Elevated expression of genes encoding a GH43 arabinoxylan arabinofuranohydrolase and an arabinose ABC transporter on MeGAX(n) but not on MeGX(n) supports a process in which arabinose may be removed extracellularly followed by its rapid assimilation.Further development of Pjdr2 for direct conversion of xylans to targeted products or introduction of these systems into fermentative strains of related bacteria may lead to biocatalysts for consolidated bioprocessing of hemicelluloses released from lignocellulose. |
| doi_str_mv | 10.1128/AEM.03523-14 |
| format | Article |
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Paenibacillus sp. strain JDR-2 (Pjdr2) efficiently depolymerizes MeGX(n) and MeGAX(n) and assimilates the generated oligosaccharides, resulting in efficient saccharification and subsequent metabolism of these polysaccharides. A xylan utilization regulon encoding a cellassociated GH10 (glycoside hydrolase family 10) endoxylanase, transcriptional regulators, ABC (ATP binding cassette) transporters, an intracellular GH67 -glucuronidase, and other glycoside hydrolases contributes to complete metabolism. This GH10/GH67 system has been proposed to account for preferential utilization of xylans compared to free oligo- and monosaccharides. To identify additional genes contributing to MeGX(n) and MeGAXn utilization, the transcriptome of Pjdr2 has been sequenced following growth on each of these substrates as well as xylose and arabinose. Increased expression of genes with different substrates identified pathways common or unique to the utilization of MeGX(n) or MeGAX(n). Coordinate upregulation of genes comprising the GH10/GH67 xylan utilization regulon is accompanied with upregulation of genes encoding a GH11 endoxylanase and a GH115 -glucuronidase, providing evidence for a novel complementary pathway for processing xylans. Elevated expression of genes encoding a GH43 arabinoxylan arabinofuranohydrolase and an arabinose ABC transporter on MeGAX(n) but not on MeGX(n) supports a process in which arabinose may be removed extracellularly followed by its rapid assimilation.Further development of Pjdr2 for direct conversion of xylans to targeted products or introduction of these systems into fermentative strains of related bacteria may lead to biocatalysts for consolidated bioprocessing of hemicelluloses released from lignocellulose.</description><identifier>ISSN: 0099-2240</identifier><identifier>EISSN: 1098-5336</identifier><identifier>EISSN: 1098-6596</identifier><identifier>DOI: 10.1128/AEM.03523-14</identifier><identifier>PMID: 25527555</identifier><identifier>CODEN: AEMIDF</identifier><language>eng</language><publisher>United States: American Society for Microbiology</publisher><subject>Bacteria ; Bacterial Proteins - genetics ; Bacterial Proteins - metabolism ; Biotechnology ; Endo-1,4-beta Xylanases - genetics ; Endo-1,4-beta Xylanases - metabolism ; Enzymes ; Gene Expression Regulation, Bacterial ; Genes ; Glucuronidase - genetics ; Glucuronidase - metabolism ; Glycoside Hydrolases - genetics ; Glycoside Hydrolases - metabolism ; Paenibacillus ; Paenibacillus - enzymology ; Paenibacillus - genetics ; Paenibacillus - metabolism ; Polymers ; Substrates ; Transcription factors ; Transcriptome ; Xylans - metabolism</subject><ispartof>Applied and Environmental Microbiology, 2015-02, Vol.81 (4), p.1490-1501</ispartof><rights>Copyright American Society for Microbiology Feb 2015</rights><rights>Copyright © 2015, American Society for Microbiology. All Rights Reserved. 2015 American Society for Microbiology</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c445t-35f9b3a271f1aa8fae274cf64bcc58ffb79db4530b99bfa84a1a06897f8d083b3</citedby><cites>FETCH-LOGICAL-c445t-35f9b3a271f1aa8fae274cf64bcc58ffb79db4530b99bfa84a1a06897f8d083b3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4309694/pdf/$$EPDF$$P50$$Gpubmedcentral$$H</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4309694/$$EHTML$$P50$$Gpubmedcentral$$H</linktohtml><link.rule.ids>230,314,723,776,780,881,3175,27901,27902,53766,53768</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/25527555$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Sawhney, Neha</creatorcontrib><creatorcontrib>Crooks, Casey</creatorcontrib><creatorcontrib>St John, Franz</creatorcontrib><creatorcontrib>Preston, James F</creatorcontrib><title>Transcriptomic analysis of xylan utilization systems in Paenibacillus sp. strain JDR-2</title><title>Applied and Environmental Microbiology</title><addtitle>Appl Environ Microbiol</addtitle><description>Xylans, including methylglucuronoxylans (MeGX(n)) and methylglucuronoarabinoxylans (MeGAXn), are the predominant polysaccharidesin hemicellulose fractions of dicots and monocots available for conversion to biofuels and chemicals. Paenibacillus sp. strain JDR-2 (Pjdr2) efficiently depolymerizes MeGX(n) and MeGAX(n) and assimilates the generated oligosaccharides, resulting in efficient saccharification and subsequent metabolism of these polysaccharides. A xylan utilization regulon encoding a cellassociated GH10 (glycoside hydrolase family 10) endoxylanase, transcriptional regulators, ABC (ATP binding cassette) transporters, an intracellular GH67 -glucuronidase, and other glycoside hydrolases contributes to complete metabolism. This GH10/GH67 system has been proposed to account for preferential utilization of xylans compared to free oligo- and monosaccharides. To identify additional genes contributing to MeGX(n) and MeGAXn utilization, the transcriptome of Pjdr2 has been sequenced following growth on each of these substrates as well as xylose and arabinose. Increased expression of genes with different substrates identified pathways common or unique to the utilization of MeGX(n) or MeGAX(n). Coordinate upregulation of genes comprising the GH10/GH67 xylan utilization regulon is accompanied with upregulation of genes encoding a GH11 endoxylanase and a GH115 -glucuronidase, providing evidence for a novel complementary pathway for processing xylans. Elevated expression of genes encoding a GH43 arabinoxylan arabinofuranohydrolase and an arabinose ABC transporter on MeGAX(n) but not on MeGX(n) supports a process in which arabinose may be removed extracellularly followed by its rapid assimilation.Further development of Pjdr2 for direct conversion of xylans to targeted products or introduction of these systems into fermentative strains of related bacteria may lead to biocatalysts for consolidated bioprocessing of hemicelluloses released from lignocellulose.</description><subject>Bacteria</subject><subject>Bacterial Proteins - genetics</subject><subject>Bacterial Proteins - metabolism</subject><subject>Biotechnology</subject><subject>Endo-1,4-beta Xylanases - genetics</subject><subject>Endo-1,4-beta Xylanases - metabolism</subject><subject>Enzymes</subject><subject>Gene Expression Regulation, Bacterial</subject><subject>Genes</subject><subject>Glucuronidase - genetics</subject><subject>Glucuronidase - metabolism</subject><subject>Glycoside Hydrolases - genetics</subject><subject>Glycoside Hydrolases - metabolism</subject><subject>Paenibacillus</subject><subject>Paenibacillus - enzymology</subject><subject>Paenibacillus - genetics</subject><subject>Paenibacillus - metabolism</subject><subject>Polymers</subject><subject>Substrates</subject><subject>Transcription factors</subject><subject>Transcriptome</subject><subject>Xylans - metabolism</subject><issn>0099-2240</issn><issn>1098-5336</issn><issn>1098-6596</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2015</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqNkb1vFDEUxK0IlByBjhpZoqFgD3_u2g1SFJIACgKhkNZ69tngaHd9sXejHH99fPkSUFG9Yn4azbxB6CUlS0qZendw9GVJuGS8oWIHLSjRqpGct0_QghCtG8YE2UPPSrkghAjSql20x6RknZRygc7PMozF5bie0hAdhhH6TYkFp4CvNz2MeJ5iH3_DFNOIy6ZMfig4jvgb-DFacLHv54LLeonLlKEKnz98b9hz9DRAX_yL-7uPfhwfnR1-bE6_nnw6PDhtnBByargM2nJgHQ0UQAXwrBMutMI6J1UIttMrKyQnVmsbQAmgUBvoLqgVUdzyffT-znc928GvnB9riN6scxwgb0yCaP5WxvjL_ExXRnCiWy2qwZt7g5wuZ18mM8TifF-b-zQXQ1vVcS4FZ_-BtkQI2rW6oq__QS_SnOtrt5SkhLGO00q9vaNcTqVkHx5zU2K225q6rbnd1tBt1Fd_dn2EH8bkN0EFn8A</recordid><startdate>20150201</startdate><enddate>20150201</enddate><creator>Sawhney, Neha</creator><creator>Crooks, Casey</creator><creator>St John, Franz</creator><creator>Preston, James F</creator><general>American Society for Microbiology</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7QL</scope><scope>7QO</scope><scope>7SN</scope><scope>7SS</scope><scope>7ST</scope><scope>7T7</scope><scope>7TM</scope><scope>7U9</scope><scope>8FD</scope><scope>C1K</scope><scope>FR3</scope><scope>H94</scope><scope>M7N</scope><scope>P64</scope><scope>RC3</scope><scope>SOI</scope><scope>7X8</scope><scope>5PM</scope></search><sort><creationdate>20150201</creationdate><title>Transcriptomic analysis of xylan utilization systems in Paenibacillus sp. strain JDR-2</title><author>Sawhney, Neha ; Crooks, Casey ; St John, Franz ; Preston, James F</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c445t-35f9b3a271f1aa8fae274cf64bcc58ffb79db4530b99bfa84a1a06897f8d083b3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2015</creationdate><topic>Bacteria</topic><topic>Bacterial Proteins - genetics</topic><topic>Bacterial Proteins - metabolism</topic><topic>Biotechnology</topic><topic>Endo-1,4-beta Xylanases - genetics</topic><topic>Endo-1,4-beta Xylanases - metabolism</topic><topic>Enzymes</topic><topic>Gene Expression Regulation, Bacterial</topic><topic>Genes</topic><topic>Glucuronidase - genetics</topic><topic>Glucuronidase - metabolism</topic><topic>Glycoside Hydrolases - genetics</topic><topic>Glycoside Hydrolases - metabolism</topic><topic>Paenibacillus</topic><topic>Paenibacillus - enzymology</topic><topic>Paenibacillus - genetics</topic><topic>Paenibacillus - metabolism</topic><topic>Polymers</topic><topic>Substrates</topic><topic>Transcription factors</topic><topic>Transcriptome</topic><topic>Xylans - metabolism</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Sawhney, Neha</creatorcontrib><creatorcontrib>Crooks, Casey</creatorcontrib><creatorcontrib>St John, Franz</creatorcontrib><creatorcontrib>Preston, James F</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Bacteriology Abstracts (Microbiology B)</collection><collection>Biotechnology Research Abstracts</collection><collection>Ecology Abstracts</collection><collection>Entomology Abstracts (Full archive)</collection><collection>Environment Abstracts</collection><collection>Industrial and Applied Microbiology Abstracts (Microbiology A)</collection><collection>Nucleic Acids Abstracts</collection><collection>Virology and AIDS Abstracts</collection><collection>Technology Research Database</collection><collection>Environmental Sciences and Pollution Management</collection><collection>Engineering Research Database</collection><collection>AIDS and Cancer Research Abstracts</collection><collection>Algology Mycology and Protozoology Abstracts (Microbiology C)</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Genetics Abstracts</collection><collection>Environment Abstracts</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Applied and Environmental Microbiology</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Sawhney, Neha</au><au>Crooks, Casey</au><au>St John, Franz</au><au>Preston, James F</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Transcriptomic analysis of xylan utilization systems in Paenibacillus sp. strain JDR-2</atitle><jtitle>Applied and Environmental Microbiology</jtitle><addtitle>Appl Environ Microbiol</addtitle><date>2015-02-01</date><risdate>2015</risdate><volume>81</volume><issue>4</issue><spage>1490</spage><epage>1501</epage><pages>1490-1501</pages><issn>0099-2240</issn><eissn>1098-5336</eissn><eissn>1098-6596</eissn><coden>AEMIDF</coden><abstract>Xylans, including methylglucuronoxylans (MeGX(n)) and methylglucuronoarabinoxylans (MeGAXn), are the predominant polysaccharidesin hemicellulose fractions of dicots and monocots available for conversion to biofuels and chemicals. Paenibacillus sp. strain JDR-2 (Pjdr2) efficiently depolymerizes MeGX(n) and MeGAX(n) and assimilates the generated oligosaccharides, resulting in efficient saccharification and subsequent metabolism of these polysaccharides. A xylan utilization regulon encoding a cellassociated GH10 (glycoside hydrolase family 10) endoxylanase, transcriptional regulators, ABC (ATP binding cassette) transporters, an intracellular GH67 -glucuronidase, and other glycoside hydrolases contributes to complete metabolism. This GH10/GH67 system has been proposed to account for preferential utilization of xylans compared to free oligo- and monosaccharides. To identify additional genes contributing to MeGX(n) and MeGAXn utilization, the transcriptome of Pjdr2 has been sequenced following growth on each of these substrates as well as xylose and arabinose. Increased expression of genes with different substrates identified pathways common or unique to the utilization of MeGX(n) or MeGAX(n). Coordinate upregulation of genes comprising the GH10/GH67 xylan utilization regulon is accompanied with upregulation of genes encoding a GH11 endoxylanase and a GH115 -glucuronidase, providing evidence for a novel complementary pathway for processing xylans. Elevated expression of genes encoding a GH43 arabinoxylan arabinofuranohydrolase and an arabinose ABC transporter on MeGAX(n) but not on MeGX(n) supports a process in which arabinose may be removed extracellularly followed by its rapid assimilation.Further development of Pjdr2 for direct conversion of xylans to targeted products or introduction of these systems into fermentative strains of related bacteria may lead to biocatalysts for consolidated bioprocessing of hemicelluloses released from lignocellulose.</abstract><cop>United States</cop><pub>American Society for Microbiology</pub><pmid>25527555</pmid><doi>10.1128/AEM.03523-14</doi><tpages>12</tpages><oa>free_for_read</oa></addata></record> |
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| subjects | Bacteria Bacterial Proteins - genetics Bacterial Proteins - metabolism Biotechnology Endo-1,4-beta Xylanases - genetics Endo-1,4-beta Xylanases - metabolism Enzymes Gene Expression Regulation, Bacterial Genes Glucuronidase - genetics Glucuronidase - metabolism Glycoside Hydrolases - genetics Glycoside Hydrolases - metabolism Paenibacillus Paenibacillus - enzymology Paenibacillus - genetics Paenibacillus - metabolism Polymers Substrates Transcription factors Transcriptome Xylans - metabolism |
| title | Transcriptomic analysis of xylan utilization systems in Paenibacillus sp. strain JDR-2 |
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