Investigation, Expression, and Molecular Modeling of ORF2, a Metagenomic Lipolytic Enzyme
One clone exhibiting lipolytic activity was selected among 30 positives from a metagenomic library of a microbe consortium specialized in petroleum hydrocarbon degradation. From this clone, a sublibrary was constructed and a metagenome contig was assembled and analyzed using the ORF Finder; thus, it...
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| Veröffentlicht in: | Applied biochemistry and biotechnology 2015-04, Vol.175 (8), p.3875-3887 |
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| creator | Garcia, Rosmeriana Afnis Marioto Pereira, Mariana Rangel Maester, Thaís Carvalho de Macedo Lemos, Eliana Gertrudes |
| description | One clone exhibiting lipolytic activity was selected among 30 positives from a metagenomic library of a microbe consortium specialized in petroleum hydrocarbon degradation. From this clone, a sublibrary was constructed and a metagenome contig was assembled and analyzed using the ORF Finder; thus, it was possible to identify a potential ORF that encodes a lipolytic enzyme, denoted ORF2. This ORF is composed of 1035-bp 345 amino acids and displayed 98 % identity with an alpha/beta hydrolase from Pseudomonas nitroreducens (accession number WP024765380.1). When analyzed against a metagenome database, ORF2 also showed 76 % of sequence identity with a hypothetical protein from a marine metagenome (accession number ECT55726.1). The ProtParam analyses indicated that the recombinant protein ORF2 has a molecular mass approximately 39 kDa, as expected from its amino acid sequence, and based on phylogenetic analysis and molecular modeling, it was possible to suggest that ORF2 is a new member from family V. This enzyme exhibits the catalytic triad and conserved motifs typical from this family, wherein the serine residue is located in the central position of the conserved motif GASMGG. The orf2 gene was cloned in the expression vector pET28a, and the recombinant protein was superexpressed in Escherichia coli BL21(DE3) cells. The lipolytic activity of protein bands presented in a SDS-PAGE gel was confirmed by zymogram analyses, indicating ORF2 activity. These discoveries raise the possibility of employing this protein in biotechnological applications, such as bioremediation. |
| doi_str_mv | 10.1007/s12010-015-1556-8 |
| format | Article |
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From this clone, a sublibrary was constructed and a metagenome contig was assembled and analyzed using the ORF Finder; thus, it was possible to identify a potential ORF that encodes a lipolytic enzyme, denoted ORF2. This ORF is composed of 1035-bp 345 amino acids and displayed 98 % identity with an alpha/beta hydrolase from Pseudomonas nitroreducens (accession number WP024765380.1). When analyzed against a metagenome database, ORF2 also showed 76 % of sequence identity with a hypothetical protein from a marine metagenome (accession number ECT55726.1). The ProtParam analyses indicated that the recombinant protein ORF2 has a molecular mass approximately 39 kDa, as expected from its amino acid sequence, and based on phylogenetic analysis and molecular modeling, it was possible to suggest that ORF2 is a new member from family V. This enzyme exhibits the catalytic triad and conserved motifs typical from this family, wherein the serine residue is located in the central position of the conserved motif GASMGG. The orf2 gene was cloned in the expression vector pET28a, and the recombinant protein was superexpressed in Escherichia coli BL21(DE3) cells. The lipolytic activity of protein bands presented in a SDS-PAGE gel was confirmed by zymogram analyses, indicating ORF2 activity. These discoveries raise the possibility of employing this protein in biotechnological applications, such as bioremediation.</description><identifier>ISSN: 0273-2289</identifier><identifier>EISSN: 1559-0291</identifier><identifier>DOI: 10.1007/s12010-015-1556-8</identifier><identifier>PMID: 25764223</identifier><language>eng</language><publisher>Boston: Springer-Verlag</publisher><subject>Amino Acid Sequence ; amino acid sequences ; Amino acids ; Bacterial Proteins - biosynthesis ; Bacterial Proteins - chemistry ; Bacterial Proteins - genetics ; Bacterial Proteins - isolation & purification ; Biochemistry ; Bioremediation ; Biotechnology ; Chemistry ; Chemistry and Materials Science ; Cloning, Molecular ; E coli ; Enzymes ; Escherichia coli ; Gene Expression Regulation, Bacterial - genetics ; genes ; genomic libraries ; Metagenome - genetics ; Metagenomics ; Models, Molecular ; Molecular biology ; molecular models ; molecular weight ; open reading frames ; petroleum ; Petroleum - metabolism ; Petroleum - microbiology ; Petroleum hydrocarbons ; Phylogeny ; polyacrylamide gel electrophoresis ; Proteins ; Pseudomonas - enzymology ; Pseudomonas - genetics ; Pseudomonas nitroreducens ; recombinant proteins ; Sequence Alignment ; sequence analysis ; serine ; Substrate Specificity</subject><ispartof>Applied biochemistry and biotechnology, 2015-04, Vol.175 (8), p.3875-3887</ispartof><rights>Springer Science+Business Media New York 2015</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c499t-c7e7183274ecfdff35e34af54dc9d9a4e179cb656a0e6593b9d60220ef4117283</citedby><cites>FETCH-LOGICAL-c499t-c7e7183274ecfdff35e34af54dc9d9a4e179cb656a0e6593b9d60220ef4117283</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/s12010-015-1556-8$$EPDF$$P50$$Gspringer$$H</linktopdf><linktohtml>$$Uhttps://link.springer.com/10.1007/s12010-015-1556-8$$EHTML$$P50$$Gspringer$$H</linktohtml><link.rule.ids>314,780,784,27924,27925,41488,42557,51319</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/25764223$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Garcia, Rosmeriana Afnis Marioto</creatorcontrib><creatorcontrib>Pereira, Mariana Rangel</creatorcontrib><creatorcontrib>Maester, Thaís Carvalho</creatorcontrib><creatorcontrib>de Macedo Lemos, Eliana Gertrudes</creatorcontrib><title>Investigation, Expression, and Molecular Modeling of ORF2, a Metagenomic Lipolytic Enzyme</title><title>Applied biochemistry and biotechnology</title><addtitle>Appl Biochem Biotechnol</addtitle><addtitle>Appl Biochem Biotechnol</addtitle><description>One clone exhibiting lipolytic activity was selected among 30 positives from a metagenomic library of a microbe consortium specialized in petroleum hydrocarbon degradation. From this clone, a sublibrary was constructed and a metagenome contig was assembled and analyzed using the ORF Finder; thus, it was possible to identify a potential ORF that encodes a lipolytic enzyme, denoted ORF2. This ORF is composed of 1035-bp 345 amino acids and displayed 98 % identity with an alpha/beta hydrolase from Pseudomonas nitroreducens (accession number WP024765380.1). When analyzed against a metagenome database, ORF2 also showed 76 % of sequence identity with a hypothetical protein from a marine metagenome (accession number ECT55726.1). The ProtParam analyses indicated that the recombinant protein ORF2 has a molecular mass approximately 39 kDa, as expected from its amino acid sequence, and based on phylogenetic analysis and molecular modeling, it was possible to suggest that ORF2 is a new member from family V. This enzyme exhibits the catalytic triad and conserved motifs typical from this family, wherein the serine residue is located in the central position of the conserved motif GASMGG. The orf2 gene was cloned in the expression vector pET28a, and the recombinant protein was superexpressed in Escherichia coli BL21(DE3) cells. The lipolytic activity of protein bands presented in a SDS-PAGE gel was confirmed by zymogram analyses, indicating ORF2 activity. These discoveries raise the possibility of employing this protein in biotechnological applications, such as bioremediation.</description><subject>Amino Acid Sequence</subject><subject>amino acid sequences</subject><subject>Amino acids</subject><subject>Bacterial Proteins - biosynthesis</subject><subject>Bacterial Proteins - chemistry</subject><subject>Bacterial Proteins - genetics</subject><subject>Bacterial Proteins - isolation & purification</subject><subject>Biochemistry</subject><subject>Bioremediation</subject><subject>Biotechnology</subject><subject>Chemistry</subject><subject>Chemistry and Materials Science</subject><subject>Cloning, Molecular</subject><subject>E coli</subject><subject>Enzymes</subject><subject>Escherichia coli</subject><subject>Gene Expression Regulation, Bacterial - genetics</subject><subject>genes</subject><subject>genomic libraries</subject><subject>Metagenome - genetics</subject><subject>Metagenomics</subject><subject>Models, Molecular</subject><subject>Molecular biology</subject><subject>molecular models</subject><subject>molecular weight</subject><subject>open reading frames</subject><subject>petroleum</subject><subject>Petroleum - metabolism</subject><subject>Petroleum - microbiology</subject><subject>Petroleum hydrocarbons</subject><subject>Phylogeny</subject><subject>polyacrylamide gel electrophoresis</subject><subject>Proteins</subject><subject>Pseudomonas - enzymology</subject><subject>Pseudomonas - genetics</subject><subject>Pseudomonas nitroreducens</subject><subject>recombinant proteins</subject><subject>Sequence Alignment</subject><subject>sequence analysis</subject><subject>serine</subject><subject>Substrate Specificity</subject><issn>0273-2289</issn><issn>1559-0291</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2015</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>ABUWG</sourceid><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><sourceid>GNUQQ</sourceid><recordid>eNqNkU1v1DAQhi0EokvhB3CBSFw4EPD3xxFVW6i0VSWgB06W1xlHqZJ4sRPE9tfX25Sq4oB68ivNM-MZPQi9JvgjwVh9yoRigmtMRE2EkLV-glYlmBpTQ56iFaaK1ZRqc4Re5HyFMaFaqOfoiAolOaVshX6ejb8hT13rpi6OH6r1n12CnG-zG5vqPPbg596lkhrou7GtYqguvp3SUq_OYXItjHHofLXpdrHfTyWtx-v9AC_Rs-D6DK_u3mN0ebr-cfK13lx8OTv5vKk9N2aqvQJFNKOKgw9NCEwA4y4I3njTGMeBKOO3UkiHQQrDtqaRmFIMgROiqGbH6P0yd5fir7ncYocue-h7N0KcsyVSY840VuwRqFRGaipxQd_9g17FOY3lkAOliREc00KRhfIp5pwg2F3qBpf2lmB7UGQXRbYosgdF9rDvm7vJ83aA5r7jr5MC0AXIpTS2kB58_Z-pb5em4KJ1beqyvfxeIFGkS2mUZDeMtaK-</recordid><startdate>20150401</startdate><enddate>20150401</enddate><creator>Garcia, Rosmeriana Afnis Marioto</creator><creator>Pereira, Mariana Rangel</creator><creator>Maester, Thaís Carvalho</creator><creator>de Macedo Lemos, Eliana Gertrudes</creator><general>Springer-Verlag</general><general>Springer US</general><general>Springer Nature B.V</general><scope>FBQ</scope><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>3V.</scope><scope>7ST</scope><scope>7T7</scope><scope>7TM</scope><scope>7X7</scope><scope>7XB</scope><scope>88A</scope><scope>88E</scope><scope>88I</scope><scope>8AO</scope><scope>8FD</scope><scope>8FE</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABUWG</scope><scope>AFKRA</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BHPHI</scope><scope>C1K</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>FR3</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>LK8</scope><scope>M0S</scope><scope>M1P</scope><scope>M2P</scope><scope>M7P</scope><scope>P64</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>Q9U</scope><scope>RC3</scope><scope>SOI</scope><scope>7X8</scope><scope>7QO</scope><scope>7TN</scope><scope>F1W</scope><scope>H95</scope><scope>L.G</scope></search><sort><creationdate>20150401</creationdate><title>Investigation, Expression, and Molecular Modeling of ORF2, a Metagenomic Lipolytic Enzyme</title><author>Garcia, Rosmeriana Afnis Marioto ; Pereira, Mariana Rangel ; Maester, Thaís Carvalho ; de Macedo Lemos, Eliana Gertrudes</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c499t-c7e7183274ecfdff35e34af54dc9d9a4e179cb656a0e6593b9d60220ef4117283</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2015</creationdate><topic>Amino Acid Sequence</topic><topic>amino acid sequences</topic><topic>Amino acids</topic><topic>Bacterial Proteins - 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enzymology</topic><topic>Pseudomonas - genetics</topic><topic>Pseudomonas nitroreducens</topic><topic>recombinant proteins</topic><topic>Sequence Alignment</topic><topic>sequence analysis</topic><topic>serine</topic><topic>Substrate Specificity</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Garcia, Rosmeriana Afnis Marioto</creatorcontrib><creatorcontrib>Pereira, Mariana Rangel</creatorcontrib><creatorcontrib>Maester, Thaís Carvalho</creatorcontrib><creatorcontrib>de Macedo Lemos, Eliana Gertrudes</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>ProQuest Central (Corporate)</collection><collection>Environment Abstracts</collection><collection>Industrial and Applied Microbiology Abstracts (Microbiology A)</collection><collection>Nucleic Acids Abstracts</collection><collection>Health & Medical Collection</collection><collection>ProQuest Central (purchase pre-March 2016)</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>ProQuest Central (Alumni Edition)</collection><collection>ProQuest Central UK/Ireland</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>ProQuest Central</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>Health Research Premium Collection</collection><collection>Health Research Premium Collection (Alumni)</collection><collection>ProQuest Central Student</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>ProQuest Biological Science Collection</collection><collection>Health & Medical Collection (Alumni Edition)</collection><collection>Medical Database</collection><collection>Science Database</collection><collection>Biological Science Database</collection><collection>Biotechnology and BioEngineering Abstracts</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>Genetics Abstracts</collection><collection>Environment Abstracts</collection><collection>MEDLINE - Academic</collection><collection>Biotechnology Research Abstracts</collection><collection>Oceanic Abstracts</collection><collection>ASFA: Aquatic Sciences and Fisheries Abstracts</collection><collection>Aquatic Science & Fisheries Abstracts (ASFA) 1: Biological Sciences & Living Resources</collection><collection>Aquatic Science & Fisheries Abstracts (ASFA) Professional</collection><jtitle>Applied biochemistry and biotechnology</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Garcia, Rosmeriana Afnis Marioto</au><au>Pereira, Mariana Rangel</au><au>Maester, Thaís Carvalho</au><au>de Macedo Lemos, Eliana Gertrudes</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Investigation, Expression, and Molecular Modeling of ORF2, a Metagenomic Lipolytic Enzyme</atitle><jtitle>Applied biochemistry and biotechnology</jtitle><stitle>Appl Biochem Biotechnol</stitle><addtitle>Appl Biochem Biotechnol</addtitle><date>2015-04-01</date><risdate>2015</risdate><volume>175</volume><issue>8</issue><spage>3875</spage><epage>3887</epage><pages>3875-3887</pages><issn>0273-2289</issn><eissn>1559-0291</eissn><abstract>One clone exhibiting lipolytic activity was selected among 30 positives from a metagenomic library of a microbe consortium specialized in petroleum hydrocarbon degradation. From this clone, a sublibrary was constructed and a metagenome contig was assembled and analyzed using the ORF Finder; thus, it was possible to identify a potential ORF that encodes a lipolytic enzyme, denoted ORF2. This ORF is composed of 1035-bp 345 amino acids and displayed 98 % identity with an alpha/beta hydrolase from Pseudomonas nitroreducens (accession number WP024765380.1). When analyzed against a metagenome database, ORF2 also showed 76 % of sequence identity with a hypothetical protein from a marine metagenome (accession number ECT55726.1). The ProtParam analyses indicated that the recombinant protein ORF2 has a molecular mass approximately 39 kDa, as expected from its amino acid sequence, and based on phylogenetic analysis and molecular modeling, it was possible to suggest that ORF2 is a new member from family V. This enzyme exhibits the catalytic triad and conserved motifs typical from this family, wherein the serine residue is located in the central position of the conserved motif GASMGG. The orf2 gene was cloned in the expression vector pET28a, and the recombinant protein was superexpressed in Escherichia coli BL21(DE3) cells. The lipolytic activity of protein bands presented in a SDS-PAGE gel was confirmed by zymogram analyses, indicating ORF2 activity. These discoveries raise the possibility of employing this protein in biotechnological applications, such as bioremediation.</abstract><cop>Boston</cop><pub>Springer-Verlag</pub><pmid>25764223</pmid><doi>10.1007/s12010-015-1556-8</doi><tpages>13</tpages></addata></record> |
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| subjects | Amino Acid Sequence amino acid sequences Amino acids Bacterial Proteins - biosynthesis Bacterial Proteins - chemistry Bacterial Proteins - genetics Bacterial Proteins - isolation & purification Biochemistry Bioremediation Biotechnology Chemistry Chemistry and Materials Science Cloning, Molecular E coli Enzymes Escherichia coli Gene Expression Regulation, Bacterial - genetics genes genomic libraries Metagenome - genetics Metagenomics Models, Molecular Molecular biology molecular models molecular weight open reading frames petroleum Petroleum - metabolism Petroleum - microbiology Petroleum hydrocarbons Phylogeny polyacrylamide gel electrophoresis Proteins Pseudomonas - enzymology Pseudomonas - genetics Pseudomonas nitroreducens recombinant proteins Sequence Alignment sequence analysis serine Substrate Specificity |
| title | Investigation, Expression, and Molecular Modeling of ORF2, a Metagenomic Lipolytic Enzyme |
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