Sequence-based approach to finding functional lipases from microbial genome databases
Abstract A sequence-based approach was used to retrieve functional lipases from microbial genome databases. Many novel genes assigned as putative lipases were tested using the criteria of the typical lipase sequence rule, based on a consensus sequence of a catalytic triad (Ser, Asp, His) and oxyanio...
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| Veröffentlicht in: | FEMS microbiology letters 2004-06, Vol.235 (2), p.349-355 |
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| creator | Kwoun Kim, Hyung Jung, Yeo-Jin Choi, Won-Chan Ryu, Hyoung Seok Oh, Tae-Kwang Lee, Jung-Kee |
| description | Abstract
A sequence-based approach was used to retrieve functional lipases from microbial genome databases. Many novel genes assigned as putative lipases were tested using the criteria of the typical lipase sequence rule, based on a consensus sequence of a catalytic triad (Ser, Asp, His) and oxyanion hole sequence (HG). To obtain the lipase genes satisfying the sequence rule, PCR cloning was performed, while the lipase activities were tested using a tributyrin/tricaprylin plate and p-nitrophenyl caproate. Among nine putative lipases from four strains, five functional lipolytic proteins were obtained from Archaeoglobus fulgidus, Deinococcus radiodurans, and Agrobacterium tumefaciens. All five lipases exhibited a relatively low sequence similarity (less than 26.7%) with known lipases and turned out to belong to different lipase families. Accordingly, the current results indicate that the proposed strategic approach based on the microbial genome is an efficient and rapid method for finding novel and functional lipases. |
| doi_str_mv | 10.1111/j.1574-6968.2004.tb09609.x |
| format | Article |
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A sequence-based approach was used to retrieve functional lipases from microbial genome databases. Many novel genes assigned as putative lipases were tested using the criteria of the typical lipase sequence rule, based on a consensus sequence of a catalytic triad (Ser, Asp, His) and oxyanion hole sequence (HG). To obtain the lipase genes satisfying the sequence rule, PCR cloning was performed, while the lipase activities were tested using a tributyrin/tricaprylin plate and p-nitrophenyl caproate. Among nine putative lipases from four strains, five functional lipolytic proteins were obtained from Archaeoglobus fulgidus, Deinococcus radiodurans, and Agrobacterium tumefaciens. All five lipases exhibited a relatively low sequence similarity (less than 26.7%) with known lipases and turned out to belong to different lipase families. Accordingly, the current results indicate that the proposed strategic approach based on the microbial genome is an efficient and rapid method for finding novel and functional lipases.</description><identifier>ISSN: 0378-1097</identifier><identifier>EISSN: 1574-6968</identifier><identifier>DOI: 10.1111/j.1574-6968.2004.tb09609.x</identifier><language>eng</language><publisher>Oxford, UK: Blackwell Publishing Ltd</publisher><subject>Agrobacterium tumefaciens ; Archaeoglobus fulgidus ; Cloning ; Conserved sequence ; Deinococcus radiodurans ; Genes ; Genomes ; Lipase ; Microbial genome database ; Microbiology ; Microorganisms ; Nucleotide sequence ; p-Nitrophenyl-caproic acid</subject><ispartof>FEMS microbiology letters, 2004-06, Vol.235 (2), p.349-355</ispartof><rights>2004 Federation of European Microbiological Societies 2004</rights><rights>2004 Federation of European Microbiological Societies</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c3559-9c4efa281ae9f85eedd4dd5d170800039c62f1d1308e7e8ce7bef76e1391c7663</citedby><cites>FETCH-LOGICAL-c3559-9c4efa281ae9f85eedd4dd5d170800039c62f1d1308e7e8ce7bef76e1391c7663</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://onlinelibrary.wiley.com/doi/pdf/10.1111%2Fj.1574-6968.2004.tb09609.x$$EPDF$$P50$$Gwiley$$H</linktopdf><linktohtml>$$Uhttps://onlinelibrary.wiley.com/doi/full/10.1111%2Fj.1574-6968.2004.tb09609.x$$EHTML$$P50$$Gwiley$$H</linktohtml><link.rule.ids>314,780,784,1417,27923,27924,45573,45574</link.rule.ids></links><search><creatorcontrib>Kwoun Kim, Hyung</creatorcontrib><creatorcontrib>Jung, Yeo-Jin</creatorcontrib><creatorcontrib>Choi, Won-Chan</creatorcontrib><creatorcontrib>Ryu, Hyoung Seok</creatorcontrib><creatorcontrib>Oh, Tae-Kwang</creatorcontrib><creatorcontrib>Lee, Jung-Kee</creatorcontrib><title>Sequence-based approach to finding functional lipases from microbial genome databases</title><title>FEMS microbiology letters</title><description>Abstract
A sequence-based approach was used to retrieve functional lipases from microbial genome databases. Many novel genes assigned as putative lipases were tested using the criteria of the typical lipase sequence rule, based on a consensus sequence of a catalytic triad (Ser, Asp, His) and oxyanion hole sequence (HG). To obtain the lipase genes satisfying the sequence rule, PCR cloning was performed, while the lipase activities were tested using a tributyrin/tricaprylin plate and p-nitrophenyl caproate. Among nine putative lipases from four strains, five functional lipolytic proteins were obtained from Archaeoglobus fulgidus, Deinococcus radiodurans, and Agrobacterium tumefaciens. All five lipases exhibited a relatively low sequence similarity (less than 26.7%) with known lipases and turned out to belong to different lipase families. Accordingly, the current results indicate that the proposed strategic approach based on the microbial genome is an efficient and rapid method for finding novel and functional lipases.</description><subject>Agrobacterium tumefaciens</subject><subject>Archaeoglobus fulgidus</subject><subject>Cloning</subject><subject>Conserved sequence</subject><subject>Deinococcus radiodurans</subject><subject>Genes</subject><subject>Genomes</subject><subject>Lipase</subject><subject>Microbial genome database</subject><subject>Microbiology</subject><subject>Microorganisms</subject><subject>Nucleotide sequence</subject><subject>p-Nitrophenyl-caproic acid</subject><issn>0378-1097</issn><issn>1574-6968</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2004</creationdate><recordtype>article</recordtype><sourceid>ABUWG</sourceid><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><sourceid>GNUQQ</sourceid><recordid>eNqVkM1KxDAUhYMoOI6-Q9F1a9K0TeNCEHFUGHGhsw5pcjOm9M-mxZm3N6WDK12YzYXknJNzP4QuCY6IP9dlRFKWhBnP8ijGOImGAvMM82h3hBY_T8dogSnLQ4I5O0VnzpXYa2OcLdDmDT5HaBSEhXSgA9l1fSvVRzC0gbGNts02MGOjBts2sgoq23mZC0zf1kFtVd8W1l9voWlrCLQc5BTjztGJkZWDi8Ncos3q4f3-KVy_Pj7f361DRdOUh1wlYGScEwnc5CmA1onWqSYM574h5SqLDdGE4hwY5ApYAYZlQCgnimUZXaKrOdeX9mu4QZTt2PuiTsQUM8LihBKvuplVvq5zPRjR9baW_V4QLCaMohQTKzGxEhNGccAodt58O5u_bAX7fzjF6mVNE-4D0jmgHbs_7OFvH38D4ZWLRw</recordid><startdate>20040601</startdate><enddate>20040601</enddate><creator>Kwoun Kim, Hyung</creator><creator>Jung, Yeo-Jin</creator><creator>Choi, Won-Chan</creator><creator>Ryu, Hyoung Seok</creator><creator>Oh, Tae-Kwang</creator><creator>Lee, Jung-Kee</creator><general>Blackwell Publishing Ltd</general><general>Oxford University Press</general><scope>AAYXX</scope><scope>CITATION</scope><scope>3V.</scope><scope>7QL</scope><scope>7T7</scope><scope>7TK</scope><scope>7TM</scope><scope>7U9</scope><scope>7X7</scope><scope>7XB</scope><scope>88E</scope><scope>8AO</scope><scope>8C1</scope><scope>8FD</scope><scope>8FE</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABUWG</scope><scope>AEUYN</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>H94</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>LK8</scope><scope>M0S</scope><scope>M1P</scope><scope>M7N</scope><scope>M7P</scope><scope>P64</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>RC3</scope></search><sort><creationdate>20040601</creationdate><title>Sequence-based approach to finding functional lipases from microbial genome databases</title><author>Kwoun Kim, Hyung ; 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A sequence-based approach was used to retrieve functional lipases from microbial genome databases. Many novel genes assigned as putative lipases were tested using the criteria of the typical lipase sequence rule, based on a consensus sequence of a catalytic triad (Ser, Asp, His) and oxyanion hole sequence (HG). To obtain the lipase genes satisfying the sequence rule, PCR cloning was performed, while the lipase activities were tested using a tributyrin/tricaprylin plate and p-nitrophenyl caproate. Among nine putative lipases from four strains, five functional lipolytic proteins were obtained from Archaeoglobus fulgidus, Deinococcus radiodurans, and Agrobacterium tumefaciens. All five lipases exhibited a relatively low sequence similarity (less than 26.7%) with known lipases and turned out to belong to different lipase families. Accordingly, the current results indicate that the proposed strategic approach based on the microbial genome is an efficient and rapid method for finding novel and functional lipases.</abstract><cop>Oxford, UK</cop><pub>Blackwell Publishing Ltd</pub><doi>10.1111/j.1574-6968.2004.tb09609.x</doi><tpages>7</tpages><oa>free_for_read</oa></addata></record> |
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| ispartof | FEMS microbiology letters, 2004-06, Vol.235 (2), p.349-355 |
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| source | Oxford University Press Journals All Titles (1996-Current); Wiley Online Library All Journals; Alma/SFX Local Collection |
| subjects | Agrobacterium tumefaciens Archaeoglobus fulgidus Cloning Conserved sequence Deinococcus radiodurans Genes Genomes Lipase Microbial genome database Microbiology Microorganisms Nucleotide sequence p-Nitrophenyl-caproic acid |
| title | Sequence-based approach to finding functional lipases from microbial genome databases |
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