Carbohydrate-active enzymes identified by metagenomic analysis of deep-sea sediment bacteria
Klippel B, Sahm K, Basner A, Wiebusch S, John P, Lorenz U, Peters A, Abe F, Takahashi K, Kaiser O, Goesmann A, et al. (2014)
Extremophiles 18(5): 853-863.
Zeitschriftenaufsatz
| Veröffentlicht | Englisch
Download
Es wurden keine Dateien hochgeladen. Nur Publikationsnachweis!
Autor*in
Klippel, Barbara;
Sahm, Kerstin;
Basner, Alexander;
Wiebusch, Sigrid;
John, Patrick;
Lorenz, Ute;
Peters, Anke;
Abe, Fumiyoshi;
Takahashi, Kyoma;
Kaiser, Olaf;
Goesmann, AlexanderUniBi 
;
Jaenicke, SebastianUniBi
Alle
;
Jaenicke, SebastianUniBi
Alle
Einrichtung
Abstract / Bemerkung
Subseafloor sediment samples derived from a sediment core of 60m length were used to enrich psychrophilic aerobic bacteria on cellulose, xylan, chitin, and starch. A variety of species belonging to Alpha- and Gammaproteobacteria and to Flavobacteria were isolated from sediment depths between 12 and 42mbsf. Metagenomic DNA purified from the pooled enrichments was sequenced and analyzed for phylogenetic composition and presence of genes encoding carbohydrate-active enzymes. More than 200 open reading frames coding for glycoside hydrolases were identified, and more than 60 of them relevant for enzymatic degradation of lignocellulose. Four genes encoding beta-glucosidases with less than 52% identities to characterized enzymes were chosen for recombinant expression in Escherichia coli. In addition one endomannanase, two endoxylanases, and three beta-xylosidases were produced recombinantly. All genes could be actively expressed. Functional analysis revealed discrepancies and additional variability for the recombinant enzymes as compared to the sequence-based predictions.
Erscheinungsjahr
2014
Zeitschriftentitel
Extremophiles
Band
18
Ausgabe
5
Seite(n)
853-863
ISSN
1431-0651
eISSN
1433-4909
Page URI
https://pub.uni-bielefeld.de/record/2691732
Zitieren
Klippel B, Sahm K, Basner A, et al. Carbohydrate-active enzymes identified by metagenomic analysis of deep-sea sediment bacteria. Extremophiles. 2014;18(5):853-863.
Klippel, B., Sahm, K., Basner, A., Wiebusch, S., John, P., Lorenz, U., Peters, A., et al. (2014). Carbohydrate-active enzymes identified by metagenomic analysis of deep-sea sediment bacteria. Extremophiles, 18(5), 853-863. doi:10.1007/s00792-014-0676-3
Klippel, Barbara, Sahm, Kerstin, Basner, Alexander, Wiebusch, Sigrid, John, Patrick, Lorenz, Ute, Peters, Anke, et al. 2014. “Carbohydrate-active enzymes identified by metagenomic analysis of deep-sea sediment bacteria”. Extremophiles 18 (5): 853-863.
Klippel, B., Sahm, K., Basner, A., Wiebusch, S., John, P., Lorenz, U., Peters, A., Abe, F., Takahashi, K., Kaiser, O., et al. (2014). Carbohydrate-active enzymes identified by metagenomic analysis of deep-sea sediment bacteria. Extremophiles 18, 853-863.
Klippel, B., et al., 2014. Carbohydrate-active enzymes identified by metagenomic analysis of deep-sea sediment bacteria. Extremophiles, 18(5), p 853-863.
B. Klippel, et al., “Carbohydrate-active enzymes identified by metagenomic analysis of deep-sea sediment bacteria”, Extremophiles, vol. 18, 2014, pp. 853-863.
Klippel, B., Sahm, K., Basner, A., Wiebusch, S., John, P., Lorenz, U., Peters, A., Abe, F., Takahashi, K., Kaiser, O., Goesmann, A., Jaenicke, S., Grote, R., Horikoshi, K., Antranikian, G.: Carbohydrate-active enzymes identified by metagenomic analysis of deep-sea sediment bacteria. Extremophiles. 18, 853-863 (2014).
Klippel, Barbara, Sahm, Kerstin, Basner, Alexander, Wiebusch, Sigrid, John, Patrick, Lorenz, Ute, Peters, Anke, Abe, Fumiyoshi, Takahashi, Kyoma, Kaiser, Olaf, Goesmann, Alexander, Jaenicke, Sebastian, Grote, Ralf, Horikoshi, Koki, and Antranikian, Garabed. “Carbohydrate-active enzymes identified by metagenomic analysis of deep-sea sediment bacteria”. Extremophiles 18.5 (2014): 853-863.
Daten bereitgestellt von European Bioinformatics Institute (EBI)
8 Zitationen in Europe PMC
Daten bereitgestellt von Europe PubMed Central.
Microbial Organic Matter Degradation Potential in Baltic Sea Sediments Is Influenced by Depositional Conditions and In Situ Geochemistry.
Zinke LA, Glombitza C, Bird JT, Røy H, Jørgensen BB, Lloyd KG, Amend JP, Reese BK., Appl Environ Microbiol 85(4), 2019
PMID: 30504213
Zinke LA, Glombitza C, Bird JT, Røy H, Jørgensen BB, Lloyd KG, Amend JP, Reese BK., Appl Environ Microbiol 85(4), 2019
PMID: 30504213
Complete genome sequence of Lutibacter profundi LP1T isolated from an Arctic deep-sea hydrothermal vent system.
Wissuwa J, Bauer SL, Steen IH, Stokke R., Stand Genomic Sci 12(), 2017
PMID: 28078050
Wissuwa J, Bauer SL, Steen IH, Stokke R., Stand Genomic Sci 12(), 2017
PMID: 28078050
Diversity of Microbial Carbohydrate-Active enZYmes (CAZYmes) Associated with Freshwater and Soil Samples from Caatinga Biome.
Andrade AC, Fróes A, Lopes FÁC, Thompson FL, Krüger RH, Dinsdale E, Bruce T., Microb Ecol 74(1), 2017
PMID: 28070679
Andrade AC, Fróes A, Lopes FÁC, Thompson FL, Krüger RH, Dinsdale E, Bruce T., Microb Ecol 74(1), 2017
PMID: 28070679
Microbial Diversity in Extreme Marine Habitats and Their Biomolecules.
Poli A, Finore I, Romano I, Gioiello A, Lama L, Nicolaus B., Microorganisms 5(2), 2017
PMID: 28509857
Poli A, Finore I, Romano I, Gioiello A, Lama L, Nicolaus B., Microorganisms 5(2), 2017
PMID: 28509857
Novel archaeal thermostable cellulases from an oil reservoir metagenome.
Lewin A, Zhou J, Pham VTT, Haugen T, Zeiny ME, Aarstad O, Liebl W, Wentzel A, Liles MR., AMB Express 7(1), 2017
PMID: 28963711
Lewin A, Zhou J, Pham VTT, Haugen T, Zeiny ME, Aarstad O, Liebl W, Wentzel A, Liles MR., AMB Express 7(1), 2017
PMID: 28963711
Metagenomics: novel enzymes from non-culturable microbes.
Berini F, Casciello C, Marcone GL, Marinelli F., FEMS Microbiol Lett 364(21), 2017
PMID: 29029060
Berini F, Casciello C, Marcone GL, Marinelli F., FEMS Microbiol Lett 364(21), 2017
PMID: 29029060
Metagenomics for the development of new biocatalysts to advance lignocellulose saccharification for bioeconomic development.
Montella S, Amore A, Faraco V., Crit Rev Biotechnol 36(6), 2016
PMID: 26381035
Montella S, Amore A, Faraco V., Crit Rev Biotechnol 36(6), 2016
PMID: 26381035
International conference on extremophiles 2014.
Antranikian G, Bonch-Osmolovskaya E, Atomi H, Oren A, Adams MW, Santos H., Extremophiles 18(5), 2014
PMID: 25159180
Antranikian G, Bonch-Osmolovskaya E, Atomi H, Oren A, Adams MW, Santos H., Extremophiles 18(5), 2014
PMID: 25159180
49 References
Daten bereitgestellt von Europe PubMed Central.
Enzyme system of Clostridium stercorarium for hydrolysis of arabinoxylan: reconstitution of the in vivo system from recombinant enzymes.
Adelsberger H, Hertel C, Glawischnig E, Zverlov VV, Schwarz WH., Microbiology (Reading, Engl.) 150(Pt 7), 2004
PMID: 15256568
Adelsberger H, Hertel C, Glawischnig E, Zverlov VV, Schwarz WH., Microbiology (Reading, Engl.) 150(Pt 7), 2004
PMID: 15256568
Basic local alignment search tool.
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ., J. Mol. Biol. 215(3), 1990
PMID: 2231712
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ., J. Mol. Biol. 215(3), 1990
PMID: 2231712
Competition for polymers among heterotrophic bacteria, isolated from particles of the Equatorial Atlantic.
Berkenheger I, Fischer U., Int. Microbiol. 7(1), 2004
PMID: 15179602
Berkenheger I, Fischer U., Int. Microbiol. 7(1), 2004
PMID: 15179602
Insights into bacterial cellulose biosynthesis by functional metagenomics on Antarctic soil samples.
Berlemont R, Delsaute M, Pipers D, D'Amico S, Feller G, Galleni M, Power P., ISME J 3(9), 2009
PMID: 19458657
Berlemont R, Delsaute M, Pipers D, D'Amico S, Feller G, Galleni M, Power P., ISME J 3(9), 2009
PMID: 19458657
P, Methods Enzymol 1(), 1955
A, Mar Ecol Prog Ser 140(), 1996
The Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics.
Cantarel BL, Coutinho PM, Rancurel C, Bernard T, Lombard V, Henrissat B., Nucleic Acids Res. 37(Database issue), 2008
PMID: 18838391
Cantarel BL, Coutinho PM, Rancurel C, Bernard T, Lombard V, Henrissat B., Nucleic Acids Res. 37(Database issue), 2008
PMID: 18838391
Maribacter arcticus sp. nov., isolated from Arctic marine sediment.
Cho KH, Hong SG, Cho HH, Lee YK, Chun J, Lee HK., Int. J. Syst. Evol. Microbiol. 58(Pt 6), 2008
PMID: 18523168
Cho KH, Hong SG, Cho HH, Lee YK, Chun J, Lee HK., Int. J. Syst. Evol. Microbiol. 58(Pt 6), 2008
PMID: 18523168
Identification of carbohydrate metabolism genes in the metagenome of a marine biofilm community shown to be dominated by gammaproteobacteria and bacteroidetes.
Edwards JL, Smith DL, Connolly J, McDonald JE, Cox MJ, Joint I, Edwards C, McCarthy AJ., Genes (Basel) 1(3), 2010
PMID: 24710093
Edwards JL, Smith DL, Connolly J, McDonald JE, Cox MJ, Joint I, Edwards C, McCarthy AJ., Genes (Basel) 1(3), 2010
PMID: 24710093
E, Boletin de la Sociedad Geol Mexicana 61(1), 2009
Prokaryotic biodiversity and activity in the deep subseafloor biosphere.
Fry JC, Parkes RJ, Cragg BA, Weightman AJ, Webster G., FEMS Microbiol. Ecol. 66(2), 2008
PMID: 18752622
Fry JC, Parkes RJ, Cragg BA, Weightman AJ, Webster G., FEMS Microbiol. Ecol. 66(2), 2008
PMID: 18752622
Marine microbial genomics in Europe: current status and perspectives.
Glockner FO, Joint I., Microb Biotechnol 3(5), 2010
PMID: 20953416
Glockner FO, Joint I., Microb Biotechnol 3(5), 2010
PMID: 20953416
Gene cloning, expression and characterization of a new cold-active and salt-tolerant endo-beta-1,4-xylanase from marine Glaciecola mesophila KMM 241.
Guo B, Chen XL, Sun CY, Zhou BC, Zhang YZ., Appl. Microbiol. Biotechnol. 84(6), 2009
PMID: 19506861
Guo B, Chen XL, Sun CY, Zhou BC, Zhang YZ., Appl. Microbiol. Biotechnol. 84(6), 2009
PMID: 19506861
Gene cloning, expression and characterization of a novel xylanase from the marine bacterium, Glaciecola mesophila KMM241.
Guo B, Li PY, Yue YS, Zhao HL, Dong S, Song XY, Sun CY, Zhang WX, Chen XL, Zhang XY, Zhou BC, Zhang YZ., Mar Drugs 11(4), 2013
PMID: 23567318
Guo B, Li PY, Yue YS, Zhao HL, Dong S, Song XY, Sun CY, Zhang WX, Chen XL, Zhang XY, Zhou BC, Zhang YZ., Mar Drugs 11(4), 2013
PMID: 23567318
Genome sequence of Rheinheimera sp. strain A13L, isolated from Pangong Lake, India.
Gupta HK, Gupta RD, Singh A, Chauhan NS, Sharma R., J. Bacteriol. 193(20), 2011
PMID: 21742876
Gupta HK, Gupta RD, Singh A, Chauhan NS, Sharma R., J. Bacteriol. 193(20), 2011
PMID: 21742876
Crystal structure of a key enzyme in the agarolytic pathway, α-neoagarobiose hydrolase from Saccharophagus degradans 2-40.
Ha SC, Lee S, Lee J, Kim HT, Ko HJ, Kim KH, Choi IG., Biochem. Biophys. Res. Commun. 412(2), 2011
PMID: 21810409
Ha SC, Lee S, Lee J, Kim HT, Ko HJ, Kim KH, Choi IG., Biochem. Biophys. Res. Commun. 412(2), 2011
PMID: 21810409
B, Biochem J 280(Pt 2), 1991
Classification of glycoside hydrolases and glycosyltransferases from hyperthermophiles.
Henrissat B, Coutinho PM., Meth. Enzymol. 330(), 2001
PMID: 11210498
Henrissat B, Coutinho PM., Meth. Enzymol. 330(), 2001
PMID: 11210498
Microbial communities associated with geological horizons in coastal subseafloor sediments from the sea of okhotsk.
Inagaki F, Suzuki M, Takai K, Oida H, Sakamoto T, Aoki K, Nealson KH, Horikoshi K., Appl. Environ. Microbiol. 69(12), 2003
PMID: 14660370
Inagaki F, Suzuki M, Takai K, Oida H, Sakamoto T, Aoki K, Nealson KH, Horikoshi K., Appl. Environ. Microbiol. 69(12), 2003
PMID: 14660370
Feast and famine--microbial life in the deep-sea bed.
Jorgensen BB, Boetius A., Nat. Rev. Microbiol. 5(10), 2007
PMID: 17828281
Jorgensen BB, Boetius A., Nat. Rev. Microbiol. 5(10), 2007
PMID: 17828281
C, Polar Biol 32(), 2008
Complete genome sequence of the marine cellulose- and xylan-degrading bacterium Glaciecola sp. strain 4H-3-7+YE-5.
Klippel B, Lochner A, Bruce DC, Davenport KW, Detter C, Goodwin LA, Han J, Han S, Land ML, Mikhailova N, Nolan M, Pennacchio L, Pitluck S, Tapia R, Woyke T, Wiebusch S, Basner A, Abe F, Horikoshi K, Keller M, Antranikian G., J. Bacteriol. 193(17), 2011
PMID: 21705587
Klippel B, Lochner A, Bruce DC, Davenport KW, Detter C, Goodwin LA, Han J, Han S, Land ML, Mikhailova N, Nolan M, Pennacchio L, Pitluck S, Tapia R, Woyke T, Wiebusch S, Basner A, Abe F, Horikoshi K, Keller M, Antranikian G., J. Bacteriol. 193(17), 2011
PMID: 21705587
Molecular analysis of deep subsurface microbial communities in Nankai Trough sediments (ODP Leg 190, Site 1176).
Kormas KA, Smith DC, Edgcomb V, Teske A., FEMS Microbiol. Ecol. 45(2), 2003
PMID: 19719622
Kormas KA, Smith DC, Edgcomb V, Teske A., FEMS Microbiol. Ecol. 45(2), 2003
PMID: 19719622
Sequence of the Clostridium thermocellum mannanase gene man26B and characterization of the translated product.
Kurokawa J, Hemjinda E, Arai T, Karita S, Kimura T, Sakka K, Ohmiya K., Biosci. Biotechnol. Biochem. 65(3), 2001
PMID: 11330667
Kurokawa J, Hemjinda E, Arai T, Karita S, Kimura T, Sakka K, Ohmiya K., Biosci. Biotechnol. Biochem. 65(3), 2001
PMID: 11330667
Divalent metal activation of a GH43 β-xylosidase.
Lee CC, Braker JD, Grigorescu AA, Wagschal K, Jordan DB., Enzyme Microb. Technol. 52(2), 2012
PMID: 23273276
Lee CC, Braker JD, Grigorescu AA, Wagschal K, Jordan DB., Enzyme Microb. Technol. 52(2), 2012
PMID: 23273276
Bacterial diversity in surface sediments from the Pacific Arctic Ocean.
Li H, Yu Y, Luo W, Zeng Y, Chen B., Extremophiles 13(2), 2009
PMID: 19153801
Li H, Yu Y, Luo W, Zeng Y, Chen B., Extremophiles 13(2), 2009
PMID: 19153801
Rheinheimera nanhaiensis sp. nov., isolated from marine sediments, and emended description of the genus Rheinheimera Brettar et al. 2002 emend. Merchant et al. 2007.
Li HJ, Zhang XY, Zhang YJ, Zhou MY, Gao ZM, Chen XL, Dang HY, Zhang YZ., Int. J. Syst. Evol. Microbiol. 61(Pt 5), 2010
PMID: 20511463
Li HJ, Zhang XY, Zhang YJ, Zhou MY, Gao ZM, Chen XL, Dang HY, Zhang YZ., Int. J. Syst. Evol. Microbiol. 61(Pt 5), 2010
PMID: 20511463
AUTHOR UNKNOWN, 0
The carbohydrate-active enzymes database (CAZy) in 2013.
Lombard V, Golaconda Ramulu H, Drula E, Coutinho PM, Henrissat B., Nucleic Acids Res. 42(Database issue), 2013
PMID: 24270786
Lombard V, Golaconda Ramulu H, Drula E, Coutinho PM, Henrissat B., Nucleic Acids Res. 42(Database issue), 2013
PMID: 24270786
M, J Oceanogr 49(), 1993
BA, Proc Natl Acad Sci USA 102(31), 2005
GenDB--an open source genome annotation system for prokaryote genomes.
Meyer F, Goesmann A, McHardy AC, Bartels D, Bekel T, Clausen J, Kalinowski J, Linke B, Rupp O, Giegerich R, Puhler A., Nucleic Acids Res. 31(8), 2003
PMID: 12682369
Meyer F, Goesmann A, McHardy AC, Bartels D, Bekel T, Clausen J, Kalinowski J, Linke B, Rupp O, Giegerich R, Puhler A., Nucleic Acids Res. 31(8), 2003
PMID: 12682369
G, 1998
T, Geochem J 24(), 1990
Colwellia piezophila sp. nov., a novel piezophilic species from deep-sea sediments of the Japan Trench.
Nogi Y, Hosoya S, Kato C, Horikoshi K., Int. J. Syst. Evol. Microbiol. 54(Pt 5), 2004
PMID: 15388720
Nogi Y, Hosoya S, Kato C, Horikoshi K., Int. J. Syst. Evol. Microbiol. 54(Pt 5), 2004
PMID: 15388720
Coupled high-throughput functional screening and next generation sequencing for identification of plant polymer decomposing enzymes in metagenomic libraries.
Nyyssonen M, Tran HM, Karaoz U, Weihe C, Hadi MZ, Martiny JB, Martiny AC, Brodie EL., Front Microbiol 4(), 2013
PMID: 24069019
Nyyssonen M, Tran HM, Karaoz U, Weihe C, Hadi MZ, Martiny JB, Martiny AC, Brodie EL., Front Microbiol 4(), 2013
PMID: 24069019
CAZymes Analysis Toolkit (CAT): web service for searching and analyzing carbohydrate-active enzymes in a newly sequenced organism using CAZy database.
Park BH, Karpinets TV, Syed MH, Leuze MR, Uberbacher EC., Glycobiology 20(12), 2010
PMID: 20696711
Park BH, Karpinets TV, Syed MH, Leuze MR, Uberbacher EC., Glycobiology 20(12), 2010
PMID: 20696711
RJ, Hydrogeol J 8(), 2000
Comparative genomics reveals a deep-sea sediment-adapted life style of Pseudoalteromonas sp. SM9913.
Qin QL, Li Y, Zhang YJ, Zhou ZM, Zhang WX, Chen XL, Zhang XY, Zhou BC, Wang L, Zhang YZ., ISME J 5(2), 2010
PMID: 20703316
Qin QL, Li Y, Zhang YJ, Zhou ZM, Zhang WX, Chen XL, Zhang XY, Zhou BC, Wang L, Zhang YZ., ISME J 5(2), 2010
PMID: 20703316
Microbial communities from methane hydrate-bearing deep marine sediments in a forearc basin.
Reed DW, Fujita Y, Delwiche ME, Blackwelder DB, Sheridan PP, Uchida T, Colwell FS., Appl. Environ. Microbiol. 68(8), 2002
PMID: 12147470
Reed DW, Fujita Y, Delwiche ME, Blackwelder DB, Sheridan PP, Uchida T, Colwell FS., Appl. Environ. Microbiol. 68(8), 2002
PMID: 12147470
JE, Biochem J 285(Pt 3), 1992
B, Deep Sea Res Part II 47(), 2000
Lacinutrix himadriensis sp. nov., a psychrophilic bacterium isolated from a marine sediment, and emended description of the genus Lacinutrix.
Srinivas TN, Prasad S, Manasa P, Sailaja B, Begum Z, Shivaji S., Int. J. Syst. Evol. Microbiol. 63(Pt 2), 2012
PMID: 22561589
Srinivas TN, Prasad S, Manasa P, Sailaja B, Begum Z, Shivaji S., Int. J. Syst. Evol. Microbiol. 63(Pt 2), 2012
PMID: 22561589
Molecular monitoring of culturable bacteria from deep-sea sediment of the Nankai Trough, Leg 190 Ocean Drilling Program.
Toffin L, Webster G, Weightman AJ, Fry JC, Prieur D., FEMS Microbiol. Ecol. 48(3), 2004
PMID: 19712305
Toffin L, Webster G, Weightman AJ, Fry JC, Prieur D., FEMS Microbiol. Ecol. 48(3), 2004
PMID: 19712305
Cloning and characterization of a novel cold-active glycoside hydrolase family 1 enzyme with β-glucosidase, β-fucosidase and β-galactosidase activities.
Wierzbicka-Wos A, Bartasun P, Cieslinski H, Kur J., BMC Biotechnol. 13(), 2013
PMID: 23497058
Wierzbicka-Wos A, Bartasun P, Cieslinski H, Kur J., BMC Biotechnol. 13(), 2013
PMID: 23497058
Y, Nucleic Acids Res 40(Web Server issu), 2012
InterProScan--an integration platform for the signature-recognition methods in InterPro.
Zdobnov EM, Apweiler R., Bioinformatics 17(9), 2001
PMID: 11590104
Zdobnov EM, Apweiler R., Bioinformatics 17(9), 2001
PMID: 11590104
Research and application of marine microbial enzymes: status and prospects.
Zhang C, Kim SK., Mar Drugs 8(6), 2010
PMID: 20631875
Zhang C, Kim SK., Mar Drugs 8(6), 2010
PMID: 20631875
DNA recovery from soils of diverse composition.
Zhou J, Bruns MA, Tiedje JM., Appl. Environ. Microbiol. 62(2), 1996
PMID: 8593035
Zhou J, Bruns MA, Tiedje JM., Appl. Environ. Microbiol. 62(2), 1996
PMID: 8593035
Export
Markieren/ Markierung löschen
Markierte Publikationen
Web of Science
Dieser Datensatz im Web of Science®Quellen
PMID: 25108363
PubMed | Europe PMC
Suchen in
Google Scholar