메뉴 건너뛰기




Volumn 7, Issue 8, 2012, Pages

Phylogenetic diversity and environment-specific distributions of glycosyl hydrolase family 10 xylanases in geographically distant soils

Author keywords

[No Author keywords available]

Indexed keywords

OXYGEN; XYLAN; XYLAN ENDO 1,3 BETA XYLOSIDASE;

EID: 84865069028     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0043480     Document Type: Article
Times cited : (19)

References (48)
  • 1
    • 0030642144 scopus 로고    scopus 로고
    • Xylanolytic enzymes from fungi and bacteria
    • Sunna A, Antranikian G, ((1997)) Xylanolytic enzymes from fungi and bacteria. Crit Rev Biotechnol 17:: 39--67.
    • (1997) Crit Rev Biotechnol , vol.17 , pp. 39-67
    • Sunna, A.1    Antranikian, G.2
  • 2
    • 0032984477 scopus 로고    scopus 로고
    • Molecular and biotechnological aspects of xylanases
    • Kulkarni N, Shendye A, Rao M, ((1999)) Molecular and biotechnological aspects of xylanases. FEMS Microbiol Rev 23:: 411--456.
    • (1999) FEMS Microbiol Rev , vol.23 , pp. 411-456
    • Kulkarni, N.1    Shendye, A.2    Rao, M.3
  • 3
    • 12144282020 scopus 로고    scopus 로고
    • Xylanases, xylanase families and extremophilic xylanases
    • Collins T, Gerday C, Feller G, ((2005)) Xylanases, xylanase families and extremophilic xylanases. FEMS Microbiol Rev 29:: 3--23.
    • (2005) FEMS Microbiol Rev , vol.29 , pp. 3-23
    • Collins, T.1    Gerday, C.2    Feller, G.3
  • 4
    • 0001719868 scopus 로고
    • Xylan structure, microbial xylanases, and their mode of action
    • Bastawde KB, ((1992)) Xylan structure, microbial xylanases, and their mode of action. World J Microbiol Biotechnol 8:: 353--368.
    • (1992) World J Microbiol Biotechnol , vol.8 , pp. 353-368
    • Bastawde, K.B.1
  • 5
    • 0027345153 scopus 로고
    • Molecular biology of xylan degradation
    • Thomson JA, ((1993)) Molecular biology of xylan degradation. FEMS Microbiol Rev 10:: 65--82.
    • (1993) FEMS Microbiol Rev , vol.10 , pp. 65-82
    • Thomson, J.A.1
  • 7
    • 64949116944 scopus 로고    scopus 로고
    • Characterization of a putative endoxylanase in the migratory plant-parasitic nematode Radopholus similis
    • Haegeman A, Vanholme B, Gheysen G, ((2009)) Characterization of a putative endoxylanase in the migratory plant-parasitic nematode Radopholus similis. Mol Plant Pathol 10:: 389--401.
    • (2009) Mol Plant Pathol , vol.10 , pp. 389-401
    • Haegeman, A.1    Vanholme, B.2    Gheysen, G.3
  • 8
    • 77952879995 scopus 로고    scopus 로고
    • Molecular cloning and characterization of the novel acidic xylanase XYLD from Bispora sp. MEY-1 that is homologous to family 30 glycosyl hydrolases
    • Luo H, Yang J, Li J, Shi P, Huang H, et al. ((2010)) Molecular cloning and characterization of the novel acidic xylanase XYLD from Bispora sp. MEY-1 that is homologous to family 30 glycosyl hydrolases. Appl Microbiol Biotechnol 86:: 1829--1839.
    • (2010) Appl Microbiol Biotechnol , vol.86 , pp. 1829-1839
    • Luo, H.1    Yang, J.2    Li, J.3    Shi, P.4    Huang, H.5
  • 9
    • 0343036237 scopus 로고    scopus 로고
    • Endo-β-1,4-xylanase families: differences in catalytic properties
    • Biely P, Vrsanska M, Tenkanen M, Kluepfel D, ((1997)) Endo-β-1,4-xylanase families: differences in catalytic properties. J Biotechnol 57:: 151--166.
    • (1997) J Biotechnol , vol.57 , pp. 151-166
    • Biely, P.1    Vrsanska, M.2    Tenkanen, M.3    Kluepfel, D.4
  • 10
    • 0029937320 scopus 로고    scopus 로고
    • Biochemistry and genetics of microbial xylanases
    • Jeffries TW, ((1996)) Biochemistry and genetics of microbial xylanases. Curr Opin Biotechnol 7:: 337--342.
    • (1996) Curr Opin Biotechnol , vol.7 , pp. 337-342
    • Jeffries, T.W.1
  • 11
    • 79251587455 scopus 로고    scopus 로고
    • Metagenomic discovery of biomass-degrading genes and genomes from cow rumen
    • Hess M, Sczyrba A, Egan R, Kim TW, Chokhawala H, et al. ((2011)) Metagenomic discovery of biomass-degrading genes and genomes from cow rumen. Science 331:: 463--467.
    • (2011) Science , vol.331 , pp. 463-467
    • Hess, M.1    Sczyrba, A.2    Egan, R.3    Kim, T.W.4    Chokhawala, H.5
  • 12
    • 36549000721 scopus 로고    scopus 로고
    • Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termite
    • Warnecke F, Luginbuhl P, Ivanova N, Ghassemian M, Richardson TH, et al. ((2007)) Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termite. Nature 450:: 560--565.
    • (2007) Nature , vol.450 , pp. 560-565
    • Warnecke, F.1    Luginbuhl, P.2    Ivanova, N.3    Ghassemian, M.4    Richardson, T.H.5
  • 13
    • 77955553683 scopus 로고    scopus 로고
    • Molecular detection and diversity of xylanase genes in alpine tundra soil
    • Wang G, Wang Y, Yang P, Luo H, Huang H, et al. ((2010)) Molecular detection and diversity of xylanase genes in alpine tundra soil. Appl Microbiol Biotechnol 87:: 1383--1393.
    • (2010) Appl Microbiol Biotechnol , vol.87 , pp. 1383-1393
    • Wang, G.1    Wang, Y.2    Yang, P.3    Luo, H.4    Huang, H.5
  • 15
    • 78751503817 scopus 로고    scopus 로고
    • Soil biodiversity and carbon cycling: a review and synthesis of studies examining diversity-function relationships
    • Nielsen UN, Ayres E, Wall DH, Bardgett RD, ((2011)) Soil biodiversity and carbon cycling: a review and synthesis of studies examining diversity-function relationships. Eur J Soil Sci 62:: 105--116.
    • (2011) Eur J Soil Sci , vol.62 , pp. 105-116
    • Nielsen, U.N.1    Ayres, E.2    Wall, D.H.3    Bardgett, R.D.4
  • 16
    • 30344453391 scopus 로고    scopus 로고
    • Biodiversity and litter decomposition in terrestrial ecosystems
    • Hättenschwiler S, Tiunov AV, Scheu S, ((2005)) Biodiversity and litter decomposition in terrestrial ecosystems. Annu Rev Ecol Evol Syst 36:: 191--218.
    • (2005) Annu Rev Ecol Evol Syst , vol.36 , pp. 191-218
    • Hättenschwiler, S.1    Tiunov, A.V.2    Scheu, S.3
  • 17
    • 79958071580 scopus 로고    scopus 로고
    • Functional diversity of terrestrial microbial decomposers and their substrates
    • Hattenschwiler S, Fromin N, Barantal S, ((2011)) Functional diversity of terrestrial microbial decomposers and their substrates. C R Biol 334:: 393--402.
    • (2011) C R Biol , vol.334 , pp. 393-402
    • Hattenschwiler, S.1    Fromin, N.2    Barantal, S.3
  • 18
    • 2942576144 scopus 로고    scopus 로고
    • The soil metagenome-a rich resource for the discovery of novel natural products
    • Daniel R, ((2004)) The soil metagenome-a rich resource for the discovery of novel natural products. Curr Opin Biotechnol 15:: 199--204.
    • (2004) Curr Opin Biotechnol , vol.15 , pp. 199-204
    • Daniel, R.1
  • 19
    • 19144366982 scopus 로고    scopus 로고
    • The metagenomics of soil
    • Daniel R, ((2005)) The metagenomics of soil. Nat Rev Microbiol 3:: 470--478.
    • (2005) Nat Rev Microbiol , vol.3 , pp. 470-478
    • Daniel, R.1
  • 20
    • 51849161161 scopus 로고    scopus 로고
    • Cloning and enzymatic characterization of a xylanase gene from a soil-derived metagenomic library with an efficient approach
    • Hu Y, Zhang G, Li A, Chen J, Ma L, ((2008)) Cloning and enzymatic characterization of a xylanase gene from a soil-derived metagenomic library with an efficient approach. Appl Microbiol Biotechnol 80:: 823--830.
    • (2008) Appl Microbiol Biotechnol , vol.80 , pp. 823-830
    • Hu, Y.1    Zhang, G.2    Li, A.3    Chen, J.4    Ma, L.5
  • 21
    • 0038725668 scopus 로고    scopus 로고
    • A gene encoding a novel extremely thermostable 1,4-β-xylanase isolated directly from an environmental DNA sample
    • Sunna A, Bergquist PL, ((2003)) A gene encoding a novel extremely thermostable 1,4-β-xylanase isolated directly from an environmental DNA sample. Extremophiles 7:: 63--70.
    • (2003) Extremophiles , vol.7 , pp. 63-70
    • Sunna, A.1    Bergquist, P.L.2
  • 23
    • 79751476499 scopus 로고    scopus 로고
    • High genetic diversity and different distributions of glycosyl hydrolase family 10 and 11 xylanases in the goat rumen
    • Wang G, Luo H, Meng K, Wang Y, Huang H, et al. ((2011)) High genetic diversity and different distributions of glycosyl hydrolase family 10 and 11 xylanases in the goat rumen. PLoS ONE 6:: e16731.
    • (2011) PLoS ONE , vol.6
    • Wang, G.1    Luo, H.2    Meng, K.3    Wang, Y.4    Huang, H.5
  • 24
    • 34447631523 scopus 로고    scopus 로고
    • Structure-specificity relationships of an intracellular xylanase from Geobacillus stearothermophilus
    • Solomon V, Teplitsky A, Shulami S, Zolotnitsky G, Shoham Y, et al. ((2007)) Structure-specificity relationships of an intracellular xylanase from Geobacillus stearothermophilus. Acta Crystallogr Sect D 63:: 845--859.
    • (2007) Acta Crystallogr Sect D , vol.63 , pp. 845-859
    • Solomon, V.1    Teplitsky, A.2    Shulami, S.3    Zolotnitsky, G.4    Shoham, Y.5
  • 25
    • 33745634395 scopus 로고    scopus 로고
    • Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences
    • Li W, Godzik A, ((2006)) Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 22:: 1658--1659.
    • (2006) Bioinformatics , vol.22 , pp. 1658-1659
    • Li, W.1    Godzik, A.2
  • 26
    • 40449095397 scopus 로고    scopus 로고
    • Genome of the actinomycete plant pathogen Clavibacter michiganensis subsp. sepedonicus suggests recent niche adaptation
    • Bentley SD, Corton C, Brown SE, Barron A, Clark L, et al. ((2008)) Genome of the actinomycete plant pathogen Clavibacter michiganensis subsp. sepedonicus suggests recent niche adaptation. J Bacteriol 190:: 2150--2160.
    • (2008) J Bacteriol , vol.190 , pp. 2150-2160
    • Bentley, S.D.1    Corton, C.2    Brown, S.E.3    Barron, A.4    Clark, L.5
  • 27
    • 0031031865 scopus 로고    scopus 로고
    • Interrupted catalytic domain structures in xylanases from two distantly related strains of Prevotella ruminicola
    • Flint HJ, Whitehead TR, Martin JC, Gasparic A, ((1997)) Interrupted catalytic domain structures in xylanases from two distantly related strains of Prevotella ruminicola. Biochim Biophys Acta 1337:: 161--165.
    • (1997) Biochim Biophys Acta , vol.1337 , pp. 161-165
    • Flint, H.J.1    Whitehead, T.R.2    Martin, J.C.3    Gasparic, A.4
  • 28
    • 15444362001 scopus 로고    scopus 로고
    • Introducing DOTUR, a computer program for defining operational taxonomic units and estimating species richness
    • Schloss PD, Handelsman J, ((2005)) Introducing DOTUR, a computer program for defining operational taxonomic units and estimating species richness. Appl Environ Microbiol 71:: 1501--1506.
    • (2005) Appl Environ Microbiol , vol.71 , pp. 1501-1506
    • Schloss, P.D.1    Handelsman, J.2
  • 29
    • 0029176314 scopus 로고
    • Cloning, sequencing, and expression of a xylanase gene from the extreme thermophile Dictyoglomus thermophilum Rt46B.1 and activity of the enzyme on fiber-bound substrate
    • Gibbs MD, Reeves RA, Bergquist PL, ((1995)) Cloning, sequencing, and expression of a xylanase gene from the extreme thermophile Dictyoglomus thermophilum Rt46B.1 and activity of the enzyme on fiber-bound substrate. Appl Environ Microbiol 61:: 4403--4408.
    • (1995) Appl Environ Microbiol , vol.61 , pp. 4403-4408
    • Gibbs, M.D.1    Reeves, R.A.2    Bergquist, P.L.3
  • 31
    • 2442709377 scopus 로고    scopus 로고
    • Seasonal changes in an alpine soil bacterial community in the colorado rocky mountains
    • Lipson DA, Schmidt SK, ((2004)) Seasonal changes in an alpine soil bacterial community in the colorado rocky mountains. Appl Environ Microbiol 70:: 2867--2879.
    • (2004) Appl Environ Microbiol , vol.70 , pp. 2867-2879
    • Lipson, D.A.1    Schmidt, S.K.2
  • 33
    • 65549112969 scopus 로고    scopus 로고
    • Biochemical analysis of a β-d-xylosidase and a bifunctional xylanase-ferulic acid esterase from a xylanolytic gene cluster in Prevotella ruminicola 23
    • Dodd D, Kocherginskaya SA, Spies MA, Beery KE, Abbas CA, et al. ((2009)) Biochemical analysis of a β-d-xylosidase and a bifunctional xylanase-ferulic acid esterase from a xylanolytic gene cluster in Prevotella ruminicola 23. J Bacteriol 191:: 3328--3338.
    • (2009) J Bacteriol , vol.191 , pp. 3328-3338
    • Dodd, D.1    Kocherginskaya, S.A.2    Spies, M.A.3    Beery, K.E.4    Abbas, C.A.5
  • 34
    • 0028834548 scopus 로고
    • Novel cellulose-binding domains, NodB homologues and conserved modular architecture in xylanases from the aerobic soil bacteria Pseudomonas fluorescens subsp. cellulosa and Cellvibrio mixtus
    • Millward-Sadler SJ, Davidson K, Hazlewood GP, Black GW, Gilbert HJ, et al. ((1995)) Novel cellulose-binding domains, NodB homologues and conserved modular architecture in xylanases from the aerobic soil bacteria Pseudomonas fluorescens subsp. cellulosa and Cellvibrio mixtus. Biochem J 312 (Pt 1):: 39--48.
    • (1995) Biochem J , vol.312 , Issue.Pt 1 , pp. 39-48
    • Millward-Sadler, S.J.1    Davidson, K.2    Hazlewood, G.P.3    Black, G.W.4    Gilbert, H.J.5
  • 35
    • 33645295532 scopus 로고    scopus 로고
    • Horizontal gene transfer from Bacteria to rumen Ciliates indicates adaptation to their anaerobic, carbohydrates-rich environment
    • Ricard G, McEwan NR, Dutilh BE, Jouany JP, Macheboeuf D, et al. ((2006)) Horizontal gene transfer from Bacteria to rumen Ciliates indicates adaptation to their anaerobic, carbohydrates-rich environment. BMC Genomics 7:: 22.
    • (2006) BMC Genomics , vol.7 , pp. 22
    • Ricard, G.1    McEwan, N.R.2    Dutilh, B.E.3    Jouany, J.P.4    Macheboeuf, D.5
  • 37
    • 29144464937 scopus 로고    scopus 로고
    • UniFrac: a new phylogenetic method for comparing microbial communities
    • Lozupone C, Knight R, ((2005)) UniFrac: a new phylogenetic method for comparing microbial communities. Appl Environ Microbiol 71:: 8228--8235.
    • (2005) Appl Environ Microbiol , vol.71 , pp. 8228-8235
    • Lozupone, C.1    Knight, R.2
  • 38
    • 34547844152 scopus 로고    scopus 로고
    • Fingerprinting and diversity of bacterial copA genes in response to soil types, soil organic status and copper contamination
    • Lejon DP, Nowak V, Bouko S, Pascault N, Mougel C, et al. ((2007)) Fingerprinting and diversity of bacterial copA genes in response to soil types, soil organic status and copper contamination. FEMS Microbiol Ecol 61:: 424--437.
    • (2007) FEMS Microbiol Ecol , vol.61 , pp. 424-437
    • Lejon, D.P.1    Nowak, V.2    Bouko, S.3    Pascault, N.4    Mougel, C.5
  • 39
    • 79951810368 scopus 로고    scopus 로고
    • Functional gene diversity of soil microbial communities from five oil-contaminated fields in China
    • Liang Y, Van Nostrand JD, Deng Y, He Z, Wu L, et al. ((2011)) Functional gene diversity of soil microbial communities from five oil-contaminated fields in China. ISME J 5:: 403--413.
    • (2011) ISME J , vol.5 , pp. 403-413
    • Liang, Y.1    Van Nostrand, J.D.2    Deng, Y.3    He, Z.4    Wu, L.5
  • 41
    • 10444221885 scopus 로고    scopus 로고
    • Chitinase gene sequences retrieved from diverse aquatic habitats reveal environment-specific distributions
    • LeCleir GR, Buchan A, Hollibaugh JT, ((2004)) Chitinase gene sequences retrieved from diverse aquatic habitats reveal environment-specific distributions. Appl Environ Microbiol 70:: 6977--6983.
    • (2004) Appl Environ Microbiol , vol.70 , pp. 6977-6983
    • LeCleir, G.R.1    Buchan, A.2    Hollibaugh, J.T.3
  • 42
    • 49649087440 scopus 로고    scopus 로고
    • Simultaneous assessment of soil microbial community structure and function through analysis of the meta-transcriptome
    • Urich T, Lanzen A, Qi J, Huson DH, Schleper C, et al. ((2008)) Simultaneous assessment of soil microbial community structure and function through analysis of the meta-transcriptome. PLoS ONE 3:: e2527.
    • (2008) PLoS ONE , vol.3
    • Urich, T.1    Lanzen, A.2    Qi, J.3    Huson, D.H.4    Schleper, C.5
  • 43
    • 84855464743 scopus 로고    scopus 로고
    • Metatranscriptomics reveals the diversity of genes expressed by eukaryotes in forest soils
    • Damon C, Lehembre F, Oger-Desfeux C, Luis P, Ranger J, et al. ((2012)) Metatranscriptomics reveals the diversity of genes expressed by eukaryotes in forest soils. PLoS ONE 7:: e28967.
    • (2012) PLoS ONE , vol.7
    • Damon, C.1    Lehembre, F.2    Oger-Desfeux, C.3    Luis, P.4    Ranger, J.5
  • 44
    • 52449114817 scopus 로고    scopus 로고
    • Detection of large numbers of novel sequences in the metatranscriptomes of complex marine microbial communities
    • Gilbert JA, Field D, Huang Y, Edwards R, Li W, et al. ((2008)) Detection of large numbers of novel sequences in the metatranscriptomes of complex marine microbial communities. PLoS ONE 3:: e3042.
    • (2008) PLoS ONE , vol.3
    • Gilbert, J.A.1    Field, D.2    Huang, Y.3    Edwards, R.4    Li, W.5
  • 45
  • 46
    • 34250220631 scopus 로고    scopus 로고
    • Construction of soil environmental DNA cosmid libraries and screening for clones that produce biologically active small molecules
    • Brady SF, ((2007)) Construction of soil environmental DNA cosmid libraries and screening for clones that produce biologically active small molecules. Nat Protoc 2:: 1297--1305.
    • (2007) Nat Protoc , vol.2 , pp. 1297-1305
    • Brady, S.F.1
  • 47
    • 39149120619 scopus 로고    scopus 로고
    • Figaro a novel statistical method for vector sequence removal
    • White JR, Roberts M, Yorke JA, Pop M, ((2008)) Figaro a novel statistical method for vector sequence removal. Bioinformatics 24:: 462--467.
    • (2008) Bioinformatics , vol.24 , pp. 462-467
    • White, J.R.1    Roberts, M.2    Yorke, J.A.3    Pop, M.4
  • 48
    • 34547781750 scopus 로고    scopus 로고
    • MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0
    • Tamura K, Dudley J, Nei M, Kumar S, ((2007)) MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol Biol Evol 24:: 1596--1599.
    • (2007) Mol Biol Evol , vol.24 , pp. 1596-1599
    • Tamura, K.1    Dudley, J.2    Nei, M.3    Kumar, S.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.