High phylogenetic diversity of glycosyl hydrolase family 10 and 11 xylanases in the sediment of Lake Dabusu in China

PLoS ONE

Volumn 9, Issue 11, 2014, Pages

  Wang, Guozeng ^a   Huang, Xiaoyun ^a   Ng, Tzi Bun ^b   Lin, Juan ^a   Ye, Xiu Yun ^a  

^a FUZHOU UNIVERSITY   (China)

^b and Hong Kong Branch of CAS Center for Excellence in Animal Evolution and Genetics   (Hong Kong)

Author keywords

[No Author keywords available]

Indexed keywords

GLYCOSIDASE; RECOMBINANT ENZYME; XYLAN ENDO 1,3 BETA XYLOSIDASE; BACTERIAL PROTEIN; ENDO 1,4 BETA XYLANASE; ISOENZYME; RECOMBINANT PROTEIN;

ACTINOBACTERIA; ALKALINITY; ARTICLE; BACTEROIDETES; CHINA; ENZYME ACTIVITY; ESCHERICHIA COLI; FIRMICUTES; FUNGUS; GENE EXPRESSION; GENE IDENTIFICATION; GENE STRUCTURE; GENETIC VARIABILITY; LAKE SEDIMENT; MOLECULAR CLONING; NONHUMAN; PH; PHYLOGENY; PROTEIN FAMILY; PROTEOBACTERIA; SALINITY; SEQUENCE HOMOLOGY; VERRUCOMICROBIA; BIODIVERSITY; CLASSIFICATION; ENZYME ASSAY; ENZYMOLOGY; GENETICS; LAKE; METABOLISM; MICROBIAL CONSORTIUM; MICROBIOLOGY; SEDIMENT;

ACTINOBACTERIA; BACTERIAL PROTEINS; BACTEROIDETES; BIODIVERSITY; CHINA; ENDO-1,4-BETA XYLANASES; ENZYME ASSAYS; ESCHERICHIA COLI; GENE EXPRESSION; GEOLOGIC SEDIMENTS; HYDROGEN-ION CONCENTRATION; ISOENZYMES; LAKES; MICROBIAL CONSORTIA; PHYLOGENY; PROTEOBACTERIA; RECOMBINANT PROTEINS; SALINITY;

EID: 84911918265     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0112798     Document Type: Article

References (41)

1. Kulkarni N, Shendye A, Rao M (1999) Molecular and biotechnological aspects of xylanases. FEMS Microbiol Rev 23: 411-456.
2. Sunna A, Antranikian G (1997) Xylanolytic enzymes from fungi and bacteria. Crit Rev Biotechnol 17: 39-67.
3. Collins T, Gerday C, Feller G (2005) Xylanases, xylanase families and extremophilic xylanases. FEMS Microbiol Rev 29: 3-23.
4. Cantarel BL, Coutinho PM, Rancurel C, Bernard T, Lombard V, et al. (2009) The Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics. Nucl Acids Res 37: D233-238.
5. Biely P, Vrsanska M, Tenkanen M, Kluepfel D (1997) Endo-beta-1,4-xylanase families: differences in catalytic properties. J Biotechnol 57: 151-166.
6. Jeffries TW (1996) Biochemistry and genetics of microbial xylanases. Curr Opin Biotechnol 7: 337-342.
7. Beg QK, Kapoor M, Mahajan L, Hoondal GS (2001) Microbial xylanases and their industrial applications: a review. Appl Microbiol Biotechnol 56: 326-338.
8. Polizeli ML, Rizzatti AC, Monti R, Terenzi HF, Jorge JA, et al. (2005) Xylanases from fungi: properties and industrial applications. Appl Microbiol Biotechnol 67: 577-591.
9. Martin-Sampedro R, Rodriguez A, Ferrer A, Garcia-Fuentevilla LL, Eugenio ME (2012) Biobleaching of pulp from oil palm empty fruit bunches with laccase and xylanase. Bioresour Technol 110: 371-378.
10. Khandeparkar R, Bhosle NB (2007) Application of thermoalkalophilic xylanase from Arthrobacter sp. MTCC 5214 in biobleaching of kraft pulp. Bioresour Technol 98: 897-903.
11. Verma D, Kawarabayasi Y, Miyazaki K, Satyanarayana T (2013) Cloning, expression and characteristics of a novel alkalistable and thermostable xylanase encoding gene (Mxyl) retrieved from compost-soil metagenome. PLoS ONE 8: e52459.
12. Simkhada JR, Yoo HY, Choi YH, Kim SW, Yoo JC (2012) An extremely alkaline novel xylanase from a newly isolated Streptomyces strain cultivated in corncob medium. Appl Biochem Biotechnol 168: 2017-2027.
13. Mamo G, Delgado O, Martinez A, Mattiasson B, Hatti-Kaul R (2006) Cloning, sequence analysis, and expression of a gene encoding an endoxylanase from Bacillus halodurans S7. Mol Biotechnol 33: 149-159.
14. Gessesse A, Mamo G (1998) Purification and characterization of an alkaline xylanase from alkaliphilic Micrococcus sp AR-135. Journal of Industrial Microbiology and Biotechnology 20: 210-214.
15. Gessesse A (1998) Purification and properties of two thermostable alkaline xylanases from an alkaliphilic bacillus sp. Appl Environ Microbiol 64: 3533-3535.
16. Antony CP, Kumaresan D, Hunger S, Drake HL, Murrell JC, et al. (2013) Microbiology of Lonar Lake and other soda lakes. ISME J 7: 468-476.
17. Jones BE, Grant WD, Duckworth AW, Owenson GG (1998) Microbial diversity of soda lakes. Extremophiles 2: 191-200.
18. Zhao B, Chen S (2012) Alkalitalea saponilacus gen. nov., sp. nov., an obligately anaerobic, alkaliphilic, xylanolytic bacterium from a meromictic soda lake. Int J Syst Evol Microbiol 62: 2618-2623.
19. Rees HC, Grant WD, Jones BE, Heaphy S (2004) Diversity of Kenyan soda lake alkaliphiles assessed by molecular methods. Extremophiles 8: 63-71.
20. Foti MJ, Sorokin DY, Zacharova EE, Pimenov NV, Kuenen JG, et al. (2008) Bacterial diversity and activity along a salinity gradient in soda lakes of the Kulunda Steppe (Altai, Russia). Extremophiles 12: 133-145.
21. Lanzen A, Simachew A, Gessesse A, Chmolowska D, Jonassen I, et al. (2013) Surprising prokaryotic and eukaryotic diversity, community structure and biogeography of Ethiopian soda lakes. PLoS ONE 8: e72577.
22. Lin JL, Joye SB, Scholten JC, Schafer H, McDonald IR, et al. (2005) Analysis of methane monooxygenase genes in mono lake suggests that increased methane oxidation activity may correlate with a change in methanotroph community structure. Appl Environ Microbiol 71: 6458-6462.
23. Kovaleva OL, Tourova TP, Muyzer G, Kolganova TV, Sorokin DY (2011) Diversity of RuBisCO and ATP citrate lyase genes in soda lake sediments. FEMS Microbiol Ecol 75: 37-47.
24. Wang G, Meng K, Luo H, Wang Y, Huang H, et al. (2012) Phylogenetic diversity and environment-specific distributions of glycosyl hydrolase family 10 xylanases in geographically distant soils. PLoS ONE 7: e43480.
25. Shen J, Cao JT, Wu YH (2001) Paieoclimatic changes in Dabusu Lake. Chin J Oceanol Limnol 19: 91-96.
26. 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.
27. 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.
28. White JR, Roberts M, Yorke JA, Pop M (2008) Figaro: a novel statistical method for vector sequence removal. Bioinformatics 24: 462-467.
29. 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.
30. 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.
31. Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4: 406-425.
32. 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.
33. Huang H, Wang G, Zhao Y, Shi P, Luo H, et al. Direct and efficient cloning of full-length genes from environmental DNA by RT-qPCR and modified TAILPCR. Appl Microbiol Biotechnol 87: 1141-1149.
34. Petersen TN, Brunak S, von Heijne G, Nielsen H (2011) SignalP 4.0: discriminating signal peptides from transmembrane regions. Nat Methods 8: 785-786.
35. Miller GL, Blum R, Glennon WE, Burton AL (1960) Measurement of carboxymethylcellulase activity. Analytical Biochemistry 1: 127-132.
36. Solomon V, Teplitsky A, Shulami S, Zolotnitsky G, Shoham Y, et al. (2007) Structure-specificity relationships of an intracellular xylanase from Geobacillus stearothermophilus. Acta Crystallographica Section D 63: 845-859.
37. Ma Y, Zhang W, Xue Y, Zhou P, Ventosa A, et al. (2004) Bacterial diversity of the Inner Mongolian Baer Soda Lake as revealed by 16S rRNA gene sequence analyses. Extremophiles 8: 45-51.
38. Joshi AA, Kanekar PP, Kelkar AS, Shouche YS, Vani AA, et al. (2008) Cultivable bacterial diversity of alkaline Lonar lake, India. Microb Ecol 55: 163-172.
39. Pagaling E, Wang H, Venables M, Wallace A, Grant WD, et al. (2009) Microbial biogeography of six salt lakes in Inner Mongolia, China, and a salt lake in Argentina. Appl Environ Microbiol 75: 5750-5760.
40. Al-Zarban SS, Abbas I, Al-Musallam AA, Steiner U, Stackebrandt E, et al. (2002) Nocardiopsis halotolerans sp. nov., isolated from salt marsh soil in Kuwait. Int J Syst Evol Microbiol 52: 525-529.
41. Blanco J, Coque JJ, Velasco J, Martin JF (1997) Cloning, expression in Streptomyces lividans and biochemical characterization of a thermostable endobeta- 1,4-xylanase of Thermomonospora alba ULJB1 with cellulose-binding ability. Appl Microbiol Biotechnol 48: 208-217.