Successful heterologous expression of a novel chitinase identified by sequence analyses of the metagenome from a chitin-enriched soil sample

Stoeveken J, Singh R, Kolkenbrock S, Zakrzewski M, Wibberg D, Eikmeyer FG, Pühler A, Schlüter A, Moerschbacher BM (2015)
Journal of Biotechnology 201: 60-68.

Zeitschriftenaufsatz | Veröffentlicht | Englisch
Es wurden keine Dateien hochgeladen. Nur Publikationsnachweis!
Stoeveken, J.; Singh, R.; Kolkenbrock, S.; Zakrzewski, MarthaUniBi; Wibberg, DanielUniBi; Eikmeyer, Felix GregorUniBi ; Pühler, AlfredUniBi ; Schlüter, AndreasUniBi ; Moerschbacher, B. M.
Abstract / Bemerkung
Chitin and its derivative chitosan are abundant natural polysaccharides with many potential industrial applications. Metagenomic analysis of chitin-enriched soil samples using the Roche Genome Sequencer FLX platform led to the identification of several novel genes for chitin and chitosan modifying enzymes (CCMEs) which may be used to produce novel chitosans. The sequencing approach yielded 2,281,090 reads with an average length of 378 bp amounting to a total sequence information of approximately 851Mb. Assembly of the obtained sequences comprised 699,710 reads representing 30.68% of all reads. A total of 6625 contigs larger than 500 bp containing 16,289 predicted genes are included in the assembly. Taxonomic profiling of the indigenous microbial community by applying the software CARMA revealed that 96.1% of the reads were of bacterial origin including 17% assigned to the family Xanthomonadaceae. Several putative genes encoding CCMEs were identified by comparison against the GenBank database, inclusive a full-length chitinase gene which was codon optimized for Escherichia coli and heterologously synthesized as a Strep-tagged protein in E. coli Rosetta 2 using the pET vector system. Approximately 5 mg of the novel active chitinase was purified as demonstrated by dot assay analysis using glycol chitin as a substrate. Next generation metagenomic sequencing, thus, emerges as a new and powerful tool for the identification of potentially novel biocatalysts of biotechnological value. (C) 2014 Elsevier B.V. All rights reserved.
Dot assay; metagenomic sequencing; Next generation; Soil; Chitin/chitosan modifying enzymes; Chitinase
Journal of Biotechnology
Page URI


Stoeveken J, Singh R, Kolkenbrock S, et al. Successful heterologous expression of a novel chitinase identified by sequence analyses of the metagenome from a chitin-enriched soil sample. Journal of Biotechnology. 2015;201:60-68.
Stoeveken, J., Singh, R., Kolkenbrock, S., Zakrzewski, M., Wibberg, D., Eikmeyer, F. G., Pühler, A., et al. (2015). Successful heterologous expression of a novel chitinase identified by sequence analyses of the metagenome from a chitin-enriched soil sample. Journal of Biotechnology, 201, 60-68. doi:10.1016/j.jbiotec.2014.09.010
Stoeveken, J., Singh, R., Kolkenbrock, S., Zakrzewski, M., Wibberg, D., Eikmeyer, F. G., Pühler, A., Schlüter, A., and Moerschbacher, B. M. (2015). Successful heterologous expression of a novel chitinase identified by sequence analyses of the metagenome from a chitin-enriched soil sample. Journal of Biotechnology 201, 60-68.
Stoeveken, J., et al., 2015. Successful heterologous expression of a novel chitinase identified by sequence analyses of the metagenome from a chitin-enriched soil sample. Journal of Biotechnology, 201, p 60-68.
J. Stoeveken, et al., “Successful heterologous expression of a novel chitinase identified by sequence analyses of the metagenome from a chitin-enriched soil sample”, Journal of Biotechnology, vol. 201, 2015, pp. 60-68.
Stoeveken, J., Singh, R., Kolkenbrock, S., Zakrzewski, M., Wibberg, D., Eikmeyer, F.G., Pühler, A., Schlüter, A., Moerschbacher, B.M.: Successful heterologous expression of a novel chitinase identified by sequence analyses of the metagenome from a chitin-enriched soil sample. Journal of Biotechnology. 201, 60-68 (2015).
Stoeveken, J., Singh, R., Kolkenbrock, S., Zakrzewski, Martha, Wibberg, Daniel, Eikmeyer, Felix Gregor, Pühler, Alfred, Schlüter, Andreas, and Moerschbacher, B. M. “Successful heterologous expression of a novel chitinase identified by sequence analyses of the metagenome from a chitin-enriched soil sample”. Journal of Biotechnology 201 (2015): 60-68.

8 Zitationen in Europe PMC

Daten bereitgestellt von Europe PubMed Central.

A flavin-dependent halogenase from metagenomic analysis prefers bromination over chlorination.
Neubauer PR, Widmann C, Wibberg D, Schröder L, Frese M, Kottke T, Kalinowski J, Niemann HH, Sewald N., PLoS One 13(5), 2018
PMID: 29746521
A broad pH range and processive chitinase from a metagenome library.
Thimoteo SS, Glogauer A, Faoro H, de Souza EM, Huergo LF, Moerschbacher BM, Pedrosa FO., Braz J Med Biol Res 50(1), 2017
PMID: 28076454
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
Production and characterization of a novel antifungal chitinase identified by functional screening of a suppressive-soil metagenome.
Berini F, Presti I, Beltrametti F, Pedroli M, Vårum KM, Pollegioni L, Sjöling S, Marinelli F., Microb Cell Fact 16(1), 2017
PMID: 28137256
Expression studies of Bacillus licheniformis chitin deacetylase in E. coli Rosetta cells.
Raval R, Simsa R, Raval K., Int J Biol Macromol 104(pt b), 2017
PMID: 28223214
Metagenomics: novel enzymes from non-culturable microbes.
Berini F, Casciello C, Marcone GL, Marinelli F., FEMS Microbiol Lett 364(21), 2017
PMID: 29029060
Cloning and characterization of three ketoreductases from soil metagenome for preparing optically active alcohols.
Zhao Z, Wang H, Zhang Y, Chen L, Wu K, Wei D., Biotechnol Lett 38(10), 2016
PMID: 27383399
Chitinases Are Essential for Cell Separation in Ustilago maydis.
Langner T, Öztürk M, Hartmann S, Cord-Landwehr S, Moerschbacher B, Walton JD, Göhre V., Eukaryot Cell 14(9), 2015
PMID: 25934689

62 References

Daten bereitgestellt von Europe PubMed Central.

Basic local alignment search tool.
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ., J. Mol. Biol. 215(3), 1990
PMID: 2231712
Chitosan Oligomers and Copper Sulfate Induce Grapevine Defense Reactions and Resistance to Gray Mold and Downy Mildew
Aziz A, Trotel-Aziz P, Dhuicq L, Jeandet P, Couderchet M, Vernet G., Phytopathology 96(11), 2006
PMID: IND43857208
Bacterial chitinases: properties and potential.
Bhattacharya D, Nagpure A, Gupta RK., Crit. Rev. Biotechnol. 27(1), 2007
PMID: 17364687
Genomic signatures in microbes – properties and applications
Bohlin, Sci. World J. 11(), 2011
Metagenomic gene discovery: past, present and future.
Cowan D, Meyer Q, Stafford W, Muyanga S, Cameron R, Wittwer P., Trends Biotechnol. 23(6), 2005
PMID: 15922085
Mining of unexplored habitats for novel chitinases--chiA as a helper gene proxy in metagenomics.
Cretoiu MS, Kielak AM, Abu Al-Soud W, Sorensen SJ, van Elsas JD., Appl. Microbiol. Biotechnol. 94(5), 2012
PMID: 22526805
The utilization of N-acetyloglucosamine and chitin as sources of carbon and nitrogen by planktonic and benthic bacteria in Lake Jeziorak
Donderski, Pol. J. Environ. Stud. 12(), 2003
Glycoside hydrolases from a targeted compost metagenome, activity-screening and functional characterization.
Dougherty MJ, D'haeseleer P, Hazen TC, Simmons BA, Adams PD, Hadi MZ., BMC Biotechnol. 12(), 2012
PMID: 22759983
Exploring cultivable bacteria from the prokaryotic community associated to the carnivorous sponge Asbestopluma hypogea
Dupont, FEMS Microbiol. Ecol. (), 2014
The complete genome sequences of four new IncN plasmids from wastewater treatment plant effluent provide new insights into IncN plasmid diversity and evolution.
Eikmeyer F, Hadiati A, Szczepanowski R, Wibberg D, Schneiker-Bekel S, Rogers LM, Brown CJ, Top EM, Puhler A, Schluter A., Plasmid 68(1), 2012
PMID: 22326849
WebCARMA: a web application for the functional and taxonomic classification of unassembled metagenomic reads.
Gerlach W, Junemann S, Tille F, Goesmann A, Stoye J., BMC Bioinformatics 10(), 2009
PMID: 20021646
Taxonomic classification of metagenomic shotgun sequences with CARMA3.
Gerlach W, Stoye J., Nucleic Acids Res. 39(14), 2011
PMID: 21586583
Human macrophage activation triggered by chitotriosidase-mediated chitin and chitosan degradation.
Gorzelanny C, Poppelmann B, Pappelbaum K, Moerschbacher BM, Schneider SW., Biomaterials 31(33), 2010
PMID: 20797781
Specific interaction between chitosan and matrix metalloprotease 2 decreases the invasive activity of human melanoma cells.
Gorzelanny C, Poppelmann B, Strozyk E, Moerschbacher BM, Schneider SW., Biomacromolecules 8(10), 2007
PMID: 17845054
Enzymatic sequencing of partially acetylated chitosan oligomers.
Hamer SN, Moerschbacher BM, Kolkenbrock S., Carbohydr. Res. 392(), 2014
PMID: 24824785
Metagenomics: application of genomics to uncultured microorganisms.
Handelsman J., Microbiol. Mol. Biol. Rev. 68(4), 2004
PMID: 15590779
The GH18 family of chitinases: their domain architectures, functions and evolutions.
Huang QS, Xie XL, Liang G, Gong F, Wang Y, Wei XQ, Wang Q, Ji ZL, Chen QX., Glycobiology 22(1), 2011
PMID: 21750098
Comparative and joint analysis of two metagenomic datasets from a biogas fermenter obtained by 454-pyrosequencing.
Jaenicke S, Ander C, Bekel T, Bisdorf R, Droge M, Gartemann KH, Junemann S, Kaiser O, Krause L, Tille F, Zakrzewski M, Puhler A, Schluter A, Goesmann A., PLoS ONE 6(1), 2011
PMID: 21297863
Analysis of the metagenome from a biogas-producing microbial community by means of bioinformatics methods
Jaenicke, 2011
Biomaterials based on chitin and chitosan in wound dressing applications.
Jayakumar R, Prabaharan M, Sudheesh Kumar PT, Nair SV, Tamura H., Biotechnol. Adv. 29(3), 2011
PMID: 21262336
Evolution of family 18 glycoside hydrolases: diversity, domain structures and phylogenetic relationships.
Karlsson M, Stenlid J., J. Mol. Microbiol. Biotechnol. 16(3-4), 2008
PMID: 18679019
A new approach for discovering cold-active enzymes in a cell mixture of pure-cultured bacteria
Kim, Biotechnol. Lett. (), 2013
Analytical tools and databases for metagenomics in the next-generation sequencing era.
Kim M, Lee KH, Yoon SW, Kim BS, Chun J, Yi H., Genomics Inform 11(3), 2013
PMID: 24124405
Enzymatic production and biological activities of chitosan oligosaccharides (COS): a review
Kim, Carbohydr. Polym. 62(), 2005
Finding novel genes in bacterial communities isolated from the environment.
Krause L, Diaz NN, Bartels D, Edwards RA, Puhler A, Rohwer F, Meyer F, Stoye J., Bioinformatics 22(14), 2006
PMID: 16873483
Taxonomic composition and gene content of a methane-producing microbial community isolated from a biogas reactor.
Krause L, Diaz NN, Edwards RA, Gartemann KH, Kromeke H, Neuweger H, Puhler A, Runte KJ, Schluter A, Stoye J, Szczepanowski R, Tauch A, Goesmann A., J. Biotechnol. 136(1-2), 2008
PMID: 18611419
Phylogenetic classification of short environmental DNA fragments.
Krause L, Diaz NN, Goesmann A, Kelley S, Nattkemper TW, Rohwer F, Edwards RA, Stoye J., Nucleic Acids Res. 36(7), 2008
PMID: 18285365
Phylogenetic characterization of a biogas plant microbial community integrating clone library 16S-rDNA sequences and metagenome sequence data obtained by 454-pyrosequencing.
Krober M, Bekel T, Diaz NN, Goesmann A, Jaenicke S, Krause L, Miller D, Runte KJ, Viehover P, Puhler A, Schluter A., J. Biotechnol. 142(1), 2009
PMID: 19480946
Bioprospecting potential of the soil metagenome: novel enzymes and bioactivities
Lee, Genomis Inform. 11(), 2013
REGANOR: a gene prediction server for prokaryotic genomes and a database of high quality gene predictions for prokaryotes.
Linke B, McHardy AC, Neuweger H, Krause L, Meyer F., Appl. Bioinformatics 5(3), 2006
PMID: 16922601
Molecular analysis of a bacterial chitinolytic community in an upland pasture.
Metcalfe AC, Krsek M, Gooday GW, Prosser JI, Wellington EM., Appl. Environ. Microbiol. 68(10), 2002
PMID: 12324355
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
Effects of molecular weight and deacetylation degree of chitin/chitosan on wound healing
Minagawa, Carbohydr. Polym. 67(), 2007
Sequence assembly demystified.
Nagarajan N, Pop M., Nat. Rev. Genet. 14(3), 2013
PMID: 23358380
KEGG: Kyoto Encyclopedia of Genes and Genomes.
Ogata H, Goto S, Sato K, Fujibuchi W, Bono H, Kanehisa M., Nucleic Acids Res. 27(1), 1999
PMID: 9847135
Interactive metagenomic visualization in a Web browser.
Ondov BD, Bergman NH, Phillippy AM., BMC Bioinformatics 12(), 2011
PMID: 21961884
Establishment of a reliable protocol for the quantification of an oxidative burst in suspension-cultured wheat cells upon elicitation.
Ortmann I, Sumowski G, Bauknecht H, Moerschbacher BM., Physiol. Mol. Plant Pathol. 64(5), 2004
PMID: IND43690613
Meta-IDBA: a de Novo assembler for metagenomic data.
Peng Y, Leung HC, Yiu SM, Chin FY., Bioinformatics 27(13), 2011
PMID: 21685107
Chitin and chitosan: properties and applications
Rinaudo, Prog. Polym. Sci. 31(), 2006
The metagenome of a biogas-producing microbial community of a production-scale biogas plant fermenter analysed by the 454-pyrosequencing technology.
Schluter A, Bekel T, Diaz NN, Dondrup M, Eichenlaub R, Gartemann KH, Krahn I, Krause L, Kromeke H, Kruse O, Mussgnug JH, Neuweger H, Niehaus K, Puhler A, Runte KJ, Szczepanowski R, Tauch A, Tilker A, Viehover P, Goesmann A., J. Biotechnol. 136(1-2), 2008
PMID: 18597880
Genetic diversity and composition of a plasmid metagenome from a wastewater treatment plant.
Schluter A, Krause L, Szczepanowski R, Goesmann A, Puhler A., J. Biotechnol. 136(1-2), 2008
PMID: 18603322
Metagenomics, biotechnology with non-culturable microbes.
Schmeisser C, Steele H, Streit WR., Appl. Microbiol. Biotechnol. 75(5), 2007
PMID: 17396253
The genetic causes of convergent evolution.
Stern DL., Nat. Rev. Genet. 14(11), 2013
PMID: 24105273
Protein production by auto-induction in high density shaking cultures.
Studier FW., Protein Expr. Purif. 41(1), 2005
PMID: 15915565
Insight into the plasmid metagenome of wastewater treatment plant bacteria showing reduced susceptibility to antimicrobial drugs analysed by the 454-pyrosequencing technology.
Szczepanowski R, Bekel T, Goesmann A, Krause L, Kromeke H, Kaiser O, Eichler W, Puhler A, Schluter A., J. Biotechnol. 136(1-2), 2008
PMID: 18586057
MEGA6: Molecular Evolutionary Genetics Analysis version 6.0.
Tamura K, Stecher G, Peterson D, Filipski A, Kumar S., Mol. Biol. Evol. 30(12), 2013
PMID: 24132122
Chemical preparation and structural characterization of a homogeneous series of chitin/chitosan oligomers.
Trombotto S, Ladaviere C, Delolme F, Domard A., Biomacromolecules 9(7), 2008
PMID: 18547106
Complete genome sequencing of Agrobacterium sp. H13-3, the former Rhizobium lupini H13-3, reveals a tripartite genome consisting of a circular and a linear chromosome and an accessory plasmid but lacking a tumor-inducing Ti-plasmid.
Wibberg D, Blom J, Jaenicke S, Kollin F, Rupp O, Scharf B, Schneiker-Bekel S, Sczcepanowski R, Goesmann A, Setubal JC, Schmitt R, Puhler A, Schluter A., J. Biotechnol. 155(1), 2011
PMID: 21329740
A primer on metagenomics.
Wooley JC, Godzik A, Friedberg I., PLoS Comput. Biol. 6(2), 2010
PMID: 20195499
MetaSAMS--a novel software platform for taxonomic classification, functional annotation and comparative analysis of metagenome datasets.
Zakrzewski M, Bekel T, Ander C, Puhler A, Rupp O, Stoye J, Schluter A, Goesmann A., J. Biotechnol. 167(2), 2012
PMID: 23026555
Chitosan modification and pharmaceutical/biomedical applications.
Zhang J, Xia W, Liu P, Cheng Q, Tahirou T, Gu W, Li B., Mar Drugs 8(7), 2010
PMID: 20714418
Chitin deacetylases: properties and applications.
Zhao Y, Park RD, Muzzarelli RA., Mar Drugs 8(1), 2010
PMID: 20161969


Markieren/ Markierung löschen
Markierte Publikationen

Open Data PUB

Web of Science

Dieser Datensatz im Web of Science®


PMID: 25240439
PubMed | Europe PMC

Suchen in

Google Scholar