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Evolution, substrate specificity and subfamily classification of glycoside hydrolase family 5 (GH5)
KTH, School of Biotechnology (BIO), Glycoscience.ORCID iD: 0000-0002-8576-4370
KTH, School of Biotechnology (BIO), Glycoscience.
KTH, School of Biotechnology (BIO), Glycoscience.
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2012 (English)In: BMC Evolutionary Biology, ISSN 1471-2148, E-ISSN 1471-2148, Vol. 12, no 1, 186- p.Article in journal (Refereed) Published
Abstract [en]

Background: The large Glycoside Hydrolase family 5 (GH5) groups together a wide range of enzymes acting on beta-linked oligo- and polysaccharides, and glycoconjugates from a large spectrum of organisms. The long and complex evolution of this family of enzymes and its broad sequence diversity limits functional prediction. With the objective of improving the differentiation of enzyme specificities in a knowledge-based context, and to obtain new evolutionary insights, we present here a new, robust subfamily classification of family GH5. Results: About 80% of the current sequences were assigned into 51 subfamilies in a global analysis of all publicly available GH5 sequences and associated biochemical data. Examination of subfamilies with catalytically-active members revealed that one third are monospecific (containing a single enzyme activity), although new functions may be discovered with biochemical characterization in the future. Furthermore, twenty subfamilies presently have no characterization whatsoever and many others have only limited structural and biochemical data. Mapping of functional knowledge onto the GH5 phylogenetic tree revealed that the sequence space of this historical and industrially important family is far from well dispersed, highlighting targets in need of further study. The analysis also uncovered a number of GH5 proteins which have lost their catalytic machinery, indicating evolution towards novel functions. Conclusion: Overall, the subfamily division of GH5 provides an actively curated resource for large-scale protein sequence annotation for glycogenomics; the subfamily assignments are openly accessible via the Carbohydrate-Active Enzyme database at http://www.cazy.org/GH5.html.

Place, publisher, year, edition, pages
2012. Vol. 12, no 1, 186- p.
Keyword [en]
Protein evolution, Enzyme evolution, Functional prediction, Glycogenomics, Glycoside hydrolase family 5, Phylogenetic analysis, Subfamily classification
National Category
Bioinformatics and Systems Biology
Identifiers
URN: urn:nbn:se:kth:diva-109742DOI: 10.1186/1471-2148-12-186ISI: 000312732100001PubMedID: 22992189Scopus ID: 2-s2.0-84866500048OAI: oai:DiVA.org:kth-109742DiVA: diva2:583951
Funder
Swedish Research Council FormasSwedish Foundation for Strategic Research
Note

QC 20130201

Available from: 2013-01-08 Created: 2013-01-08 Last updated: 2017-12-06Bibliographically approved
In thesis
1. Exploring glycoside hydrolase family 5 (GH5) enzymes
Open this publication in new window or tab >>Exploring glycoside hydrolase family 5 (GH5) enzymes
2013 (English)Licentiate thesis, comprehensive summary (Other academic)
Abstract [en]

In 1990, the classification of carbohydrate-active enzymes (CAZymes) was introduced by the scientist Bernard Henrissat. According to sequence similarity, these enzymes were separated into families with conserved structures and reaction mechanisms. One interesting class of CAZymes is the group of glycoside hydrolases (GHs) containing more than 138000 modules divided into 131 families as of February 2013. One of the most versatile and the largest of these GH families, containing enzymes with numerous biomass-deconstructing activities, is glycoside hydrolase family 5 (GH5). However, for large and diverse families like the GH5 family, another layer of classification is required to get a better understanding of the evolution of diverse enzyme activities. In Paper I, a new subfamily classification of GH5 is presented in order to sort the family members into distinct groups with predictive power. In total, 51 subfamilies were defined. Despite the fact that several hundred GH5 enzymes have been characterized, 20 subfamilies lacking biochemically characterized enzymes and 38 subfamilies without structural data were identified. These highlighted subfamilies contain interesting targets for future investigation.

The GH5 family includes endo-β-mannanases catalyzing the hydrolysis of the β-1,4-linked backbone of mannan polysaccharides, which are common hemicelluloses found as storage and structural polymers in plant cell walls. Mannans are commonly utilized as raw biomaterials in food, feed, paper, textile and cosmetic industries, and mannanases are often applied for modifying and controlling the property of mannan polysaccharides in such applications. The overwhelming majority of characterized mannanases are from microbial origin. The situation for plant mannanases is quite different, as the catalytic properties for only a handful have been determined. Paper II describes the first characterization of a heterologously expressed Arabidopsis β-mannanase.

Abstract [sv]

År 1990 introducerade forskaren Bernard Henrissat en klassificering av kolhydrataktiva enzymer (CAZymer), enligt vilken enzymerna - baserat på sekvenslikhet - delades in i familjer med konserverade strukturer och reaktionsmekanismer. En intressant CAZym-klass är glykosidhydrolaserna (GH), en klass som i februari 2013 innehöll fler än 138000 katalytiska moduler indelade i 131 olika familjer. En av de största och mest varierade av GH-familjerna är glykosidhydrolasfamilj 5 (GH5), vilken innehåller en mångfald av identifierade enzymaktiviteter relevanta för nedbrytning av biomassa. För stora och diversifierade familjer som GH5 krävs det dock ytterligare en klassificeringsnivå för att bättre förstå evolutionen och uppkomsten av de många förekommande enzymaktiviteterna. I manuskript I presenteras en ny uppdelning av GH5 enzymer i subfamiljer med syfte att dela upp familjemedlemmarna i distinkta grupper som representerar olika funktioner. Utifrån denna klassificering kan sedan ett enzyms funktion förutsägas baserat på vilken subfamilj det tillhör. Totalt definierades 51 subfamiljer. Trots att hundratals GH5 enzymer har karaktäristerats så visade det sig att 20 av subfamiljerna helt saknar biokemiskt karaktäriserade enzymer och 38 av dem saknar publicerade proteinstrukturer. Dessa subfamiljer är särskilt intressanta för framtida studier.

GH5-familjen inkluderar endo-β-mannanaser som katalyserar hydrolysen av den β-1,4-länkade huvudkedjan i mannanpolysackarider. Dessa växtpolymerer som ingår i hemicellulosagruppen är vanligt förekommande i cellväggarna, där de fungerar som energilagringsmolekyler eller har en strukturell funktion. Mannaner används ofta som råmaterial för industriell livs- och djurfodersproduktion, papper, textilier och kosmetika. I dessa processer behövs ofta mannanaser för modifiering och kontroll av egenskaperna hos dessa polysackarider. Den överväldigande majoriteten av alla karaktäriserade mannanaser kommer från mikroorganismer. Endast för ett fåtal växtmannanaser har de katalytiska egenskaperna analyserats. Manuskript II beskriver den första karaktäriseringen av ett heterologt uttryckt β-mannanas från Arabidopsis.

Place, publisher, year, edition, pages
Stockholm: KTH Royal Institute of Technology, 2013. 41 p.
Series
Trita-BIO-Report, ISSN 1654-2312 ; 2013:8
Keyword
GH5, glycoside hydrolase, subfamily classification, mannans, polysaccharides, mannanases, cell wall, GH5, glykosidhydrolas, subfamiljklassificering, mannaner, polysackarider, mannanaser, cellvägg
National Category
Engineering and Technology Natural Sciences
Research subject
SRA - Molecular Bioscience
Identifiers
urn:nbn:se:kth:diva-121537 (URN)978-91-7501-719-8 (ISBN)
Presentation
2013-05-28, FP41, AlbaNova Universitetscentrum, Roslagstullsbacken 33, Stockholm, 10:30 (English)
Opponent
Supervisors
Funder
Swedish Foundation for Strategic Research
Note

QC 20130506

Available from: 2013-05-06 Created: 2013-04-30 Last updated: 2013-05-06Bibliographically approved
2. Discovery and investigation of glycoside hydrolase family 5 enzymes with potential use in biomass conversion
Open this publication in new window or tab >>Discovery and investigation of glycoside hydrolase family 5 enzymes with potential use in biomass conversion
2015 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Glycoside hydrolases (GHs) cleave glycosidic bonds in glycoconjugates, oligosaccharides and polysaccharides such as cellulose and various hemicelluloses. Mannan is a major group of hemicelluloses. In higher plants, they usually serve as storage carbohydrates in seeds and tubers or as structural polysaccharides cross-linking with cellulose/lignin in cell walls. In industrial fields, this renewable biomass component can be used in various areas such as production of biofuels and health-benefit manno-oligosaccharides; and mannan degrading enzymes, especially mannanases, are important molecular tools for controlling mannan polysaccharides properties in biomass conversion. In this thesis, the evolution, substrate specificity and subfamily classification of the most important GH family, i.e., glycoside hydrolase family 5 (GH5), are presented providing a powerful tool for exploring GH5 enzymes in search for enzymes with interesting properties for sustainable biomass conversion. Additionally, three GH5_7 mannanases from Arabidopsis thaliana (AtMan5-1, AtMan5-2 and AtMan5-6) were investigated in the present study. Bioinformatics tools, heterologous expression, and enzymology were applied in order to reveal the catalytic properties of the target enzymes, increase understanding of plant mannanase evolution, and evaluate their potential use in biomass conversion. This approach revealed: (1) AtMan5-1 exhibits mannan hydrolase/transglycosylase activity (MHT), (2) AtMan5-2 preferably degrades mannans with a glucomannan backbone, and (3) AtMan5-6 is a relatively thermotolerant enzyme showing high catalytic efficiency for conversion of glucomannan and galactomannan making this plant mannanase an interesting candidate for biotechnological applications of digesting various mannans. Moreover, these studies suggest an evolutionary diversification of plant mannanase enzymatic function.

Place, publisher, year, edition, pages
Stockholm: KTH Royal Institute of Technology, 2015. 51 p.
Series
TRITA-BIO-Report, ISSN 1654-2312 ; 2015:5
Keyword
plant cell wall, biomass, hemicellulose, mannans, glycoside hydrolase, subfamily classification, Arabidopsis, mannanase, transglycosylase, enzymatic characterization.
National Category
Biocatalysis and Enzyme Technology Plant Biotechnology Biochemistry and Molecular Biology
Research subject
Biotechnology
Identifiers
urn:nbn:se:kth:diva-160538 (URN)978-91-7595-439-4 (ISBN)
Public defence
2015-03-20, FD41, AlbaNova University Center, Roslagstullsbacken 21, Stockholm, 13:00 (English)
Opponent
Supervisors
Funder
Swedish Foundation for Strategic Research Swedish Research Council Formas
Note

QC 20150224

Available from: 2015-02-24 Created: 2015-02-23 Last updated: 2015-02-24Bibliographically approved

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