A holistic approach to understanding CAZy families through reductionist methods
2009 (English)Licentiate thesis, comprehensive summary (Other academic)
In a time when the amount of biological data present in the public domain is becoming increasingly vast, the need for good classification systems has never been greater. In the field of glycoscience the necessity of a good classification for the enzymes involved in the biosynthesis, modification and degradation of polysaccharides is even more pronounced than in other fields. This is due to the complexity of the substrates, the polysaccharides, as the theoretical number of possible hexa-oligosaccharides from only hexoses exceeds 1012 isomers!
An initiative to classify enzymes acting on carbohydrates began around 1990 by the French scientist Bernard Henrissat. The resulting database, the Carbohydrate Active enzymes database (CAZy), classifies enzymes by sequence similarity into families allowing the inference of structure and catalytic mechanism. What CAZy does not provide however, are means to understand how members of a family are related, and in what way they differ from each other. The top-down approach used in this thesis, combining phylogenetic analysis of whole CAZy families, or sub-families, with structural determinations and detailed kinetic analysis allows for exactly that.
Finding determinants for transglycosylation versus hydrolysis within the xth gene product family of GH16 as well as restricting the hydrolytic enzymes to a well defined clade are integral parts of paper I. In paper II a new bacterial sub-clade within CE8 was discovered. The structural determination of theEscherichia coli outer membrane lipoprotein YbhC from from the new sub-clade explained the difference in specificity. The information provided in the two papers of this thesis gives a better understanding of the development of different specificities of diverse CAZY families as well as it aids in future gene product annotations. Furthermore this work has begun to fill the white spots uncovered in the phylogenetic trees.
Place, publisher, year, edition, pages
Stockholm: KTH , 2009. , viii, 55 p.
Trita-BIO-Report, ISSN 1654-2312 ; 2009:5
Carbohydrate esterase family 8, XET, PME, YbhC
Biochemistry and Molecular Biology
IdentifiersURN: urn:nbn:se:kth:diva-10183ISBN: 978-91-7415-269-2OAI: oai:DiVA.org:kth-10183DiVA: diva2:210065
2009-04-29, FA31, Albanova University Center, Stockholm, 14:00 (English)
Nygren, Per-Åke, Ph.DArvestad, Lars, Ph.D.
Brumer, Harry, Ph.D.
List of papers