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A study of the origin of orphans in the fungi lineage
Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
Manuscript (Other academic)
Identifiers
URN: urn:nbn:se:su:diva-25579OAI: oai:DiVA.org:su-25579DiVA: diva2:200003
Note
Part of urn:nbn:se:su:diva-8295Available from: 2008-11-06 Created: 2008-10-27 Last updated: 2010-01-13Bibliographically approved
In thesis
1. Domain rearrangement and creation in protein evolution
Open this publication in new window or tab >>Domain rearrangement and creation in protein evolution
2008 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Proteins are composed of domains, recurrent protein fragments with distinct structure, function and evolutionary history. Some domains exist only as single domain proteins, however, a majority of them are also combined with other domains. Domain rearrangements are important in the evolution of new proteins as new functionalities can arise in a single evolutionary event. In addition, the domain repertoire can be expanded through mutations of existing domains and de novo creation. The processes of domain rearrangement and creation have been the focus of this thesis.

According to our estimates about 65% of the eukaryotic and 40% of the prokaryotic proteins are of multidomain type. We found that insertion of a single domain at the N- or C-terminus was the most common event in the creation of novel multidomain architectures. However, domain repeats deviate from this pattern and are often expanded through duplications of several domains. Next, by mapping domain combinations onto an evolutionary tree we estimated that roughly one domain architecture has been created per million years, with the highest rates in metazoa. Much of this so called explosion of new architectures in metazoa seems to be explained by a set of domains amenable to exon shuffling. In contrast to domain architectures, most known domain families evolved early. However, many proteins have incomplete domain coverage, and could hence contain de novo created domains. In Saccharomyces cerevisiae, however, species specific sequences constitute only a minor fraction of the proteome, and are often short, disordered sequences located at the protein termini.

Place, publisher, year, edition, pages
Stockholm: Institutionen för biokemi och biofysik, 2008. 50 p.
National Category
Bioinformatics (Computational Biology)
Research subject
Biochemistry
Identifiers
urn:nbn:se:su:diva-8295 (URN)978-91-7155-767-4 (ISBN)
Public defence
2008-11-28, Magnélisalen, Kemiska övningslaboratoriet, Svante Arrhenius väg 12 A, Stockholm, 10:00
Opponent
Supervisors
Available from: 2008-11-06 Created: 2008-10-27Bibliographically approved

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Citation style
  • apa
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