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Nilsson, Johan
Publications (3 of 3) Show all publications
Nilsson, J., Grahn, M. & Wright, A. P. (2011). Proteome-wide evidence for enhanced positive Darwinian selection within intrinsically disordered regions in proteins. Genome Biology, 12(7), R65
Open this publication in new window or tab >>Proteome-wide evidence for enhanced positive Darwinian selection within intrinsically disordered regions in proteins
2011 (English)In: Genome Biology, ISSN 1465-6906, E-ISSN 1474-760X, Vol. 12, no 7, p. R65-Article in journal (Refereed) Published
Abstract [en]

ABSTRACT: BACKGROUND: Understanding the adaptive changes that alter the function of proteins during evolution is an important question for biology and medicine. The increasing number of completely sequenced genomes from closely related organisms, as well as individuals within species, facilitates systematic detection of recent selection events by means of comparative genomics. RESULTS: We have used genome-wide strain-specific single nucleotide polymorphism data from 64 strains of budding yeast (Saccharomyces cerevisiae or Saccharomyces paradoxus) to determine whether adaptive positive selection is correlated with protein regions showing propensity for different classes of structure conformation. Data from phylogenetic and population genetic analysis of 3746 gene alignments consistently shows a significantly higher degree of positive Darwinian selection in intrinsically disordered regions of proteins compared to regions of alpha helix, beta sheet or tertiary structure. Evidence of positive selection is significantly enriched in classes of proteins whose functions and molecular mechanisms can be coupled to adaptive processes and these classes tend to have a higher average content of intrinsically unstructured protein regions. CONCLUSIONS: We suggest that intrinsically disordered protein regions may be important for the production and maintenance of genetic variation with adaptive potential and that they may thus be of central significance for the evolvability of the organism or cell in which they occur.

National Category
Bioinformatics and Systems Biology
Identifiers
urn:nbn:se:sh:diva-9985 (URN)10.1186/gb-2011-12-7-r65 (DOI)000296648400004 ()21771306 (PubMedID)2-s2.0-79960555958 (Scopus ID)
Available from: 2011-09-05 Created: 2011-07-27 Last updated: 2017-07-17Bibliographically approved
Ferreira, M. E., Berndt, K. D., Nilsson, J. & Wright, A. P. H. (2010). WD40 Domain Divergence Is Important for Functional Differences between he Fission Yeast Tup11 and Tup12 Co-Repressor Proteins. PLOS ONE, 5(6), Article ID e11009.
Open this publication in new window or tab >>WD40 Domain Divergence Is Important for Functional Differences between he Fission Yeast Tup11 and Tup12 Co-Repressor Proteins
2010 (English)In: PLOS ONE, E-ISSN 1932-6203, Vol. 5, no 6, article id e11009Article in journal (Refereed) Published
Abstract [en]

We have previously demonstrated that subsets of Ssn6/Tup target genes ave distinct requirements for the Schizosaccharomyces pombe homologs of he Tup1/Groucho/TLE co-repressor proteins, Tup11 and Tup12. The very igh level of divergence in the histone interacting repression domains f the two proteins suggested that determinants distinguishing Tup11 and up12 might be located in this domain. Here we have combined hylogenetic and structural analysis as well as phenotypic haracterization, under stress conditions that specifically require up12, to identify and characterize the domains involved in up12-specific action. The results indicate that divergence in the epression domain is not generally relevant for Tup12-specific function. nstead, we show that the more highly conserved C-terminal WD40 repeat omain of Tup12 is important for Tup12-specific function. Surface amino cid residues specific for the WD40 repeat domain of Tup12 proteins in ifferent fission yeasts are clustered in blade 3 of the propeller-like tructure that is characteristic of WD40 repeat domains. The Tup11 and up12 proteins in fission yeasts thus provide an excellent model system or studying the functional divergence of WD40 repeat domains.

National Category
Biochemistry and Molecular Biology
Identifiers
urn:nbn:se:sh:diva-13706 (URN)10.1371/journal.pone.0011009 (DOI)000278494900021 ()2-s2.0-77955193861 (Scopus ID)
Available from: 2011-12-06 Created: 2011-12-06 Last updated: 2021-06-14Bibliographically approved
Ferreira, M. E., Nilsson, J., Berndt, K. D. & Wright, A. P. H.Protein domains underlying functional divergence between the Tup11 and Tup12 co-repressor proteins in fission yeast.
Open this publication in new window or tab >>Protein domains underlying functional divergence between the Tup11 and Tup12 co-repressor proteins in fission yeast
(English)Manuscript (preprint) (Other academic)
National Category
Biochemistry and Molecular Biology
Identifiers
urn:nbn:se:sh:diva-31105 (URN)
Note

Som manuskript i avhandling. As manuscript in dissertation.

Available from: 2016-11-09 Created: 2016-11-09 Last updated: 2017-06-29Bibliographically approved
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