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Identifying and Quantifying Orphan Protein Sequences in Fungi
Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för biokemi och biofysik.
Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för biokemi och biofysik.ORCID-id: 0000-0002-7115-9751
2010 (Engelska)Ingår i: Journal of Molecular Biology, ISSN 0022-2836, E-ISSN 1089-8638, Vol. 396, nr 2, s. 396-405Artikel i tidskrift (Refereegranskat) Published
Abstract [en]

For large regions of many proteins, and even entire proteins, no homology to known domains or proteins can be detected. These sequences are often referred to as orphans. Surprisingly, it has been reported that the large number of orphans is sustained in spite of a rapid increase of available genomic sequences. However, it is believed that de novo creation of coding sequences is rare in comparison to mechanisms such as domain shuffling and gene duplication; hence, most sequences should have homologs in other genomes. To investigate this, the sequences of 19 complete fungi genomes were compared. By using the phylogenetic relationship between these genomes, we could identify potentially de novo created orphans in Saccharomyces cerevisiae. We found that only a small fraction, <2%, of the S. cerevisiae proteome is orphan, which confirms that de novo creation of coding sequences is indeed rare. Furthermore, we found it necessary to compare the most closely related species to distinguish between de novo created sequences and rapidly evolving sequences where homologs are present but cannot be detected. Next, the orphan proteins (OPs) and orphan domains (ODs) were characterized. First, it was observed that both OPs and ODs are short. In addition, at least some of the OPs have been shown to be functional in experimental assays, showing that they are not pseudogenes. Furthermore, in contrast to what has been reported before and what is seen for older orphans, S. cerevisiae specific ODs and proteins are not more disordered than other proteins. This might indicate that many of the older, and earlier classified, orphans indeed are fast-evolving sequences. Finally, >90% of the detected ODs are located at the protein termini, which suggests that these orphans could have been created by mutations that have affected the start or stop codons.

Ort, förlag, år, upplaga, sidor
2010. Vol. 396, nr 2, s. 396-405
Nyckelord [en]
evolution, protein domain, orphan protein, fungi
Nationell ämneskategori
Naturvetenskap
Identifikatorer
URN: urn:nbn:se:su:diva-49277DOI: 10.1016/j.jmb.2009.11.053ISI: 000274980400013OAI: oai:DiVA.org:su-49277DiVA, id: diva2:379359
Forskningsfinansiär
Stiftelsen för strategisk forskning (SSF)VetenskapsrådetEU, FP7, Sjunde ramprogrammet, 503567; 512092
Anmärkning

authorCount :2

Tillgänglig från: 2010-12-17 Skapad: 2010-12-13 Senast uppdaterad: 2017-12-11Bibliografiskt granskad

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Ekman, DianaElofsson, Arne
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