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Protein Families02:47

Protein Families

Protein families are groups of homologous proteins; that is, they have similarities in amino acid sequences and three-dimensional structures. Protein families usually occur because of gene duplication, where an additional copy of a gene is inserted into the genome of an organism.   Mutations that change the amino acids but still allow the protein to be properly synthesized, will lead to new protein family members.   If these new proteins contain similar amino acids in key locations, protein...
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Identification of protein complexes with quantitative proteomics in S. cerevisiae
11:12

Identification of protein complexes with quantitative proteomics in S. cerevisiae

Published on: March 4, 2009

Identifying and quantifying orphan protein sequences in fungi.

Diana Ekman1, Arne Elofsson

  • 1Stockholm Bioinformatics Center/Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden.

Journal of Molecular Biology
|December 1, 2009
PubMed
Summary

Newly identified orphan proteins in Saccharomyces cerevisiae are rare, comprising less than 2% of the proteome. These proteins are short, functional, and not necessarily disordered, suggesting novel evolutionary origins.

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Area of Science:

  • Genomics
  • Proteomics
  • Evolutionary Biology

Background:

  • Large protein regions or entire proteins lacking homology to known sequences are termed orphans.
  • Despite increasing genomic data, the number of orphan sequences remains high.
  • De novo creation of coding sequences is considered rare compared to domain shuffling and gene duplication.

Purpose of the Study:

  • To investigate the prevalence and characteristics of orphan proteins and domains in Saccharomyces cerevisiae.
  • To determine if de novo creation of coding sequences is a significant factor in orphan sequence generation.
  • To differentiate between de novo orphans and rapidly evolving sequences with undetectable homologs.

Main Methods:

  • Comparative genomic analysis of 19 complete fungal genomes.
  • Phylogenetic analysis to identify potentially de novo created orphans in S. cerevisiae.
  • Characterization of orphan proteins (OPs) and orphan domains (ODs) for length, disorder, and location.

Main Results:

  • Only a small fraction (<2%) of the S. cerevisiae proteome consists of orphan sequences.
  • Orphan proteins and domains are generally short.
  • Some orphan proteins have been experimentally validated as functional, not pseudogenes.
  • S. cerevisiae specific orphan proteins and domains are not more disordered than other proteins.
  • >90% of detected orphan domains are located at protein termini.

Conclusions:

  • De novo creation of coding sequences is rare, as evidenced by the low percentage of orphans in S. cerevisiae.
  • Close species comparisons are crucial for distinguishing de novo orphans from rapidly evolving sequences.
  • The characteristics of S. cerevisiae orphans suggest they may arise from mutations affecting start/stop codons.
  • Older classified orphans might represent fast-evolving sequences rather than truly de novo creations.