title: A method to assess compositional bias in biological sequences and its application to prion-like glutamine/asparagine-rich domains in eukaryotic proteomes.
abstract: We have derived a novel method to assess compositional biases in biological sequences, which is based on finding the lowest-probability subsequences for a given residue-type set. As a case study, the distribution of prion-like glutamine/asparagine-rich ((Q+N)-rich) domains (which are linked to amyloidogenesis) was assessed for budding and fission yeasts and four other eukaryotes. We find more than 170 prion-like (Q+N)-rich regions in budding yeast, and, strikingly, many fewer in fission yeast. Also, some residues, such as tryptophan or isoleucine, are unlikely to form biased regions in any eukaryotic proteome.
authors.affiliation: Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Avenue, New Haven, CT 06520-8114, USA. harrison@csb.yale.edu
authors.forename: Paul M
authors.initials: PM
authors.lastname: Harrison
authors.forename: Mark
authors.initials: M
authors.lastname: Gerstein
mesh_terms: D020816:Amino Acid Motifs / Q000235:genetics; D000595:Amino Acid Sequence / Q000235:genetics; D000818:Animals; D001216:Asparagine / Q000235:genetics; D029742:Caenorhabditis elegans Proteins / Q000737:chemistry / Q000235:genetics; D019295:Computational Biology / Q000379:methods / Q000706:statistics & numerical data; D029721:Drosophila Proteins / Q000737:chemistry / Q000235:genetics; D005057:Eukaryotic Cells / Q000737:chemistry / Q000378:metabolism; D005656:Fungal Proteins / Q000737:chemistry / Q000235:genetics; D005973:Glutamine / Q000235:genetics; D006801:Humans; D008969:Molecular Sequence Data; D011328:Prions / Q000737:chemistry* / Q000235:genetics; D017434:Protein Structure, Tertiary / Q000235:genetics; D020543:Proteome / Q000235:genetics*; D004718:Saccharomycetales / Q000235:genetics; D012568:Schizosaccharomyces / Q000235:genetics; D029702:Schizosaccharomyces pombe Proteins / Q000737:chemistry / Q000235:genetics; D012641:Selection, Genetic; D020539:Sequence Analysis, Protein / Q000379:methods / Q000706:statistics & numerical data
chemical_list: D029742:Caenorhabditis elegans Proteins; D029721:Drosophila Proteins; D005656:Fungal Proteins; D011328:Prions; D020543:Proteome; D029702:Schizosaccharomyces pombe Proteins; D005973:Glutamine; D001216:Asparagine