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The Recent De Novo Origin of Protein C-Termini.

Andreatta ME, Levine JA, Foy SG, Guzman LD, Kosinski LJ, Cordes MH, Masel J - Genome Biol Evol (2015)

Bottom Line: Because we study recent additions to potentially old genes, we are able to apply a variety of stringent quality filters to our annotations of what is a true protein-coding gene, discarding the putative proteins of unknown function that are typical of recent fully de novo genes.We identify 54 examples of C-terminal extensions in Saccharomyces and 28 in Drosophila, all of them recent enough to still be polymorphic.Four of the Saccharomyces C-terminal extensions (to ADH1, ARP8, TPM2, and PIS1) that survived our quality filters are predicted to lead to significant modification of a protein domain structure.

View Article: PubMed Central - PubMed

Affiliation: Department of Ecology & Evolutionary Biology, University of Arizona Present address: Aegis Sciences, Nashville, TN.

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Three proteins with additions that may impact protein structure. (A) Alcohol dehydrogenase I from S. cerevisiae S288C, PDB ID 2HCY, chain A, residues 1–347, (B) Actin-related protein 8 from S. cerevisiae S288C, PDB ID 4AM6, chain A, residues 248-881, (C) Tropomyosin 2, homolog from O. cuniculus shown, PDB ID 2W49, chains A and B, residues 39–200. The ribbon diagram in each panel shows the portion of the protein altered by frameshift in orange, with the length of the altered region as well as the increase in sequence length indicated. Below each structure the C-terminal sequences of the reference strain and the longest version are shown, preceded by five residues of the unaltered region of sequence, shown in italics. Sequences are annotated with actual or predicted locations of α-helix (red) and β-strand (blue) secondary structures. These locations are inferred from the S. cerevisiae S288C or homologous structure in the case of the reference strain, or predicted by Jpred 3 in the case of the longest version.
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evv098-F5: Three proteins with additions that may impact protein structure. (A) Alcohol dehydrogenase I from S. cerevisiae S288C, PDB ID 2HCY, chain A, residues 1–347, (B) Actin-related protein 8 from S. cerevisiae S288C, PDB ID 4AM6, chain A, residues 248-881, (C) Tropomyosin 2, homolog from O. cuniculus shown, PDB ID 2W49, chains A and B, residues 39–200. The ribbon diagram in each panel shows the portion of the protein altered by frameshift in orange, with the length of the altered region as well as the increase in sequence length indicated. Below each structure the C-terminal sequences of the reference strain and the longest version are shown, preceded by five residues of the unaltered region of sequence, shown in italics. Sequences are annotated with actual or predicted locations of α-helix (red) and β-strand (blue) secondary structures. These locations are inferred from the S. cerevisiae S288C or homologous structure in the case of the reference strain, or predicted by Jpred 3 in the case of the longest version.

Mentions: Among our 54 addition alleles, we identified at least four cases in which the new amino acid sequence can be predicted to cause significant alteration and/or expansion of a protein domain structure. Three of these cases involve frameshift-mediated replacement of sequence integral to a protein domain structure, coupled with addition of varying amounts of sequence at the C terminus (fig. 5); a fourth case involves a pure addition with essentially no sequence replacement. In each of the four cases, secondary structure prediction using Jpred 3 (Cole et al. 2008) suggests the possibility of changes in secondary structure, either within the existing domain structure or as part of a C-terminal extension, or both. We discuss each case in more detail below.Fig. 5.—


The Recent De Novo Origin of Protein C-Termini.

Andreatta ME, Levine JA, Foy SG, Guzman LD, Kosinski LJ, Cordes MH, Masel J - Genome Biol Evol (2015)

Three proteins with additions that may impact protein structure. (A) Alcohol dehydrogenase I from S. cerevisiae S288C, PDB ID 2HCY, chain A, residues 1–347, (B) Actin-related protein 8 from S. cerevisiae S288C, PDB ID 4AM6, chain A, residues 248-881, (C) Tropomyosin 2, homolog from O. cuniculus shown, PDB ID 2W49, chains A and B, residues 39–200. The ribbon diagram in each panel shows the portion of the protein altered by frameshift in orange, with the length of the altered region as well as the increase in sequence length indicated. Below each structure the C-terminal sequences of the reference strain and the longest version are shown, preceded by five residues of the unaltered region of sequence, shown in italics. Sequences are annotated with actual or predicted locations of α-helix (red) and β-strand (blue) secondary structures. These locations are inferred from the S. cerevisiae S288C or homologous structure in the case of the reference strain, or predicted by Jpred 3 in the case of the longest version.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC4494051&req=5

evv098-F5: Three proteins with additions that may impact protein structure. (A) Alcohol dehydrogenase I from S. cerevisiae S288C, PDB ID 2HCY, chain A, residues 1–347, (B) Actin-related protein 8 from S. cerevisiae S288C, PDB ID 4AM6, chain A, residues 248-881, (C) Tropomyosin 2, homolog from O. cuniculus shown, PDB ID 2W49, chains A and B, residues 39–200. The ribbon diagram in each panel shows the portion of the protein altered by frameshift in orange, with the length of the altered region as well as the increase in sequence length indicated. Below each structure the C-terminal sequences of the reference strain and the longest version are shown, preceded by five residues of the unaltered region of sequence, shown in italics. Sequences are annotated with actual or predicted locations of α-helix (red) and β-strand (blue) secondary structures. These locations are inferred from the S. cerevisiae S288C or homologous structure in the case of the reference strain, or predicted by Jpred 3 in the case of the longest version.
Mentions: Among our 54 addition alleles, we identified at least four cases in which the new amino acid sequence can be predicted to cause significant alteration and/or expansion of a protein domain structure. Three of these cases involve frameshift-mediated replacement of sequence integral to a protein domain structure, coupled with addition of varying amounts of sequence at the C terminus (fig. 5); a fourth case involves a pure addition with essentially no sequence replacement. In each of the four cases, secondary structure prediction using Jpred 3 (Cole et al. 2008) suggests the possibility of changes in secondary structure, either within the existing domain structure or as part of a C-terminal extension, or both. We discuss each case in more detail below.Fig. 5.—

Bottom Line: Because we study recent additions to potentially old genes, we are able to apply a variety of stringent quality filters to our annotations of what is a true protein-coding gene, discarding the putative proteins of unknown function that are typical of recent fully de novo genes.We identify 54 examples of C-terminal extensions in Saccharomyces and 28 in Drosophila, all of them recent enough to still be polymorphic.Four of the Saccharomyces C-terminal extensions (to ADH1, ARP8, TPM2, and PIS1) that survived our quality filters are predicted to lead to significant modification of a protein domain structure.

View Article: PubMed Central - PubMed

Affiliation: Department of Ecology & Evolutionary Biology, University of Arizona Present address: Aegis Sciences, Nashville, TN.

Show MeSH
Related in: MedlinePlus