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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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(A) The stop codon position in the sister species was used as an outgroup to determine whether a SCP was caused by an addition to or a subtraction from the ancestral coding sequence. Additions can result either from point mutations eliminating the stop codon or from indels that knock the stop codon out of frame. In the latter case, we distinguish between added amino acids that increase the total length of the protein, and new amino acids that include all novel amino acids following the indel. (B) When the SCP involves more than two stop codon positions, inference is more complicated. Here, at least one addition took place, plus one event that could have been either an addition or a subtraction. (C) At least one addition and one subtraction must have occurred to explain this phylogeny. More complex cases with more than 3 stop codon positions were classified using the same logic. While it is in principle possible to use the strain phylogeny (Liti et al. 2009) to distinguish the order of events in these cases, there is enough outcrossing between strains (Ruderfer et al. 2006) such that the gene tree may not match the strain tree, and so this was not done.
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evv098-F1: (A) The stop codon position in the sister species was used as an outgroup to determine whether a SCP was caused by an addition to or a subtraction from the ancestral coding sequence. Additions can result either from point mutations eliminating the stop codon or from indels that knock the stop codon out of frame. In the latter case, we distinguish between added amino acids that increase the total length of the protein, and new amino acids that include all novel amino acids following the indel. (B) When the SCP involves more than two stop codon positions, inference is more complicated. Here, at least one addition took place, plus one event that could have been either an addition or a subtraction. (C) At least one addition and one subtraction must have occurred to explain this phylogeny. More complex cases with more than 3 stop codon positions were classified using the same logic. While it is in principle possible to use the strain phylogeny (Liti et al. 2009) to distinguish the order of events in these cases, there is enough outcrossing between strains (Ruderfer et al. 2006) such that the gene tree may not match the strain tree, and so this was not done.

Mentions: Nonsingleton SCP gene sequences were then realigned with their monomorphic sister reference sequences and reanalyzed for SCP. Genes were excluded if the stop codon position in the monomorphic sister species was not shared with any of the focal species alleles, reducing the number of genes to 817. The remaining genes were then classified as additions, subtractions, or ambiguous events (fig. 1). Alignments of genes that were classified as additions were manually checked for quality and poorly aligned sequences were removed. The remaining sequences were then realigned and edges were cleaned using the extend and prune algorithm described above.Fig. 1.—


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)

(A) The stop codon position in the sister species was used as an outgroup to determine whether a SCP was caused by an addition to or a subtraction from the ancestral coding sequence. Additions can result either from point mutations eliminating the stop codon or from indels that knock the stop codon out of frame. In the latter case, we distinguish between added amino acids that increase the total length of the protein, and new amino acids that include all novel amino acids following the indel. (B) When the SCP involves more than two stop codon positions, inference is more complicated. Here, at least one addition took place, plus one event that could have been either an addition or a subtraction. (C) At least one addition and one subtraction must have occurred to explain this phylogeny. More complex cases with more than 3 stop codon positions were classified using the same logic. While it is in principle possible to use the strain phylogeny (Liti et al. 2009) to distinguish the order of events in these cases, there is enough outcrossing between strains (Ruderfer et al. 2006) such that the gene tree may not match the strain tree, and so this was not done.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC4494051&req=5

evv098-F1: (A) The stop codon position in the sister species was used as an outgroup to determine whether a SCP was caused by an addition to or a subtraction from the ancestral coding sequence. Additions can result either from point mutations eliminating the stop codon or from indels that knock the stop codon out of frame. In the latter case, we distinguish between added amino acids that increase the total length of the protein, and new amino acids that include all novel amino acids following the indel. (B) When the SCP involves more than two stop codon positions, inference is more complicated. Here, at least one addition took place, plus one event that could have been either an addition or a subtraction. (C) At least one addition and one subtraction must have occurred to explain this phylogeny. More complex cases with more than 3 stop codon positions were classified using the same logic. While it is in principle possible to use the strain phylogeny (Liti et al. 2009) to distinguish the order of events in these cases, there is enough outcrossing between strains (Ruderfer et al. 2006) such that the gene tree may not match the strain tree, and so this was not done.
Mentions: Nonsingleton SCP gene sequences were then realigned with their monomorphic sister reference sequences and reanalyzed for SCP. Genes were excluded if the stop codon position in the monomorphic sister species was not shared with any of the focal species alleles, reducing the number of genes to 817. The remaining genes were then classified as additions, subtractions, or ambiguous events (fig. 1). Alignments of genes that were classified as additions were manually checked for quality and poorly aligned sequences were removed. The remaining sequences were then realigned and edges were cleaned using the extend and prune algorithm described above.Fig. 1.—

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