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Functional Significance May Underlie the Taxonomic Utility of Single Amino Acid Substitutions in Conserved Proteins

We hypothesized that some amino acid substitutions in conserved proteins that are strongly fixed by critical functional roles would show lineage-specific distributions. As an example of an archetypal conserved eukaryotic protein we considered the active site of β-tubulin. Our analysis identified one... Full description

Journal Title: Journal of Molecular Evolution 2010, Vol.70 (4), p.395-402
Main Author: Tyler, Kevin M
Other Authors: Wagner, Gerd K , Wu, Qiong , Huber, Katharina T
Format: Electronic Article Electronic Article
Language: English
Subjects:
SNP
Publisher: New York: Springer-Verlag
ID: ISSN: 0022-2844
Link: https://www.ncbi.nlm.nih.gov/pubmed/20386893
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title: Functional Significance May Underlie the Taxonomic Utility of Single Amino Acid Substitutions in Conserved Proteins
format: Article
creator:
  • Tyler, Kevin M
  • Wagner, Gerd K
  • Wu, Qiong
  • Huber, Katharina T
subjects:
  • Amino Acid Sequence
  • Amino Acid Substitution - genetics
  • Amino acids
  • Analysis
  • Animal Genetics and Genomics
  • Animals
  • Article
  • Behavior
  • Biomedical and Life Sciences
  • Cattle
  • Cell Biology
  • Conserved Sequence
  • Ecology
  • Eukaryota - genetics
  • Eukaryote
  • Eukaryotes
  • Evolution
  • Evolutionary Biology
  • Fungal Proteins - genetics
  • Genetics
  • Genomics
  • Life Sciences
  • macromolecular substances
  • Medical policy
  • Microbiology
  • Molecular Biology
  • Pharmacy
  • Phylogenetics
  • Phylogeny
  • Plant Genetics and Genomics
  • Plant Sciences
  • Polymorphism, Single Nucleotide
  • Proteins
  • Radiation
  • Sequence Alignment
  • SNP
  • Software
  • Substitution
  • Systematics
  • Tubulin
  • Tubulin - genetics
  • Tubulins
  • Unikont
  • Universities and colleges
ispartof: Journal of Molecular Evolution, 2010, Vol.70 (4), p.395-402
description: We hypothesized that some amino acid substitutions in conserved proteins that are strongly fixed by critical functional roles would show lineage-specific distributions. As an example of an archetypal conserved eukaryotic protein we considered the active site of β-tubulin. Our analysis identified one amino acid substitution—β-tubulin F224—which was highly lineage specific. Investigation of β-tubulin for other phylogenetically restricted amino acids identified several with apparent specificity for well-defined phylogenetic groups. Intriguingly, none showed specificity for “supergroups” other than the unikonts. To understand why, we analysed the β-tubulin Neighbor-Net and demonstrated a fundamental division between core β-tubulins (plant-like) and divergent β-tubulins (animal and fungal). F224 was almost completely restricted to the core β-tubulins, while divergent β-tubulins possessed Y224. Thus, our specific example offers insight into the restrictions associated with the co-evolution of β-tubulin during the radiation of eukaryotes, underlining a fundamental dichotomy between F-type, core β-tubulins and Y-type, divergent β-tubulins. More broadly our study provides proof of principle for the taxonomic utility of critical amino acids in the active sites of conserved proteins.
language: eng
source:
identifier: ISSN: 0022-2844
fulltext: no_fulltext
issn:
  • 0022-2844
  • 1432-1432
url: Link


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creatorTyler, Kevin M ; Wagner, Gerd K ; Wu, Qiong ; Huber, Katharina T
creatorcontribTyler, Kevin M ; Wagner, Gerd K ; Wu, Qiong ; Huber, Katharina T
descriptionWe hypothesized that some amino acid substitutions in conserved proteins that are strongly fixed by critical functional roles would show lineage-specific distributions. As an example of an archetypal conserved eukaryotic protein we considered the active site of β-tubulin. Our analysis identified one amino acid substitution—β-tubulin F224—which was highly lineage specific. Investigation of β-tubulin for other phylogenetically restricted amino acids identified several with apparent specificity for well-defined phylogenetic groups. Intriguingly, none showed specificity for “supergroups” other than the unikonts. To understand why, we analysed the β-tubulin Neighbor-Net and demonstrated a fundamental division between core β-tubulins (plant-like) and divergent β-tubulins (animal and fungal). F224 was almost completely restricted to the core β-tubulins, while divergent β-tubulins possessed Y224. Thus, our specific example offers insight into the restrictions associated with the co-evolution of β-tubulin during the radiation of eukaryotes, underlining a fundamental dichotomy between F-type, core β-tubulins and Y-type, divergent β-tubulins. More broadly our study provides proof of principle for the taxonomic utility of critical amino acids in the active sites of conserved proteins.
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subjectAmino Acid Sequence ; Amino Acid Substitution - genetics ; Amino acids ; Analysis ; Animal Genetics and Genomics ; Animals ; Article ; Behavior ; Biomedical and Life Sciences ; Cattle ; Cell Biology ; Conserved Sequence ; Ecology ; Eukaryota - genetics ; Eukaryote ; Eukaryotes ; Evolution ; Evolutionary Biology ; Fungal Proteins - genetics ; Genetics ; Genomics ; Life Sciences ; macromolecular substances ; Medical policy ; Microbiology ; Molecular Biology ; Pharmacy ; Phylogenetics ; Phylogeny ; Plant Genetics and Genomics ; Plant Sciences ; Polymorphism, Single Nucleotide ; Proteins ; Radiation ; Sequence Alignment ; SNP ; Software ; Substitution ; Systematics ; Tubulin ; Tubulin - genetics ; Tubulins ; Unikont ; Universities and colleges
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descriptionWe hypothesized that some amino acid substitutions in conserved proteins that are strongly fixed by critical functional roles would show lineage-specific distributions. As an example of an archetypal conserved eukaryotic protein we considered the active site of β-tubulin. Our analysis identified one amino acid substitution—β-tubulin F224—which was highly lineage specific. Investigation of β-tubulin for other phylogenetically restricted amino acids identified several with apparent specificity for well-defined phylogenetic groups. Intriguingly, none showed specificity for “supergroups” other than the unikonts. To understand why, we analysed the β-tubulin Neighbor-Net and demonstrated a fundamental division between core β-tubulins (plant-like) and divergent β-tubulins (animal and fungal). F224 was almost completely restricted to the core β-tubulins, while divergent β-tubulins possessed Y224. Thus, our specific example offers insight into the restrictions associated with the co-evolution of β-tubulin during the radiation of eukaryotes, underlining a fundamental dichotomy between F-type, core β-tubulins and Y-type, divergent β-tubulins. More broadly our study provides proof of principle for the taxonomic utility of critical amino acids in the active sites of conserved proteins.
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16Evolution
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abstractWe hypothesized that some amino acid substitutions in conserved proteins that are strongly fixed by critical functional roles would show lineage-specific distributions. As an example of an archetypal conserved eukaryotic protein we considered the active site of β-tubulin. Our analysis identified one amino acid substitution—β-tubulin F224—which was highly lineage specific. Investigation of β-tubulin for other phylogenetically restricted amino acids identified several with apparent specificity for well-defined phylogenetic groups. Intriguingly, none showed specificity for “supergroups” other than the unikonts. To understand why, we analysed the β-tubulin Neighbor-Net and demonstrated a fundamental division between core β-tubulins (plant-like) and divergent β-tubulins (animal and fungal). F224 was almost completely restricted to the core β-tubulins, while divergent β-tubulins possessed Y224. Thus, our specific example offers insight into the restrictions associated with the co-evolution of β-tubulin during the radiation of eukaryotes, underlining a fundamental dichotomy between F-type, core β-tubulins and Y-type, divergent β-tubulins. More broadly our study provides proof of principle for the taxonomic utility of critical amino acids in the active sites of conserved proteins.
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