scholarly journals APOBEC3s: history of an antiviral and mutagenic protein family

Virologie ◽  
2020 ◽  
Vol 24 (6) ◽  
pp. 381-418
Author(s):  
Cédric Verriez ◽  
Roland Marquet ◽  
Jean-Christophe Paillart ◽  
Benjamin Stupfler
Keyword(s):  
Protein Family ◽  
History Of

scholarly journals ASPEN: A methodology for reconstructing protein evolution with improved accuracy using ensemble models

2017 ◽  
Author(s):  
Roman Sloutsky ◽  
Kristen M. Naegle
Keyword(s):  
Protein Evolution ◽  
Protein Function ◽  
Evolutionary History ◽  
Phylogenetic Signal ◽  
Protein Family ◽  
Reconstruction Algorithms ◽  
Protein Families ◽  
Homologous Proteins ◽  
Extant Species ◽  
History Of

AbstractEvolutionary reconstruction algorithms produce models of the evolutionary history of proteins: the order of duplications and speciations that led to extant homologous proteins observed across species. Although they are regularly used to gain insight into protein function, these models are estimates of an unknowable truth according to the underlying assumptions inherent in each algorithm, its objective function, and the input sequences supplied for reconstruction. In practice, the generated models are highly sensitive to the sequence inputs. In this work, we asked whether we could identify stronger phylogenetic signal by capitalizing on the variance introduced by perturbing the input to evolutionary reconstruction to explore a rich space of possible models that could explain protein evolution. We subsampled from available protein orthologs, “same” proteins across multiple extant species, and produced an ensemble of topologies representing the duplication history which produced related proteins (paralogs) for simulated protein families and in a real protein family – the LacI transcription factor family. We found that two very important phenomena arise from this approach. First, the reproducibility of an all-sequence, single-alignment reconstruction, measured by comparing topologies inferred from 90% subsamples, directly correlates with the accuracy of that single-alignment reconstruction, producing a measurable value for something that has been traditionally unknowable. Second, if we take a large ensemble of trees inferred from 50% subsamples and cast the ensemble into a form that represents the distribution of pairwise leaf distances observed across the ensemble, then trees that capture the most frequently observed relationships are also the most accurate. We propose a new methodology, ASPEN, a meta-algorithm that finds and ranks the trees that are most consistent with observations across the ensemble. Top-ranked ASPEN trees are significantly more accurate than the single-alignment tree produced from all available sequences. Importantly, our findings suggest that the true tree is currently inaccessible for most real protein families. Instead, applications that rely on evolutionary models should integrate across many trees that are equally likely to represent the true evolutionary history of a protein family.

scholarly journals Acyl-CoA Dehydrogenases: Dynamic History of Protein Family Evolution

2009 ◽  
Vol 69 (2) ◽  
pp. 176-193 ◽  
Author(s):  
Zuzana Swigoňová ◽  
Al-Walid Mohsen ◽  
Jerry Vockley
Keyword(s):  
Protein Family ◽  
History Of ◽  
Acyl Coa Dehydrogenases
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