Faculty Opinions recommendation of A Shift in Aggregation Avoidance Strategy Marks a Long-Term Direction to Protein Evolution.

2019 ◽  
Author(s):  
Helen Chamberlin
Keyword(s):  
Protein Evolution ◽  
Avoidance Strategy

scholarly journals A Shift in Aggregation Avoidance Strategy Marks a Long-Term Direction to Protein Evolution

Genetics ◽  
2019 ◽  
Vol 211 (4) ◽  
pp. 1345-1355 ◽  
Author(s):  
Scott G. Foy ◽  
Benjamin A. Wilson ◽  
Jason Bertram ◽  
Matthew H. J. Cordes ◽  
Joanna Masel
Keyword(s):  
Protein Evolution ◽  
Avoidance Strategy

scholarly journals Universal constraints on protein evolution in the long-term evolution experiment with Escherichia coli

2020 ◽  
Author(s):  
Rohan Maddamsetti
Keyword(s):  
Protein Evolution ◽  
Long Term Evolution ◽  
Protein Abundance ◽  
Interacting Proteins ◽  
Protein Thermostability ◽  
Protein Protein Interaction ◽  
Term Evolution ◽  
Evolution Experiment ◽  
Positive Correlations

AbstractAlthough it is well known that highly expressed and highly interacting proteins evolve slowly across the tree of life, there is little consensus for why this is true. Here, I report that highly abundant and highly interacting proteins evolve slowly in the hypermutator populations of Lenski’s long-term evolution experiment with E. coli (LTEE). Specifically, the density of observed mutations per gene, as measured in metagenomic time series covering 60,000 generations of the LTEE, strongly anti-correlates with mRNA abundance, protein abundance, and degree of protein-protein interaction. Weaker positive correlations between protein thermostability and mutation density are observed in the hypermutator populations, counterbalanced by negative correlations between protein thermostability and mRNA and protein abundance. These results show that universal constraints on protein evolution are visible in data spanning three decades of experimental evolution. Therefore, it should be possible to design experiments to answer why highly expressed and highly interacting proteins evolve slowly.

scholarly journals Molecular function limits divergent protein evolution on planetary timescales

2017 ◽  
Author(s):  
Mariam M. Konaté ◽  
Germán Plata ◽  
Jimin Park ◽  
Dinara R. Usmanova ◽  
Harris H. Wang ◽  
...  
Keyword(s):  
Amino Acid ◽  
Protein Evolution ◽  
Molecular Function ◽  
Functional Conservation ◽  
Fitness Effects ◽  
Sequence Identity ◽  
The Past ◽  
Independent Evolution

AbstractFunctional conservation is known to constrain protein evolution. Nevertheless, the long-term divergence patterns of proteins maintaining the same molecular function and the possible limits of this divergence have not been explored in detail. We investigate these fundamental questions by characterizing the divergence between ancient protein orthologs with conserved molecular function. Our results demonstrate that the decline of sequence and structural similarities between such orthologs significantly slows down after ~1-2 billion years of independent evolution. As a result, their sequence and structural similarities have not substantially decreased for the past billion years. The effective divergence limit (>25% sequence identity) is not primarily due to protein sites universally conserved in all linages. Instead, less than four amino acid types are accepted, on average, per site in orthologs strictly conserving their molecular function. Our analysis also reveals different divergence patterns for protein sites with experimentally determined small and large fitness effects of mutations.

scholarly journals Long-Term Asymmetrical Acceleration of Protein Evolution after Gene Duplication

2014 ◽  
Vol 6 (8) ◽  
pp. 1949-1955 ◽  
Author(s):  
Oriol Pich i Roselló ◽  
Fyodor A. Kondrashov
Keyword(s):  
Gene Duplication ◽  
Protein Evolution

scholarly journals A Model of Substitution Trajectories in Sequence Space and Long-Term Protein Evolution

2014 ◽  
Vol 32 (2) ◽  
pp. 542-554 ◽  
Author(s):  
Dinara R. Usmanova ◽  
Luca Ferretti ◽  
Inna S. Povolotskaya ◽  
Peter K. Vlasov ◽  
Fyodor A. Kondrashov
Keyword(s):  
Protein Evolution ◽  
Sequence Space

scholarly journals Universal constraints on protein evolution in the long-term evolution experiment with Escherichia coli

2021 ◽  
Author(s):  
Rohan Maddamsetti
Keyword(s):  
Escherichia Coli ◽  
Protein Evolution ◽  
Long Term Evolution ◽  
Protein Abundance ◽  
Nonsynonymous Mutation ◽  
Protein Protein Interaction ◽  
Term Evolution ◽  
Mutation Density ◽  
Evolution Experiment

Abstract Although it is well known that abundant proteins evolve slowly across the tree of life, there is little consensus for why this is true. Here, I report that abundant proteins evolve slowly in the hypermutator populations of Lenski’s long-term evolution experiment with Escherichia coli (LTEE). Specifically, the density of all observed mutations per gene, as measured in metagenomic time series covering 60,000 generations of the LTEE, significantly anti-correlates with mRNA abundance, protein abundance, and degree of protein-protein interaction. The same pattern holds for nonsynonymous mutation density. However, synonymous mutation density, measured across the LTEE hypermutator populations, positively correlates with protein abundance. These results show that universal constraints on protein evolution are visible in data spanning three decades of experimental evolution. Therefore, it should be possible to design experiments to answer why abundant proteins evolve slowly.

scholarly journals Molecular function limits divergent protein evolution on planetary timescales

eLife ◽  
2019 ◽  
Vol 8 ◽  
Author(s):  
Mariam M Konaté ◽  
Germán Plata ◽  
Jimin Park ◽  
Dinara R Usmanova ◽  
Harris Wang ◽  
...  
Keyword(s):  
Protein Evolution ◽  
Protein Sequences ◽  
Editorial Note ◽  
Molecular Function ◽  
Editorial Process ◽  
Functional Conservation ◽  
Fitness Effects ◽  
Sequence Identity ◽  
The Past

Functional conservation is known to constrain protein evolution. Nevertheless, the long-term divergence patterns of proteins maintaining the same molecular function and the possible limits of this divergence have not been explored in detail. We investigate these fundamental questions by characterizing the divergence between ancient protein orthologs with conserved molecular function. Our results demonstrate that the decline of sequence and structural similarities between such orthologs significantly slows down after ~1–2 billion years of independent evolution. As a result, the sequence and structural similarities between ancient orthologs have not substantially decreased for the past billion years. The effective divergence limit (>25% sequence identity) is not primarily due to protein sites universally conserved in all linages. Instead, less than four amino acid types are accepted, on average, per site across orthologous protein sequences. Our analysis also reveals different divergence patterns for protein sites with experimentally determined small and large fitness effects of mutations.Editorial note: This article has been through an editorial process in which the authors decide how to respond to the issues raised during peer review. The Reviewing Editor's assessment is that all the issues have been addressed (<xref ref-type="decision-letter" rid="SA1">see decision letter</xref>).

scholarly journals Highly expressed genes evolve under strong epistasis from a proteome-wide scan in E. coli

2017 ◽  
Author(s):  
Eric Girard ◽  
Pouria Dasmeh ◽  
Adrian W.R. Serohijos
Keyword(s):  
Protein Evolution ◽  
Protein Unfolding ◽  
Long Term Evolution ◽  
Fitness Cost ◽  
Sequence Evolution ◽  
E Coli ◽  
Term Evolution ◽  
Highly Expressed Genes

ABSTRACTEpistasis or the non-additivity of mutational effects is a major force in protein evolution, but it has not been systematically quantified at the level of a proteome. Here, we estimated the extent of epistasis for 2,382 genes in E. coli using several hundreds of orthologs for each gene within the class Gammaproteobacteria. We found that the average epistasis is ~41% across genes in the proteome and that epistasis is stronger among highly expressed genes. This trend is quantitatively explained by the prevailing model of sequence evolution based on minimizing the fitness cost of protein unfolding and aggregation. Our results highlight the coupling between selection and epistasis in the long-term evolution of a proteome.

Therapy and prevention for mental health: What if mental diseases are mostly not brain disorders?

2019 ◽  
Vol 42 ◽  
Author(s):  
John P. A. Ioannidis
Keyword(s):  
Mental Health ◽  
Mental Disease ◽  
Brain Disorders ◽  
Social Stressors ◽  
Labor Education ◽  
Mental Diseases ◽  
Long Term Follow Up ◽  
Political Decisions

AbstractNeurobiology-based interventions for mental diseases and searches for useful biomarkers of treatment response have largely failed. Clinical trials should assess interventions related to environmental and social stressors, with long-term follow-up; social rather than biological endpoints; personalized outcomes; and suitable cluster, adaptive, and n-of-1 designs. Labor, education, financial, and other social/political decisions should be evaluated for their impacts on mental disease.

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