scholarly journals The role of evolutionary selection in the dynamics of protein structure evolution

2016 ◽  
Author(s):  
Amy I. Gilson ◽  
Ahmee Marshall-Christensen ◽  
Jeong-Mo Choi ◽  
Eugene I. Shakhnovich
Keyword(s):  
Protein Structure ◽  
Sequence Divergence ◽  
Divergent Evolution ◽  
Structure Evolution ◽  
Linear Sequence ◽  
Structure Relationship ◽  
Ancient Proteins ◽  
Evolutionary Paths ◽  
Evolutionary Simulations ◽  
Evolution Of Proteins

AbstractHomology modeling is a powerful tool for predicting a protein’s structure. This approach is successful because proteins whose sequences are only 30% identical still adopt the same structure, while structure similarity rapidly deteriorates beyond the 30% threshold. By studying the divergence of protein structure as sequence evolves in real proteins and in evolutionary simulations, we show that this non-linear sequence-structure relationship emerges as a result of selection for protein folding stability in divergent evolution. Fitness constraints prevent the emergence of unstable protein evolutionary intermediates thereby enforcing evolutionary paths that preserve protein structure despite broad sequence divergence. However on longer time scales, evolution is punctuated by rare events where the fitness barriers obstructing structure evolution are overcome and discovery of new structures occurs. We outline biophysical and evolutionary rationale for broad variation in protein family sizes, prevalence of compact structures among ancient proteins and more rapid structure evolution of proteins with lower packing density.

scholarly journals New Hepatitis B Virus of Cranes That Has an Unexpected Broad Host Range

2003 ◽  
Vol 77 (3) ◽  
pp. 1964-1976 ◽  
Author(s):  
Alexej Prassolov ◽  
Heinz Hohenberg ◽  
Tatyana Kalinina ◽  
Carola Schneider ◽  
Lucyna Cova ◽  
...  
Keyword(s):  
Hepatitis B Virus ◽  
Hepatitis B ◽  
Host Range ◽  
Sequence Divergence ◽  
Divergent Evolution ◽  
Broad Host Range ◽  
Virus Propagation ◽  
Direct Dna Sequencing ◽  
Duck Hepatitis ◽  
B Virus

ABSTRACT All hepadnaviruses known so far have a very limited host range, restricted to their natural hosts and a few closely related species. This is thought to be due mainly to sequence divergence in the large envelope protein and species-specific differences in host components essential for virus propagation. Here we report an infection of cranes with a novel hepadnavirus, designated CHBV, that has an unexpectedly broad host range and is only distantly evolutionarily related to avihepadnaviruses of related hosts. Direct DNA sequencing of amplified CHBV DNA as well a sequencing of cloned viral genomes revealed that CHBV is most closely related to, although distinct from, Ross' goose hepatitis B virus (RGHBV) and slightly less closely related to duck hepatitis B virus (DHBV). Phylogenetically, cranes are very distant from geese and ducks and are most closely related to herons and storks. Naturally occurring hepadnaviruses in the last two species are highly divergent in sequence from RGHBV and DHBV and do not infect ducks or do so only marginally. In contrast, CHBV from crane sera and recombinant CHBV produced from LMH cells infected primary duck hepatocytes almost as efficiently as DHBV did. This is the first report of a rather broad host range of an avihepadnavirus. Our data imply either usage of similar or identical entry pathways and receptors by DHBV and CHBV, unusual host and virus adaptation mechanisms, or divergent evolution of the host genomes and cellular components required for virus propagation.

scholarly journals Evolutionary assembly patterns of prokaryotic genomes

2015 ◽  
Author(s):  
Maximilian O. Press ◽  
Christine Queitsch ◽  
Elhanan Borenstein
Keyword(s):  
Evolutionary Constraints ◽  
Historical Contingency ◽  
Phenotypic Characters ◽  
Functional Relationships ◽  
Evolutionary Innovation ◽  
Gene Level ◽  
Prokaryotic Genomes ◽  
Evolutionary Paths ◽  
Evolution Of Proteins ◽  
Sequence Substitution

AbstractEvolutionary innovation must occur in the context of some genomic background, which limits available evolutionary paths. For example, protein evolution by sequence substitution is constrained by epistasis between residues. In prokaryotes, evolutionary innovation frequently happens by macrogenomic events such as horizontal gene transfer (HGT). Previous work has suggested that HGT can be influenced by ancestral genomic content, yet the extent of such gene-level constraints has not yet been systematically characterized. Here, we evaluated the evolutionary impact of such constraints in prokaryotes, using probabilistic ancestral reconstructions from 634 extant prokaryotic genomes and a novel framework for detecting evolutionary constraints on HGT events. We identified 8,228 directional dependencies between genes, and demonstrated that many such dependencies reflect known functional relationships, including, for example, evolutionary dependencies of the photosynthetic enzyme RuBisCO. Modeling all dependencies as a network, we adapted an approach from graph theory to establish chronological precedence in the acquisition of different genomic functions. Specifically, we demonstrated that specific functions tend to be gained sequentially, suggesting that evolution in prokaryotes is governed by functional assembly patterns. Finally, we showed that these dependencies are universal rather than clade-specific and are often sufficient for predicting whether or not a given ancestral genome will acquire specific genes. Combined, our results indicate that evolutionary innovation via HGT is profoundly constrained by epistasis and historical contingency, similar to the evolution of proteins and phenotypic characters, and suggest that the emergence of specific metabolic and pathological phenotypes in prokaryotes can be predictable from current genomes.

scholarly journals Chromosome size affects sequence divergence between species through the interplay of recombination and selection

2021 ◽  
Author(s):  
Anna Tigano ◽  
Ruqayya Khan ◽  
Arina D. Omer ◽  
David Weisz ◽  
Olga Dudchenko ◽  
...  
Keyword(s):  
Recombination Rate ◽  
Chromosomal Rearrangements ◽  
Genome Structure ◽  
Sequence Divergence ◽  
Great Apes ◽  
Integrative Approach ◽  
Chromosome Size ◽  
Recombination Rates ◽  
Evolutionary Simulations ◽  
The Relationship

AbstractThe structure of the genome, including the architecture, number, and size of its chromosomes, shapes the distribution of genetic diversity and sequence divergence. Importantly, smaller chromosomes experience higher recombination rates than larger ones. To investigate how the relationship between chromosome size and recombination rate affects sequence divergence between species, we adopted an integrative approach that combines empirical analyses and evolutionary simulations. We estimated pairwise sequence divergence among 15 species from three different Mammalian clades - Peromyscus rodents, Mus mice, and great apes - from chromosome-level genome assemblies. We found a strong significant negative correlation between chromosome size and sequence divergence in all species comparisons within the Peromyscus and great apes clades, but not the Mus clade, demonstrating that the dramatic chromosomal rearrangements among Mus species masked the ancestral genomic landscape of divergence in many comparisons. Moreover, our evolutionary simulations showed that the main factor determining differences in divergence among chromosomes of different size is the interplay of recombination rate and selection, with greater variation in larger populations than in smaller ones. In ancestral populations, shorter chromosomes harbor greater nucleotide diversity. As ancestral populations diverge and eventually speciate, diversity present at the onset of the split contributes to greater sequence divergence in shorter chromosomes among daughter species. The combination of empirical data and evolutionary simulations also revealed other factors that affect the relationship between chromosome size and divergence, including chromosomal rearrangements, demography, and divergence times, and deepen our understanding of the role of genome structure on the evolution of species divergence.

scholarly journals The variation among sites of protein structure divergence is shaped by mutation and scaled by selection

2020 ◽  
Author(s):  
María Laura Marcos ◽  
Julian Echave
Keyword(s):  
Protein Structure ◽  
Protein Evolution ◽  
Protein Structures ◽  
Sequence Divergence ◽  
Biophysical Model ◽  
Sequence Variability ◽  
Protein Families ◽  
Scaling Effect ◽  
Mutation And Selection

AbstractProtein structures do not evolve uniformly, but the degree of structure divergence varies among sites. The resulting site-dependent structure divergence patterns emerge from a process that involves mutation and selection, which may both, in principle, influence the emergent pattern. In contrast with sequence divergence patterns, which are known to be mainly determined by selection, the relative contributions of mutation and selection to structure divergence patterns is unclear. Here, studying 6 protein families with a mechanistic biophysical model of protein evolution, we untangle the effects of mutation and selection. We found that even in the absence of selection, structure divergence varies from site to site because the mutational sensitivity is not uniform. Selection scales the profile, increasing its amplitude, without changing its shape. This scaling effect follows from the similarity between mutational sensitivity and sequence variability profiles.

scholarly journals Snapshot of Protein Structure Evolution Reveals Conservation of Functional Dimerization through Intertwined Folding

Structure ◽  
2004 ◽  
Vol 12 (8) ◽  
pp. 1489-1494 ◽  
Author(s):  
Dimitri Y Chirgadze ◽  
Mykhaylo Demydchuk ◽  
Marion Becker ◽  
Stephen Moran ◽  
Massimo Paoli
Keyword(s):  
Protein Structure ◽  
Structure Evolution

scholarly journals Divergent Evolution of the repFII Replicon of IncF Plasmids Carrying Cytotoxic Necrotizing Factorcnf2, Cytolethal Distending ToxincdtIII, andf17AeFimbrial Variant Genes in Type 2 Necrotoxigenic Escherichia coli Isolates from Calves

2015 ◽  
Vol 82 (2) ◽  
pp. 510-517
Author(s):  
Morgan Bihannic ◽  
Marisa Haenni ◽  
Eric Oswald ◽  
Jean-Yves Madec
Keyword(s):  
Escherichia Coli ◽  
Driving Forces ◽  
Divergent Evolution ◽  
Virulence Determinants ◽  
Genetic Determinants ◽  
Content Type ◽  
E Coli ◽  
Fimbrial Adhesins ◽  
Evolutionary Paths

ABSTRACTAmong the pathovars ofEscherichia coliin cattle, necrotoxigenicE. coli(NTEC) is defined by the production of cytotoxic necrotizing factors (CNFs). In particular, type 2 NTEC (NTEC2) strains are frequent in diarrheic and septicemic calves and usually coproduce CNF type 2 (CNF2), cytolethal distending toxin type III (CDTIII), and fimbrial adhesins of the F17 family, whose genetic determinants have frequently been reported on the same Vir-like plasmid. In this study, we investigated the genetic environment of thecnf2,f17Ae, andcdtIIIgenes in a collection of fecalE. coliisolates recovered from 484 French and 58 Iranian calves. In particular, we highlighted the spread ofcnf2,f17Ae, andcdtIIIon similar 150-kb IncF plasmids harboring the newly assigned repFII replicon allele F74 in NTEC2 isolates. Interestingly, this 150-kb IncF plasmid differed from the 140-kb IncF plasmid harboring the newly assigned repFII replicon allele F75 and carryingcnf2alone. These results suggest two divergent lineages ofcnf2-carrying IncF plasmids depending on the presence of thef17AeandcdtIIIgenes. This partition was observed inE. colistrains of unrelated backgrounds, suggesting two different evolutionary paths ofcnf2-carrying IncF plasmids rather than divergent evolutions of NTEC2 clones. The driving forces for such divergent evolutions are not known, and further studies are required to clarify the selection of plasmid subtypes spreading virulence determinants inE. coli, in particular, plasmids of the IncF family.

scholarly journals The effect of dark matter on stars at the Galactic center: The paradox of youth problem

2020 ◽  
Vol 29 (08) ◽  
pp. 2050052
Author(s):  
Ebrahim Hassani ◽  
Reza Pazhouhesh ◽  
Hossein Ebadi
Keyword(s):  
Black Hole ◽  
Dark Matter ◽  
Galactic Center ◽  
Young Stars ◽  
Evolutionary Models ◽  
Massive Black Hole ◽  
Physical Conditions ◽  
Dm Effect ◽  
Evolutionary Paths ◽  
Evolutionary Simulations

Stars that evolve near the Galactic massive black hole show strange behaviors. The spectroscopic features of these stars show that they must be old. But their luminosities are much higher than the amounts that are predicted by the current stellar evolutionary models, which means that they must be active and young stars. In fact, this group of stars shows signatures of old and young stars, simultaneously. This is a paradox known as the “paradox of youth problem” (PYP). Some people tried to solve the PYP without supposing dark matter (DM) effects on stars. But, in this work, we implemented Weakly Interacting Massive Particles (WIMPs) annihilation as a new source of energy inside such stars. This implementation is logical for stars that evolve at high DM density environments. The new source of energy causes stars to follow different evolutionary paths on the H-R diagram in comparison with classical stellar evolutionary models. Increasing DM density in stellar evolutionary simulations causes the deviations from the standard H-R diagrams becomes more pronounced. By investigating the effects of WIMPs density on stellar structures and evolutions, we concluded that by considering DM effects on stars at the Galactic center, it is possible to solve the PYP. In addition to DM effect, complete solutions to PYP must consider all extreme and unique physical conditions that are present near the Galactic massive black hole.

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