scholarly journals Unprecedented Protein Divergence Within a T3SS Family

2021 ◽  
Author(s):  
Azzeldin Madkour ◽  
Bian Almessiry ◽  
Bertha González-Pedrajo ◽  
Brendan Kenny
Keyword(s):  
Protein Divergence

scholarly journals Mucosal Human Papillomaviruses Encode Four Different E5 Proteins Whose Chemistry and Phylogeny Correlate with Malignant or Benign Growth

2004 ◽  
Vol 78 (24) ◽  
pp. 13613-13626 ◽  
Author(s):  
Ignacio G. Bravo ◽  
Ángel Alonso
Keyword(s):  
Human Papillomaviruses ◽  
Structural Proteins ◽  
Phylogenetic Study ◽  
Protein Divergence ◽  
Early Proteins ◽  
Differential Involvement ◽  
E6 And E7 ◽  
Different Characteristics ◽  
L1 And L2 ◽  
Transformation Processes

ABSTRACT We performed a phylogenetic study of the E2-L2 region of human mucosal papillomaviruses (PVs) and of the proteins therein encoded. Hitherto, proteins codified in this region were known as E5 proteins. We show that many of these proteins could be spurious translations, according to phylogenetic and chemical coherence criteria between similar protein sequences. We show that there are four separate families of E5 proteins, with different characteristics of phylogeny, chemistry, and rate of evolution. For the sake of clarity, we propose a change in the present nomenclature. E5α is present in groups A5, A6, A7, A9, and A11, PVs highly associated with malignant carcinomas of the cervix and penis. E5β is present in groups A2, A3, A4, and A12, i.e., viruses associated with certain warts. E5γ is present in group A10, and E5δ is encoded in groups A1, A8, and A10, which are associated with benign transformations. The phylogenetic relationships between mucosal human PVs are the same when considering the oncoproteins E6 and E7 and the E5 proteins and differ from the phylogeny estimated for the structural proteins L1 and L2. Besides, the protein divergence rate is higher in early proteins than in late proteins, increasing in the order L1 < L2 < E6 ≈ E7 < E5. Moreover, the same proteins have diverged more rapidly in viruses associated with malignant transformations than in viruses associated with benign transformations. The E5 proteins display, therefore, evolutionary characteristics similar to those of the E6 and E7 oncoproteins. This could reflect a differential involvement of the E5 types in the transformation processes.

scholarly journals Mitochondria-encoded genes contribute to evolution of heat and cold tolerance in yeast

2019 ◽  
Vol 5 (1) ◽  
pp. eaav1848 ◽  
Author(s):  
Xueying C. Li ◽  
David Peris ◽  
Chris Todd Hittinger ◽  
Elaine A. Sia ◽  
Justin C. Fay
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Cold Tolerance ◽  
Yeast Species ◽  
Saccharomyces Uvarum ◽  
Phenotypic Differences ◽  
Protein Divergence ◽  
Thermal Growth ◽  
Genome Wide ◽  
A Genome ◽  
Moderate Effect

Genetic analysis of phenotypic differences between species is typically limited to interfertile species. Here, we conducted a genome-wide noncomplementation screen to identify genes that contribute to a major difference in thermal growth profile between two reproductively isolated yeast species,Saccharomyces cerevisiaeandSaccharomyces uvarum. The screen identified only a single nuclear-encoded gene with a moderate effect on heat tolerance, but, in contrast, revealed a large effect of mitochondrial DNA (mitotype) on both heat and cold tolerance. Recombinant mitotypes indicate that multiple genes contribute to thermal divergence, and we show that protein divergence inCOX1affects both heat and cold tolerance. Our results point to the yeast mitochondrial genome as an evolutionary hotspot for thermal divergence.

scholarly journals Adaptive protein divergence of BMP ligands takes place under developmental and evolutionary constraints

Development ◽  
2016 ◽  
Vol 143 (20) ◽  
pp. 3742-3750 ◽  
Author(s):  
Petra M. Tauscher ◽  
Jinghua Gui ◽  
Osamu Shimmi
Keyword(s):  
Evolutionary Constraints ◽  
Protein Divergence

scholarly journals Unprecedented Protein Divergence within a T3SS Family

2021 ◽  
Author(s):  
Azzeldin Madkour ◽  
Bian Almessiry ◽  
Bertha González-Pedrajo ◽  
Brendan Kenny
Keyword(s):  
Therapeutic Targets ◽  
Resistance Mechanisms ◽  
Specific Protein ◽  
Secretion System ◽  
Protein Functionality ◽  
Protein Divergence ◽  
Type Three Secretion System ◽  
Type Three Secretion ◽  
Rapid Emergence ◽  
Functional Defects

Selection pressure drives rapid emergence of antibiotic resistance mechanisms promoting searches for therapeutic targets in bacterial processes needed for virulence, not viability, which include the Type Three Secretion System (T3SS). Distinct T3SS families evolved from the flagellar export apparatus where remaining homology hinders development of anti-T3SS specific therapies. Around 15 proteins that are highly-conserved within, but not between T3SS families yet such divergence is rarely leveraged, to promote understanding, due to unknown evolutionary histories. Here we document unprecedented divergence in two ‘LEE’ T3SS family members. Interchangeability studies uncover unusual LEE biology (eg 2-orf genes) and illustrate each T3SS protein can tolerate dramatic change. Functional defects (12 proteins) and novel phenotypes enabled studies that reveal i) pathotype-specific protein functionality, ii) T3SS crosstalk with other processes, and iii) potential therapeutic targets. The work provides resources and testable predictions for further discoveries and will promote comparable studies between distinct T3SS families.

scholarly journals Regional effect on the molecular clock rate of protein evolution in Eutherian and Metatherian genomes

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Raf Huttener ◽  
Lieven Thorrez ◽  
Thomas in‘t Veld ◽  
Barney Potter ◽  
Guy Baele ◽  
...  
Keyword(s):  
Protein Evolution ◽  
Molecular Clock ◽  
Clock Rate ◽  
Regional Effect ◽  
Sliding Windows ◽  
Protein Divergence ◽  
Regional Effects ◽  
Specific Effects ◽  
A Genome ◽  
Phylogenetic Lineages

Abstract Background Different types of proteins diverge at vastly different rates. Moreover, the same type of protein has been observed to evolve with different rates in different phylogenetic lineages. In the present study we measured the rates of protein evolution in Eutheria (placental mammals) and Metatheria (marsupials) on a genome-wide basis and we propose that the gene position in the genome landscape has an important influence on the rate of protein divergence. Results We analyzed a protein-encoding gene set (n = 15,727) common to 16 mammals (12 Eutheria and 4 Metatheria). Using sliding windows that averaged regional effects of protein divergence we constructed landscapes in which strong and lineage-specific regional effects were seen on the molecular clock rate of protein divergence. Within each lineage, the relatively high rates were preferentially found in subtelomeric chromosomal regions. Such regions were observed to contain important and well-studied loci for fetal growth, uterine function and the generation of diversity in the adaptive repertoire of immunoglobulins. Conclusions A genome landscape approach visualizes lineage-specific regional differences between Eutherian and Metatherian rates of protein evolution. This phenomenon of chromosomal position is a new element that explains at least part of the lineage-specific effects and differences between proteins on the molecular clock rates.

scholarly journals The Relationship between Gene Isoform Multiplicity, Number of Exons and Protein Divergence

PLoS ONE ◽  
2013 ◽  
Vol 8 (8) ◽  
pp. e72742 ◽  
Author(s):  
Jordi Morata ◽  
Santi Béjar ◽  
David Talavera ◽  
Casandra Riera ◽  
Sergio Lois ◽  
...  
Keyword(s):  
Protein Divergence ◽  
The Relationship ◽  
Gene Isoform

scholarly journals Contingency and entrenchment in protein evolution under purifying selection

2015 ◽  
Vol 112 (25) ◽  
pp. E3226-E3235 ◽  
Author(s):  
Premal Shah ◽  
David M. McCandlish ◽  
Joshua B. Plotkin
Keyword(s):  
Ligand Binding ◽  
Protein Evolution ◽  
Protein Sequence ◽  
Computational Models ◽  
Purifying Selection ◽  
Sequence Evolution ◽  
Phenotypic Effect ◽  
Protein Divergence ◽  
Protein Sequence Evolution ◽  
Over Time

The phenotypic effect of an allele at one genetic site may depend on alleles at other sites, a phenomenon known as epistasis. Epistasis can profoundly influence the process of evolution in populations and shape the patterns of protein divergence across species. Whereas epistasis between adaptive substitutions has been studied extensively, relatively little is known about epistasis under purifying selection. Here we use computational models of thermodynamic stability in a ligand-binding protein to explore the structure of epistasis in simulations of protein sequence evolution. Even though the predicted effects on stability of random mutations are almost completely additive, the mutations that fix under purifying selection are enriched for epistasis. In particular, the mutations that fix are contingent on previous substitutions: Although nearly neutral at their time of fixation, these mutations would be deleterious in the absence of preceding substitutions. Conversely, substitutions under purifying selection are subsequently entrenched by epistasis with later substitutions: They become increasingly deleterious to revert over time. Our results imply that, even under purifying selection, protein sequence evolution is often contingent on history and so it cannot be predicted by the phenotypic effects of mutations assayed in the ancestral background.

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