Evolutionary Rate Variation in Organelle Genomes: The Role of Mutational Processes

2011 ◽  
pp. 123-146 ◽  
Author(s):  
Daniel B. Sloan ◽  
Douglas R. Taylor
Keyword(s):  
Evolutionary Rate ◽  
Rate Variation ◽  
Organelle Genomes ◽  
Mutational Processes

scholarly journals Horizontal Gene Transfer Involving Chloroplasts

2021 ◽  
Vol 22 (9) ◽  
pp. 4484
Author(s):  
Ewa Filip ◽  
Lidia Skuza
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Driving Force ◽  
Genetic Material ◽  
Adaptive Significance ◽  
Chloroplast Genomes ◽  
Organelle Genomes ◽  
Number Of Genes ◽  
Cellular Compartments

Horizontal gene transfer (HGT)- is defined as the acquisition of genetic material from another organism. However, recent findings indicate a possible role of HGT in the acquisition of traits with adaptive significance, suggesting that HGT is an important driving force in the evolution of eukaryotes as well as prokaryotes. It has been noted that, in eukaryotes, HGT is more prevalent than originally thought. Mitochondria and chloroplasts lost a large number of genes after their respective endosymbiotic events occurred. Even after this major content loss, organelle genomes still continue to lose their own genes. Many of these are subsequently acquired by intracellular gene transfer from the original plastid. The aim of our review was to elucidate the role of chloroplasts in the transfer of genes. This review also explores gene transfer involving mitochondrial and nuclear genomes, though recent studies indicate that chloroplast genomes are far more active in HGT as compared to these other two DNA-containing cellular compartments.

Disentangling the role of competition, light interception, and functional traits in tree growth rate variation in South Asian tropical moist forests

2021 ◽  
Vol 483 ◽  
pp. 118908
Author(s):  
Mizanur Rahman ◽  
Masum Billah ◽  
Md Obydur Rahman ◽  
Debit Datta ◽  
Muhammad Ahsanuzzaman ◽  
...  
Keyword(s):  
Growth Rate ◽  
Functional Traits ◽  
South Asian ◽  
Tree Growth ◽  
Light Interception ◽  
Rate Variation ◽  
Tree Growth Rate

Chromosomal location and evolutionary rate variation in enterobacterial genes

Science ◽  
1989 ◽  
Vol 246 (4931) ◽  
pp. 808-810 ◽  
Author(s):  
P. Sharp ◽  
D. Shields ◽  
K. Wolfe ◽  
W. Li
Keyword(s):  
Evolutionary Rate ◽  
Chromosomal Location ◽  
Rate Variation

scholarly journals Accessibility Over Transposable Elements Reveals Genetic Determinants of Stemness Properties in Normal and Leukemic Hematopoiesis

2021 ◽  
Author(s):  
Bettina Nadorp ◽  
Giacomo Grillo ◽  
Aditi Qamra ◽  
Amanda Mitchell ◽  
Christopher Arlidge ◽  
...  
Keyword(s):  
Stem Cells ◽  
Hematopoietic Stem Cells ◽  
Chromatin Accessibility ◽  
Genetic Determinants ◽  
Hematopoietic Stem ◽  
Transcription Regulators ◽  
Docking Sites ◽  
Cellular Hierarchy ◽  
Mutational Processes

AbstractDespite most acute myeloid leukemia (AML) patients achieving complete remission after induction chemotherapy, two thirds of patients will relapse with fatal disease within 5 years. AML is organized as a cellular hierarchy sustained by leukemia stem cells (LSC) at the apex, with LSC properties directly linked to tumor progression, therapy failure and disease relapse 1–5. Despite the central role of LSC in poor patient outcomes, little is known of the genetic determinants of their stemness properties 6–8. Although much AML research focuses on mutational processes and their impact on gene expression programs, the genetic determinants of cell state properties including stemness expand beyond mutations, relying on the genetic architecture captured in the chromatin of each cell 9–11. As LSCs share many functional and molecular properties with normal hematopoietic stem cells (HSC), we identified genetic determinants of primitive populations enriched for LSCs and HSCs in comparison with their downstream mature progeny by investigating their chromatin accessibility. Our work reveals how distinct transposable element (TE) subfamilies are used in primitive versus mature populations, functioning as docking sites for stem cell-associated regulators of genome topology, including CTCF, or lineage-specific transcription regulators in primitive and mature populations, respectively. We further show how TE subfamilies accessible in LSCs define docking sites for several oncogenic drivers in AML, namely FLI1, LYL1 and MEIS1. Using chromatin accessibility profiles from a cohort of AML patients, we further show the clinical utility of our TE accessibility-based LSCTE121 scoring scheme to identify patients with high rates of relapse. Collectively, our work reveals how different accessible TE subfamilies serve as genetic determinants of stemness properties in normal and leukemic hematopoietic stem cells.

scholarly journals Identification and Visualization of Functionally Important Domains and Residues in Herpes Simplex Virus Glycoprotein K(gK) Using a Combination of Phylogenetics and Protein Modeling

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Paul J. F. Rider ◽  
Lyndon M. Coghill ◽  
Misagh Naderi ◽  
Jeremy M. Brown ◽  
Michal Brylinski ◽  
...  
Keyword(s):  
Herpes Simplex ◽  
Evolutionary Rate ◽  
Quantitative Measure ◽  
Rate Variation ◽  
Human Pathogens ◽  
Herpes Simplex Viruses ◽  
Varicella Zoster ◽  
Conserved Sequence ◽  
Glycoprotein K ◽  
Herpes Simplex Virus Glycoprotein

Abstract Alphaherpesviruses are a subfamily of herpesviruses that include the significant human pathogens herpes simplex viruses (HSV) and varicella zoster virus (VZV). Glycoprotein K (gK), conserved in all alphaherpesviruses, is a multi-membrane spanning virion glycoprotein essential for virus entry into neuronal axons, virion assembly, and pathogenesis. Despite these critical functions, little is known about which gK domains and residues are most important for maintaining these functions across all alphaherpesviruses. Herein, we employed phylogenetic and structural analyses including the use of a novel model for evolutionary rate variation across residues to predict conserved gK functional domains. We found marked heterogeneity in the evolutionary rate at the level of both individual residues and domains, presumably as a result of varying selective constraints. To clarify the potential role of conserved sequence features, we predicted the structures of several gK orthologs. Congruent with our phylogenetic analysis, slowly evolving residues were identified at potentially structurally significant positions across domains. We found that using a quantitative measure of amino acid rate variation combined with molecular modeling we were able to identify amino acids predicted to be critical for gK protein structure/function. This analysis yields targets for the design of anti-herpesvirus therapeutic strategies across all alphaherpesvirus species that would be absent from more traditional analyses of conservation.

scholarly journals Cross-species comparison of site-specific evolutionary-rate variation in influenza haemagglutinin

2013 ◽  
Vol 368 (1614) ◽  
pp. 20120334 ◽  
Author(s):  
Austin G. Meyer ◽  
Eric T. Dawson ◽  
Claus O. Wilke
Keyword(s):  
Protein Structure ◽  
Sialic Acid ◽  
Avian Influenza ◽  
Evolutionary Rate ◽  
Solvent Accessibility ◽  
Rate Variation ◽  
Structural Constraints ◽  
Binding Region ◽  
Site Specific ◽  
Sialic Acid Binding

We investigate the causes of site-specific evolutionary-rate variation in influenza haemagglutinin (HA) between human and avian influenza, for subtypes H1, H3, and H5. By calculating the evolutionary-rate ratio, ω = d N /d S as a function of a residue's solvent accessibility in the three-dimensional protein structure, we show that solvent accessibility has a significant but relatively modest effect on site-specific rate variation. By comparing rates within HA subtypes among host species, we derive an upper limit to the amount of variation that can be explained by structural constraints of any kind. Protein structure explains only 20–40% of the variation in ω . Finally, by comparing ω at sites near the sialic-acid-binding region to ω at other sites, we show that ω near the sialic-acid-binding region is significantly elevated in both human and avian influenza, with the exception of avian H5. We conclude that protein structure, HA subtype, and host biology all impose distinct selection pressures on sites in influenza HA.

Evolutionary rate variation among vertebrate β globin genes: Implications for dating gene family duplication events

Gene ◽  
2006 ◽  
Vol 380 (1) ◽  
pp. 21-29 ◽  
Author(s):  
Gabriela Aguileta ◽  
Joseph P. Bielawski ◽  
Ziheng Yang
Keyword(s):  
Gene Family ◽  
Evolutionary Rate ◽  
Rate Variation ◽  
Globin Genes ◽  
Duplication Events
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