Article
Biochemistry & Molecular Biology
Shilpi Chaurasia, Julien Y. Dutheil
Summary: Compensatory substitutions occur when advantageous mutations restore fitness lost due to previous deleterious mutations. This study presents an atlas of intra-protein compensatory substitutions built using a phylogenetic approach and a dataset of 1,630 bacterial protein families. Through the analysis of evolutionary and structural properties, it is shown that compensatory mutations are rare but widespread in proteins. Coevolving residues are typically evolving slowly and located in the protein core, and they are more often in contact than expected by chance. The findings provide insights into the relationship between protein structure and fitness landscape.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Biochemistry & Molecular Biology
Jia Zheng, Ning Guo, Andreas Wagner
Summary: Translation errors during protein synthesis can lead to phenotypic mutations that are more frequent than DNA mutations. This study found that high mistranslation levels can amplify the fitness effects of deleterious DNA mutations and reduce a population's mutation load, but have no effect on the occurrence of beneficial mutations. This interaction between phenotypic and DNA mutations can ultimately impact a population's evolvability.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Biochemistry & Molecular Biology
Reena Debray, Nina De Luna, Britt Koskella
Summary: Bacteria and lytic viruses (phages) have a coevolutionary relationship, and this study explores how phages shape the future evolutionary trajectories of their host populations. The researchers found that some bacteria populations re-evolved phage sensitivity over time, while others acquired compensatory mutations that reduced the costs of resistance. The genetic mechanisms of resistance and the initial evolution of resistance played a significant role in these outcomes. This study highlights the importance of phages in the ecological and evolutionary dynamics of their host communities and provides insights into the genetic architecture of historical contingency.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Ecology
Dirk Metzler, Ulrich Knief, Joshua Penalba, Jochen B. W. Wolf
Summary: This study used a mathematical model to investigate the effects of assortative mating on hybrid-zone dynamics, finding that assortative mating can maintain steep clines in mating-trait loci without generalizing to genome-wide reproductive isolation.
Article
Biochemistry & Molecular Biology
Alexandre Blanckaert, Bret A. Payseur
Summary: Natural hybrid zones offer insights into the genetic basis of speciation in progress. By using genome sequence data, researchers have developed a statistical method to detect incompatibility loci and identify regions in the genome where departures from the local site frequency spectrum occur. This approach is applicable to a variety of scenarios and does not require prior knowledge of demographic history.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Multidisciplinary Sciences
Andreas Wagner
Summary: This study suggests that adaptive landscapes contain mutations that can enhance the evolvability of evolving molecules and promote the evolution of high fitness populations. The research found that these evolvability-enhancing mutations enable populations to evolve significantly higher fitness.
NATURE COMMUNICATIONS
(2023)
Article
Multidisciplinary Sciences
Christopher W. Bakerlee, Alex N. Nguyen Ba, Yekaterina Shulgina, Jose I. Rojas Echenique, Michael M. Desai
Summary: Epistasis plays a significant role in evolutionary trajectories, with idiosyncratic interactions observed among specific mutations. Protein-level fitness landscapes have shown such interactions, while genome-wide mutations demonstrate ubiquitous patterns of diminishing-returns and increasing-costs epistasis.
Article
Multidisciplinary Sciences
Alief Moulana, Thomas Dupic, Angela M. Phillips, Jeffrey Chang, Serafina Nieves, Anne A. Roffler, Allison J. Greaney, Tyler N. Starr, Jesse D. Bloom, Michael M. Desai
Summary: The Omicron BA.1 variant of SARS-CoV-2 has multiple mutations that contribute to its ability to escape antibodies. Despite individual decreases in ACE2 affinity, these mutations are compensated by interactions with other mutations that enhance affinity, allowing BA.1 to evade immunity while maintaining ACE2 binding. Compensatory epistasis plays a key role in driving substantial evolutionary change for SARS-CoV-2.
NATURE COMMUNICATIONS
(2022)
Article
Genetics & Heredity
Alexey D. Neverov, Anfisa V. Popova, Gennady G. Fedonin, Evgeny A. Cheremukhin, Galya V. Klink, Georgii A. Bazykin
Summary: The study analyzes the evolution rates and methods of protein sites in detail, finding that co-evolving sites cluster in protein structures and are influenced by epistasis and selection events. Additionally, they discovered that proteins consist of co-evolving structural blocks with specific functions.
Article
Genetics & Heredity
Catarina Serrano, Carla S. S. Teixeira, David N. Cooper, Joao Carneiro, Monica Lopes-Marques, Peter D. Stenson, Antonio Amorim, Maria J. Prata, Sergio F. Sousa, Luisa Azevedo
Summary: The study identified several candidate compensated variants in human X-chromosomally encoded proteins, especially finding strong evidence for a compensated pair of amino acids in the coagulation FIXa protein in various mammalian species. The nature of the compensatory interactions was further characterized through molecular dynamics simulations, revealing a potential mechanism for alleviating pathogenic effects of certain mutations.
Review
Genetics & Heredity
Erez Persi, Yuri Wolf, David Horn, Eytan Ruppin, Francesca Demichelis, Robert A. Gatenby, Robert J. Gillies, Eugene Koonin
Summary: Intratumour heterogeneity and phenotypic plasticity enabled by various somatic aberrations, epigenetic and metabolic adaptations, play a crucial role in helping cancers resist treatment and survive under environmental stress. Understanding the interplay between genetic aberrations, the microenvironment, and epigenetic and metabolic cellular states is essential for early detection, prevention, and development of efficient therapeutic strategies for cancer.
NATURE REVIEWS GENETICS
(2021)
Article
Multidisciplinary Sciences
Hong Wu, Zefu Wang, Yuxing Zhang, Laurent Frantz, Christian Roos, David M. Irwin, Chenglin Zhang, Xuefeng Liu, Dongdong Wu, Song Huang, Tongtong Gu, Jianquan Liu, Li Yu
Summary: It is discovered that historical hybridization occurred among a group of snub-nosed monkeys, leading to the origin of a hybrid species. The gray snub-nosed monkey has a stable mixed genomic ancestry derived from the golden snub-nosed monkey, the ancestor of black-white and black snub-nosed monkeys. Genes derived from the parental lineages have been identified, potentially contributing to the mosaic coat coloration of the hybrid and promoting reproductive isolation. This study highlights the underappreciated role of hybridization in generating species and phenotypic diversity in mammals.
Article
Multidisciplinary Sciences
Krishna B. S. Swamy, Hsin-Yi Lee, Carmina Ladra, Chien-Fu Jeff Liu, Jung-Chi Chao, Yi-Yun Chen, Jun-Yi Leu
Summary: The study reveals that impaired protein complex assembly due to destabilized hybrid protein complexes may be a general mechanism of hybrid incompatibility. These complex incompatibilities can negatively affect mitosis and meiosis, compromising the fitness of the hybrid individuals.
NATURE COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Tushar Modi, Paul Campitelli, Ismail Can Kazan, Sefika Banu Ozkan
Summary: This article discusses how conformational dynamics shape protein folding and the functional landscape during protein evolution. It emphasizes the importance of dynamic allostery in protein evolution and discusses how the protein anisotropic network can lead to allosteric and epistatic interactions.
CURRENT OPINION IN STRUCTURAL BIOLOGY
(2021)
Article
Mathematical & Computational Biology
Charlotte Nachtegael, Barbara Gravel, Arnau Dillen, Guillaume Smits, Ann Nowe, Sofia Papadimitriou, Tom Lenaerts
Summary: Improving the understanding of oligogenic nature of diseases requires high-quality FAIR data. The OLlgogenic disease DAtabase (OLIDA) presents a novel curation protocol and scoring mechanism, resulting in a new repository of 916 oligogenic variant combinations linked to 159 diseases. OLIDA follows the FAIR principles, providing detailed documentation and easy data access.
DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION
(2022)