Article
Biochemistry & Molecular Biology
Maria-Agustina Rossi, Timothy Palzkill, Fabio C. L. Almeida, Alejandro J. Vila
Summary: Protein evolution involves the adaptation of molecules to different functional challenges through the accumulation of mutations. This study focuses on CTX-M beta-lactamases and demonstrates the optimization of protein dynamics through two mutations outside the active site, which enhance the enzyme's activity against a specific substrate. NMR analysis reveals that these mutations increase backbone dynamics and the exposure to solvent of a buried beta-sheet. The conformational changes induced by the mutations in this beta-sheet trigger further changes in loops at the opposite side of the active site. These findings highlight the importance of alternative conformations in protein evolution.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Biochemistry & Molecular Biology
Matteo Bisardi, Juan Rodriguez-Rivas, Francesco Zamponi, Martin Weigt
Summary: The study proposes stochastic models of experimental protein evolution based on reconstructed data-driven fitness landscapes, predicting important features of experimentally evolved sequence libraries. It showcases the potential of the approach in determining protein structure from epistasis signals in experimental sequence libraries, offering a quantitative explanation for outcomes of recent experiments and enabling forecasts for future evolution experiments.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Plant Sciences
Alexander M. C. Bowles, Jordi Paps, Ulrike Bechtold
Summary: Drought stress is a major constraint in crop production, with intense research being conducted on drought tolerance mechanisms for future production of drought tolerant crops. The variability in definitions of drought tolerance presents a challenge for systematic assessment across the plant kingdom. Drought tolerance is a polygenic trait, and understanding its evolution may provide insights into gene gain and loss patterns in relation to diverse drought adaptations.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Infectious Diseases
Dillon Muzondiwa, Hleliwe Hlanze, Oleg N. Reva
Summary: The study reveals that different lineages of Mycobacterium tuberculosis employ different evolutionary trajectories to achieve multidrug resistance and reduce the fitness cost associated with drug resistance.
Article
Biochemical Research Methods
Tian Yang, Zhixia Ye, Michael D. Lynch
Summary: Enzyme evolution is important in biotechnology and synthetic biology but requires multiple rounds of screening to identify optimal mutant sequences. This is due to the scarcity of the fitness landscape caused by epistatic mutations. The approach proposed in this study incorporates diverse substrate analogues in the screening process to accurately identify epistatic mutant residues without testing the entire combinatorial search space.
ACS SYNTHETIC BIOLOGY
(2022)
Article
Multidisciplinary Sciences
Nicoletta Commins, Mark R. Sullivan, Kerry McGowen, Evan M. Koch, Eric J. Rubin, Maha Farhat
Summary: The molecular clock rate of Mycobacterium abscessus (Mab) slows down coincident with the emergence of phylogenetic clusters, challenging the model of person-to-person transmission and providing insights into transmission inference in emerging pathogens.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Letter
Biochemistry & Molecular Biology
Roberto Del Amparo, Miguel Arenas
Summary: Selecting the best-fitting substitution model is recommended for accurately reconstructing ancestral sequences.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Microbiology
Camilo Gomez-Garzon, Jeffrey E. Barrick, Shelley M. Payne
Summary: Iron acquisition is crucial for living organisms, and the Feo system is the most prevalent bacterial iron transporter. This study examines the evolution of the Feo transporter and suggests that FeoC, one of the accessory proteins, has been lost in many bacterial lineages. Experimental evidence supports the hypothesis that FeoC may have different functions in different species, and its loss is promoted by mutations in FeoA or by the fusion of FeoA and FeoB. The proposed evolutionary model for the Feo system is based on bioinformatic analyses and experimental data.
Article
Microbiology
Camilo Gomez-Garzon, Jeffrey E. Barrick, Shelley M. Payne
Summary: Feo, a ferrous iron transport system, is critical for virulence in certain bacterial species. The large protein FeoB facilitates iron transport into bacterial cells, while the functions of FeoA and FeoC remain unclear.
Article
Virology
Artem N. N. Bondaryuk, Olga I. I. Belykh, Evgeny I. I. Andaev, Yurij S. S. Bukin
Summary: By studying 47 genome sequences of Omsk hemorrhagic fever virus, it was found that the complete open reading frame data is more accurate than the E gene data in estimating substitution rate and divergence time. The research also revealed a declining trend in OHFV genetic diversity, but with evidence that local virus subpopulations underwent exponential growth.
Article
Biochemistry & Molecular Biology
Philip Lavretsky, Robert E. Wilson, Sandra L. Talbot, Sarah A. Sonsthagen
Summary: Insight into complex evolutionary histories is gained through comparative phylogenomic and population genomic studies, revealing that hybridization has played a crucial role in transferring genetic material and generating new species within the sea duck tribe Mergini. Despite low contemporary levels of gene flow, at least 18 putative hybrids have been identified, highlighting the significance of hybridization in shifting genetic variation between species.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2021)
Article
Genetics & Heredity
Junzong He, Zhihao Zhou, Yan Huang, Jinmei Feng, Wenxiang Li, Guitang Wang, Congjie Hua
Summary: The complete mitochondrial genome of Sinergasilus major was sequenced to explore the phylogeny and mitogenomic evolution of Copepoda. The study revealed that the nad2 gene may be a better marker for investigating phylogenetic relationships among closely related species in Copepoda than the commonly used cox1 gene. Additionally, the study recovered the sister-group relationship of Siphonostomatoida and Cyclopoida.
Article
Cell Biology
Pramod Shinde, Harry J. Whitwell, Rahul Kumar Verma, Mikhail Ivanchenko, Alexey Zaikin, Sarika Jalan
Summary: Investigating human mitochondrial genome variations can provide insights into human history and natural selection. Analysis of 24,167 human mt-genome samples from five continents revealed different co-mutation patterns among populations, with a stronger COX gene co-mutation bias in Asian and American populations. The study also showed a hierarchical modularity in the co-mutation networks and mutations clustered preferentially in known mitochondrial haplogroups.
Article
Biochemistry & Molecular Biology
Alexander G. Lucaci, Jordan D. Zehr, David Enard, Joseph W. Thornton, Sergei L. Kosakovsky Pond
Summary: Inference and interpretation of evolutionary processes are influenced by statistical models and tests. Failing to consider certain aspects of the substitution process and model variation can bias estimates of model parameters and affect selection detection. This study develops an analytical framework to incorporate multinucleotide substitutions and variation in synonymous substitution rate into selection analyses. The results show that these factors have a significant impact on the detection of positive selection, highlighting the need for their routine inclusion in selection analysis.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)
Article
Biochemistry & Molecular Biology
Olivia Kosterlitz, Nathan Grassi, Bailey Werner, Ryan Seamus Mcgee, Eva M. Top, Benjamin Kerr
Summary: This study presents a framework to examine the evolutionary consequences of host-switching in genes that undergo horizontal gene transfer (HGT). It finds that with sufficient landscape alignment, vehicles of HGT such as plasmids can enable a distributed form of genetic evolution across species within a bacterial community.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)
Editorial Material
Biochemistry & Molecular Biology
David D. Pollock
MOLECULAR BIOLOGY AND EVOLUTION
(2020)
Article
Genetics & Heredity
Jonathan A. Shortt, Robert P. Ruggiero, Corey Cox, Aaron C. Wacholder, David D. Pollock
Article
Medicine, General & Internal
Camus Nimmo, Kayleen Brien, James Millard, Alison D. Grant, Nesri Padayatchi, Alexander S. Pym, Max O'Donnell, Richard Goldstein, Judith Breuer, Francois Balloux
Article
Biochemistry & Molecular Biology
David D. Pollock, Todd A. Castoe, Blair W. Perry, Spyros Lytras, Kristen J. Wade, David L. Robertson, Edward C. Holmes, Maciej F. Boni, Sergei L. Kosakovsky Pond, Rhys Parry, Elizabeth J. Carlton, James L. N. Wood, Pleuni S. Pennings, Richard A. Goldstein
MOLECULAR BIOLOGY AND EVOLUTION
(2020)
Article
Multidisciplinary Sciences
Kenji Fukushima, David D. Pollock
NATURE COMMUNICATIONS
(2020)
Article
Virology
Christopher Ruis, Lisa C. Lindesmith, Michael L. Mallory, Paul D. Brewer-Jensen, Josephine M. Bryant, Veronica Costantini, Christopher Monit, Jan Vinje, Ralph S. Baric, Richard A. Goldstein, Judith Breuer
Article
Infectious Diseases
Zachary L. Nikolakis, Nicole R. Hales, Blair W. Perry, Drew R. Schield, Laura E. Timm, Yang Liu, Bo Zhong, Katerina J. Kechris, Elizabeth J. Carlton, David D. Pollock, Todd A. Castoe
Summary: Genomic approaches show potential in studying transmission patterns and responses to control efforts for diseases like schistosomiasis. This study demonstrates the use of whole genome amplification and sequencing to analyze individual archival schistosome larvae, providing insights into genetic diversity, relatedness, and transmission patterns. The results suggest that population-level WGS datasets for individual larvae could be valuable for disease control efforts, offering new avenues for understanding parasite biology and transmission pathways.
PLOS NEGLECTED TROPICAL DISEASES
(2021)
Article
Multidisciplinary Sciences
Steven A. Kemp, Dami A. Collier, Rawlings P. Datir, Isabella A. T. M. Ferreira, Salma Gayed, Aminu Jahun, Myra Hosmillo, Chloe Rees-Spear, Petra Mlcochova, Ines Ushiro Lumb, David J. Roberts, Anita Chandra, Nigel Temperton, Katherine Sharrocks, Elizabeth Blane, Yorgo Modis, Kendra E. Leigh, John A. G. Briggs, Marit J. van Gils, Kenneth G. C. Smith, John R. Bradley, Chris Smith, Rainer Doffinger, Lourdes Ceron-Gutierrez, Gabriela Barcenas-Morales, David D. Pollock, Richard A. Goldstein, Anna Smielewska, Jordan P. Skittrall, Theodore Gouliouris, Ian G. Goodfellow, Effrossyni Gkrania-Klotsas, Christopher J. R. Illingworth, Laura E. McCoy, Ravindra K. Gupta
Summary: Chronic infection with SARS-CoV-2 can lead to viral evolution and increased resistance to neutralizing antibodies in immunosuppressed individuals treated with convalescent plasma. During convalescent plasma therapy, there were significant shifts in the viral population structure and sensitivity, suggesting strong selection pressure on the virus during treatment.
Article
Multidisciplinary Sciences
R. Charlotte Eccleston, David D. Pollock, Richard A. Goldstein
Summary: Epistasis and cooperativity in protein folding are both influenced by networks of energetic interactions within proteins, and their selection can affect each other. Selection for cooperativity may be crucial for predicting protein structure using epistasis measurements.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Correction
Multidisciplinary Sciences
Kenji Fukushima, David D. Pollock
NATURE COMMUNICATIONS
(2021)
Editorial Material
Parasitology
Zachary L. Nikolakis, Elizabeth J. Carlton, David D. Pollock, Todd A. Castoe
Summary: Luo et al. identified genes associated with host-switching in Schistosoma japonicum, providing a guide for studying selected chromosomal genes using population genetics.
TRENDS IN PARASITOLOGY
(2022)
Article
Virology
Cristina Venturini, Juanita Pang, Asif U. Tamuri, Sunando Roy, Claire Atkinson, Paul Griffiths, Judith Breuer, Richard A. Goldstein
Summary: This study presents a new approach called HaROLD for haplotype reconstruction of slowly evolving viruses based on identifying co-varying variant frequencies using a probabilistic framework. It demonstrates high accuracy in synthetic and clinical datasets.
Article
Ecology
Kenji Fukushima, David D. Pollock
Summary: To address the problem of convergent evolution on macroevolutionary timescales, we developed a new metric called omega(C) that measures error-corrected convergence rate of protein evolution. Using gene expression data, we explored over 20 million branch combinations in vertebrate genes and identified the joint convergence of expression patterns and protein sequences with amino acid substitutions in functionally important sites, providing hypotheses on undiscovered phenotypes.
NATURE ECOLOGY & EVOLUTION
(2023)
Article
Multidisciplinary Sciences
Oscar J. Charles, Cristina Venturini, Soren Gantt, Claire Atkinson, Paul Griffiths, Richard A. Goldstein, Judith Breuer
Summary: Human cytomegalovirus (CMV), a highly variable virus, infects most of the world's population and shows both conserved and variable regions in its genome. The conserved regions and a minority of the variable regions display geographic population structure, while other variable regions are not geographically structured and are enriched for genes encoding immunomodulatory functions. This suggests the presence of at least two CMV founder populations and a second evolutionary process of balancing selection. Understanding these processes is crucial for vaccine development and drug target identification.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)