13 papers · ranked by Valyu relevance
Yanhui Hu, Ben Ewen-Campen, Aram Comjean, Jonathan Rodiger + 2 more
Paralogs are genes which arose via gene duplication, and when such paralogs retain overlapping or redundant function, this poses a challenge to functional genetics research. Recent technological advancements have made it possible to systematically probe gene function for redundant genes using dual or multiplex gene…
Jacob L. Steenwyk, Dayna C. Goltz, Thomas J. Buida, Yuanning Li + 2 more
Molecular evolution studies, such as phylogenomic studies and genome-wide surveys of positive selection, often rely on gene families of single-copy orthologs (SC-OGs). In contrast, large gene families with multiple homologs in one or more species—a phenomenon observed among several important families of genes such as…
Yibo Si, Kshitiz Adhikari, Laura E. Herring, Daniel Isom + 6 more
Paralogs engage in biological processes through both redundant and non-redundant functions. In the yeast Saccharomyces cerevisiae, approximately one-fifth of the genome consists of paralogs, with their encoded proteins involved in multiple pathways. However, the unique contributions of individual paralogs have remained…
Adele Xu, Rut Molinuevo, Elisa Fazzari, Harrison Tom + 7 more
The formation of paralogs through gene duplication is a core evolutionary process. For paralogs that encode components of protein complexes such as the ribosome, a central question is whether they encode functionally distinct proteins, or whether they exist to maintain appropriate total expression of equivalent…
Rohan Dandage, Mikhail Papkov, Brittany M. Greco, Dmytro Fishman + 9 more
Gene duplication is common across the tree of life, including yeast and humans, and contributes to genomic robustness. In this study, we examined changes in the subcellular localization and abundance of proteins in response to the deletion of their paralogs originating from the whole-genome duplication event, which is…
Brittany M. Greco, Gerardo Zapata, Rohan Dandage, Mikhail Papkov + 5 more
Whole-genome duplication (WGD) events are common across various organisms however the retention and evolution of WGD paralogs is not fully understood. Quantitative measure of protein redistribution in response to the deletion of their WGD paralog provides insight into sources of gene retention. Here, we describe PARPAL…
Saurav Mallik, Angel F. Cisneros, Christian R. Landry, Emmanuel D. Levy
Homomeric proteins are ubiquitous and mediate myriads of cellular functions. When a gene encoding a homomer duplicates, the resulting paralogs can either form distinct homomers, or evolve into a heteromer containing both paralogs. While such events have extensively shaped proteomes, the molecular mechanisms driving…
Anjan Venkatesh, Niall Quinn, Swathi Ramachandra Upadhya, Barbara De Kegel + 6 more
Proteins operate within dense interconnected networks, where interactions are necessary both for stabilising proteins and for enabling them to execute their molecular functions. Remarkably, protein-protein interaction networks operating within tumour cells continue to function despite widespread genetic perturbations.…
Raman K. Singh, Robert A. Crawford, Dheerendra P. Mall, Graham D. Pavitt + 1 more
Ribosome heterogeneity arises via the differential incorporation of ribosomal protein (RP) paralogs, post-transcriptionally modified rRNA, post-translationally modified RPs, and ribosome-associated proteins (RAPs) into ribosomes. This has led to the hypothesis that heterogeneous or “specialized” ribosomes, which…
Barbara De Kegel, Colm J. Ryan
Genomic instability is a hallmark of cancer, resulting in tumor genomes having large numbers of genetic aberrations, including homozygous deletions of protein coding genes. That tumor cells remain viable in the presence of such gene loss suggests high robustness to genetic perturbation. In model organisms and cancer…
Lukas Becker, Philipp Spohr, Gunnar W. Klau, Ilka M. Axmann + 2 more
Bioinformatics has established itself as a central pillar of modern biology. Specifically, comparative genomics enables scientists to study a vast number of genomes efficiently. These comparative analyses shed light on the evolution and potential function of genomes and genes, but are also increasingly used as a key…
Alexander S. Moffett, Andrea Falcón-Cortés, Michele Di Pierro
Gene duplication is a fundamental part of evolutionary innovation. While single-gene duplications frequently exhibit asymmetric evolutionary rates between paralogs, the extent to which this applies to multi-gene duplications remains unclear. In this study, we investigate the role of genetic context in shaping…
Alan J.S. Beavan, Bulat Fatkhullin, Juan Fontana, James O. McInerney + 2 more
Throughout eukaryotic evolution, the structure of the ribosome has been highly conserved, featuring 80 common protein gene families. However, in many eukaryotes, paralogs of these proteins are present. “Specialised ribosomes” have been documented across diverse groups of eukaryotes where they play an important role in…