scholarly journals Is Speciation Accompanied by Rapid Evolution? Insights from Comparing Reproductive and Nonreproductive Transcriptomes in Drosophila

2011 ◽  
Vol 2011 ◽  
pp. 1-11 ◽  
Author(s):  
Santosh Jagadeeshan ◽  
Wilfried Haerty ◽  
Rama S. Singh
Keyword(s):  
Molecular Phylogenetics ◽  
Rapid Evolution ◽  
Protein Coding ◽  
Diverse Range ◽  
Rates Of Evolution ◽  
Accelerated Evolution ◽  
Gradual Evolution ◽  
Interesting Pattern ◽  
Range Of Functions ◽  
Fossil Data

The tempo and mode of evolutionary change during speciation have remained contentious until recently. While much of the evidence claiming speciation is an abrupt and rapid process comes from fossil data, recent molecular phylogenetics show that the background of gradual evolution is often broken by accelerated rates of molecular evolution during speciation. However, what kinds of genes affect or are affected by speciation remains unexplored. Our analysis of 4843 protein-coding genes in five species of the Drosophila melanogaster subgroup shows that while ~70% of genes follow clock-like evolution, between 17–19.67% of loci show signatures of accelerated rates of evolution in recently formed species. These genes show 2-3-fold higher rates of substitution in recently diverged species compared to older species. This fraction of loci affects a diverse range of functions. Only a small proportion of reproductive genes experience speciation-related accelerated changes but many sex-and -reproduction related genes show an interesting pattern of persistent rapid evolution suggesting that sex-and-reproduction related genes are under constant selective pressures. The identification of loci associated with accelerated evolution allows us to address the mechanisms of rapid evolution and speciation, which in our study appears to be a combination of both selection and rapid demographical changes.

scholarly journals Revisiting Bap Multidomain Protein: More Than Sticking Bacteria Together

2020 ◽  
Vol 11 ◽  
Author(s):  
Jaione Valle ◽  
Xianyang Fang ◽  
Iñigo Lasa
Keyword(s):  
Biofilm Formation ◽  
Core Genome ◽  
Current Knowledge ◽  
Surface Proteins ◽  
Structure And Properties ◽  
Diverse Range ◽  
The Core ◽  
Self Assembling ◽  
Abiotic Surfaces ◽  
Range Of Functions

One of the major components of the staphylococcal biofilm is surface proteins that assemble as scaffold components of the biofilm matrix. Among the different surface proteins able to contribute to biofilm formation, this review is dedicated to the Biofilm Associated Protein (Bap). Bap is part of the accessory genome of Staphylococcus aureus but orthologs of Bap in other staphylococcal species belong to the core genome. When present, Bap promotes adhesion to abiotic surfaces and induces strong intercellular adhesion by self-assembling into amyloid like aggregates in response to the levels of calcium and the pH in the environment. During infection, Bap enhances the adhesion to epithelial cells where it binds directly to the host receptor Gp96 and inhibits the entry of the bacteria into the cells. To perform such diverse range of functions, Bap comprises several domains, and some of them include several motifs associated to distinct functions. Based on the knowledge accumulated with the Bap protein of S. aureus, this review aims to summarize the current knowledge of the structure and properties of each domain of Bap and their contribution to Bap functionality.

The dark matter rises: the expanding world of regulatory RNAs

2013 ◽  
Vol 54 ◽  
pp. 1-16 ◽  
Author(s):  
Michael B. Clark ◽  
Anupma Choudhary ◽  
Martin A. Smith ◽  
Ryan J. Taft ◽  
John S. Mattick
Keyword(s):  
Phenotypic Diversity ◽  
Rapid Progress ◽  
Major Area ◽  
Protein Coding ◽  
Diverse Range ◽  
Protein Coding Genes ◽  
Evolutionary Innovation ◽  
Non Coding Rnas ◽  
Cellular Pathways ◽  
Regulatory Rnas

The ability to sequence genomes and characterize their products has begun to reveal the central role for regulatory RNAs in biology, especially in complex organisms. It is now evident that the human genome contains not only protein-coding genes, but also tens of thousands of non–protein coding genes that express small and long ncRNAs (non-coding RNAs). Rapid progress in characterizing these ncRNAs has identified a diverse range of subclasses, which vary widely in size, sequence and mechanism-of-action, but share a common functional theme of regulating gene expression. ncRNAs play a crucial role in many cellular pathways, including the differentiation and development of cells and organs and, when mis-regulated, in a number of diseases. Increasing evidence suggests that these RNAs are a major area of evolutionary innovation and play an important role in determining phenotypic diversity in animals.

scholarly journals Phenotypes can be robust and evolvable if mutations have non-local effects on sequence constraints

2018 ◽  
Vol 15 (138) ◽  
pp. 20170618 ◽  
Author(s):  
Marcel Weiß ◽  
Sebastian E. Ahnert
Keyword(s):  
Rna Secondary Structure ◽  
Local Effects ◽  
Protein Coding ◽  
Diverse Range ◽  
Positive Correlation ◽  
Alternative Phenotypes ◽  
Genetic Sequences ◽  
Non Local ◽  
Sequence Constraints ◽  
Sequence Position

The mapping between biological genotypes and phenotypes plays an important role in evolution, and understanding the properties of this mapping is crucial to determine the outcome of evolutionary processes. One of the most striking properties observed in several genotype–phenotype (GP) maps is the positive correlation between the robustness and evolvability of phenotypes. This implies that a phenotype can be strongly robust against mutations and at the same time evolvable to a diverse range of alternative phenotypes. Here, we examine the causes for this positive correlation by introducing two analytically tractable GP map models that follow the principles of real biological GP maps. The first model is based on gene-like GP maps, reflecting the way in which genetic sequences are organized into protein-coding genes, and the second one is based on the GP map of RNA secondary structure. For both models, we find that a positive correlation between phenotype robustness and evolvability only emerges if mutations at one sequence position can have non-local effects on the sequence constraints at another position. This highlights that non-local effects of mutations are closely related to the coexistence of robustness and evolvability in phenotypes, and are likely to be an important feature of many biological GP maps.

scholarly journals Signatures of rapid evolution in urban and rural transcriptomes of white-footed mice (Peromyscus leucopus) in the New York metropolitan area

2013 ◽  
Author(s):  
Stephen E Harris ◽  
Jason Munshi-South ◽  
Craig Obergfell ◽  
Rachel O'Neill
Keyword(s):  
New York ◽  
Candidate Genes ◽  
High Throughput Sequencing ◽  
Peromyscus Leucopus ◽  
Rapid Evolution ◽  
Urban Ecosystems ◽  
Urban Environments ◽  
Forest Fragments ◽  
Protein Coding ◽  
Biological Phenomena

Urbanization is a major cause of ecological degradation around the world, and human settlement in large cities is accelerating. New York City (NYC) is one of the oldest and most urbanized cities in North America, but still maintains 20% vegetation cover and substantial populations of some native wildlife. The white-footed mouse, Peromyscus leucopus, is a common resident of NYC’s forest fragments and an emerging model system for examining the evolutionary consequences of urbanization. In this study, we developed transcriptomic resources for urban P. leucopus to examine evolutionary changes in protein-coding regions for an exemplar ‘urban adapter’. We used Roche 454 GS FLX+ high throughput sequencing to derive transcriptomes from multiple tissues from individuals across both urban and rural populations. From these data, we identified 31,015 SNPs and several candidate genes potentially experiencing positive selection in urban populations of P. leucopus. These candidate genes are involved in xenobiotic metabolism, innate immune response, demethylation activity, and other important biological phenomena in novel urban environments. This study is one of the first to report candidate genes exhibiting signatures of directional selection in divergent urban ecosystems.

scholarly journals CRISPR Mutants of Three Y Chromosome Genes Suggest Gradual Evolution of Fertility Functions in Drosophila melanogaster

2020 ◽  
Author(s):  
Yassi Hafezi ◽  
Samantha R. Sruba ◽  
Steven R. Tarrash ◽  
Mariana F. Wolfner ◽  
Andrew G. Clark
Keyword(s):  
Drosophila Melanogaster ◽  
Y Chromosome ◽  
Nonsynonymous Substitution ◽  
Wild Type ◽  
Protein Coding ◽  
Repeat Elements ◽  
The Third ◽  
Gradual Evolution ◽  
Complex Functions ◽  
Lines Of Evidence

ABSTRACTGene-poor, repeat-rich regions of the genome are poorly understood and have been understudied due to technical challenges and the misconception that they are degenerating “junk”. Yet multiple lines of evidence indicate these regions may be an important source of variation that could drive adaptation and species divergence, particularly through regulation of fertility. The ∼40 Mb Y chromosome of Drosophila melanogaster contains only 16 known protein-coding genes and is highly repetitive and entirely heterochromatic. Most of the genes originated from duplication of autosomal genes and have reduced nonsynonymous substitution rates, suggesting functional constraint. We devised a genetic strategy for recovering and retaining stocks with sterile Y-linked mutations and combined it with CRISPR to create mutants with deletions that disrupt three Y-linked genes. Two genes, PRY and FDY, had no previously identified functions. We found that PRY mutant males are sub-fertile, but FDY mutant males had no detectable fertility defects. FDY, the newest known gene on the Y chromosome, may have fertility effects that are conditional or too subtle to detect. The third gene, CCY, had been predicted but never formally shown to be required for male fertility. CRISPR-targeting and RNAi of CCY caused male sterility. Surprisingly, however, our CCY mutants were sterile even in the presence of an extra wild-type Y chromosome, suggesting that perturbation of the Y chromosome can lead to dominant sterility. Our approach provides an important step toward understanding the complex functions of the Y chromosome and parsing which functions are accomplished by genes versus repeat elements.

scholarly journals Negative-sense RNA viruses: An underexplored platform for examining virus–host lipid interactions

2021 ◽  
Vol 32 (20) ◽  
pp. pe1
Author(s):  
Monica L. Husby ◽  
Robert V. Stahelin
Keyword(s):  
Host Cell ◽  
Rna Viruses ◽  
Life Cycles ◽  
Diverse Range ◽  
Membrane Biology ◽  
Wide Range ◽  
Range Of Functions ◽  
Pathogenic Viruses ◽  
Pathogenic Agents ◽  
Negative Sense

Viruses are pathogenic agents that can infect all varieties of organisms, including plants, animals, and humans. These microscopic particles are genetically simple as they encode a limited number of proteins that undertake a wide range of functions. While structurally distinct, viruses often share common characteristics that have evolved to aid in their infectious life cycles. A commonly underappreciated characteristic of many deadly viruses is a lipid envelope that surrounds their protein and genetic contents. Notably, the lipid envelope is formed from the host cell the virus infects. Lipid-enveloped viruses comprise a diverse range of pathogenic viruses, which often lead to high fatality rates and many lack effective therapeutics and/or vaccines. This perspective primarily focuses on the negative-sense RNA viruses from the order Mononegavirales, which obtain their lipid envelope from the host plasma membrane. Specifically, the perspective highlights the common themes of host cell lipid and membrane biology necessary for virus replication, assembly, and budding.

scholarly journals Decreased transcription factor binding levels nearby primate pseudogenes suggests regulatory degeneration

2015 ◽  
Author(s):  
Gavin M Douglas ◽  
Michael D Wilson ◽  
Alan M Moses
Keyword(s):  
Transcription Factor ◽  
Transcription Factor Binding ◽  
Urate Oxidase ◽  
Factor Binding ◽  
Sequence Constraint ◽  
Rates Of Evolution ◽  
Accelerated Evolution ◽  
Regulatory Module ◽  
Show Evidence ◽  
Binding Level

Characteristics of pseudogene degeneration at the coding level are well-known, such as a shift towards neutral rates of nonsynonymous substitutions and gain of frameshift mutations. In contrast, degeneration of pseudogene transcriptional regulation is not well understood. Here, we test two predictions of regulatory degeneration along the pseudogenized lineage: (1) decreased transcription factor binding and (2) accelerated evolution in putative cis-regulatory regions. We find evidence for decreased TF binding levels nearby two primate pseudogenes compared to functional liver genes. We also find evidence for pseudogene-lineage-specific relaxation of sequence constraint on a fragment of the promoter of the primate pseudogene urate oxidase (Uox) and a nearby cis-regulatory module (CRM). However, the majority of TF-bound sequences nearby pseudogenes do not show evidence for lineage-specific accelerated rates of evolution. We conclude that decreases in TF binding level could be a marker for regulatory degeneration, while sequence degeneration in most CRMs may be obscured by background rates of TF binding site turnover.

scholarly journals Rapid evolution of mammalian HERC6 and independent duplication of a chimeric HERC5/6 gene in rodents and bats suggest an overlooked role of HERCs in antiviral innate immunity

2020 ◽  
Author(s):  
Stéphanie Jacquet ◽  
Dominique Pontier ◽  
Lucie Etienne
Keyword(s):  
Innate Immunity ◽  
Rapid Evolution ◽  
Chimeric Gene ◽  
Mammalian Evolution ◽  
Evolutionary Diversification ◽  
Accelerated Evolution ◽  
Independent Duplication ◽  
New Research ◽  
Herc Proteins ◽  
Antiviral Innate Immunity

AbstractThe antiviral innate immunity in mammals has evolved very rapidly in response to pathogen selective pressure. Studying the evolutionary diversification of mammalian antiviral defenses is of main importance to better understand our innate immune repertoire. The small HERC proteins are part of a multigene family including interferon-inducible antiviral effectors. Notably, HERC5 inhibits divergent viruses through the conjugation of ISG15 to diverse proteins-termed as ISGylation. Though HERC6 is the most closely-related protein of HERC5, it lacks the ISGylation function in humans. Interestingly, HERC6 is the main E3-ligase of ISG15 in mice, suggesting adaptive changes in HERC6 with implications in the innate immunity. Therefore, HERC5 and HERC6 have probably diversified through complex evolutionary history in mammals, and such characterization would require an extensive survey of mammalian evolution. Here, we performed mammalian-wide and lineage-specific phylogenetic and genomic analyses of HERC5 and HERC6. We used 83 orthologous sequences from bats, rodents, primates, artiodactyls and carnivores – the top five representative groups of mammalian evolution and the main hosts of viral diversity. We found that mammalian HERC5 has been under weak and differential positive selection in mammals, with only primate HERC5 showing evidences of pathogen-driven selection. In contrast, HERC6 has been under strong and recurrent adaptive evolution in mammals, suggesting past genetic arms-races with viral pathogens. Importantly, we found accelerated evolution in the HERC6 spacer domain, suggesting that it might be a pathogen-mammal interface, targeting a viral protein and/or being the target of virus antagonists. Finally, we identified a HERC5/6 chimeric gene that arose from independent duplication in rodent and bat lineages and encodes for a conserved HERC5 N-terminal domain and divergent HERC6 spacer and HECT domains. This duplicated chimeric gene highlights adaptations that potentially contribute to rodent and bat antiviral innate immunity. Altogether, we found major genetic innovations in mammalian HERC5 and HERC6. Our findings open new research avenues on the functions of HERC6 and HERC5/6 in mammals, and on their implication in antiviral innate immunity.

scholarly journals Characterization of a putative NsrR homologue in Streptomyces venezuelae reveals a new member of the Rrf2 superfamily

2016 ◽  
Author(s):  
John T. Munnoch ◽  
Ma Teresa Pellicer Martinez ◽  
Dimitri A. Svistunenko ◽  
Jason C. Crack ◽  
Nick E. Le Brun ◽  
...  
Keyword(s):  
Target Genes ◽  
Nitrosative Stress ◽  
Streptomyces Coelicolor ◽  
Binding Activity ◽  
Streptomyces Venezuelae ◽  
Diverse Range ◽  
Dna Binding Activity ◽  
Acid Protein ◽  
Range Of Functions

AbstractMembers of the Rrf2 superfamily of transcription factors are widespread in bacteria but their functions are largely unexplored. The few that have been characterized in detail sense nitric oxide (NsrR), iron limitation (RirA), cysteine availability (CymR) and the iron sulfur (Fe-S) cluster status of the cell (IscR). In this study we combined ChIP- and dRNA-seq with in vitro biochemistry to characterize a putative NsrR homologue in Streptomyces venezuelae. ChIP-seq analysis revealed that rather than regulating the nitrosative stress response like Streptomyces coelicolor NsrR, Sven6563 binds to a conserved motif at a different, much larger set of genes with a diverse range of functions, including a number of regulators, genes required for glutamine synthesis, NADH/NAD(P)H metabolism, as well as general DNA/RNA and amino acid/protein turn over. Our biochemical experiments further show that Sven6563 has a [2Fe-2S] cluster and that the switch between oxidized and reduced cluster controls its DNA binding activity in vitro. To our knowledge, both the sensing domain and the putative target genes are novel for an Rrf2 protein, suggesting Sven6563 represents a new member of the Rrf2 superfamily. Given the redox sensitivity of its Fe-S cluster we have tentatively named the protein RsrR for Redox sensitive response Regulator.

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