scholarly journals Recurrent Duplication and Diversification of Acrosomal Fertilization Proteins in Abalone

2021 ◽  
Author(s):  
Jolie A Carlisle ◽  
Megan A Glenski ◽  
Willie J. Swanson
Keyword(s):  
Positive Selection ◽  
Gene Array ◽  
Sequence Divergence ◽  
Coat Proteins ◽  
Reproductive Proteins ◽  
Ancestral Gene ◽  
Gamete Recognition ◽  
Duplication Events ◽  
Fertilization Proteins ◽  
Species Specific

Reproductive proteins mediating fertilization commonly exhibit rapid sequence diversification driven by positive selection. This pattern has been observed among nearly all taxonomic groups, including mammals, invertebrates, and plants, and is remarkable given the essential nature of the molecular interactions mediating fertilization. Gene duplication is another important mechanism that facilitates the generation of molecular novelty. Following duplication, paralogs may parse ancestral gene function (subfunctionalization) or acquire new roles (neofunctionalization). However, the contributions of duplication followed by sequence diversification to the molecular diversity of gamete recognition genes has been understudied in many models of fertilization. The marine gastropod mollusk abalone is a classic model for fertilization. Its two acrosomal proteins (lysin and sp18) are ancient gene duplicates with unique gamete recognition functions. Through detailed genomic and bioinformatic analyses we show how duplication events followed by sequence diversification has played an ongoing role in the evolution of abalone acrosomal proteins. The common ancestor of abalone had four members of its acrosomal protein family in a tandem gene array that repeatedly experienced positive selection. We find that both sp18 paralogs contain positively selected sites located in different regions of the paralogs, consistent with a subfunctionalization model where selection acted upon distinct binding interfaces in each paralog. Further, a more recent species-specific duplication of both lysin and sp18 in the European abalone H. tuberculata is described. Despite clade-specific acrosomal protein paralogs, there are no concomitant duplications of egg coat proteins in H. tuberculata, indicating that duplication of egg proteins per se is not responsible for retention of duplicated acrosomal proteins. We hypothesize that, in a manner analogous to host/pathogen evolution, sperm proteins are selected for increased diversity through extensive sequence divergence and recurrent duplication driven by conflict mechanisms.

scholarly journals Odorant receptor copy number change, co-expression, and positive selection establish peripheral coding differences between fly species

2021 ◽  
Author(s):  
Thomas O. Auer ◽  
Raquel Álvarez-Ocaña ◽  
Steeve Cruchet ◽  
Richard Benton ◽  
J. Roman Arguello
Keyword(s):  
Positive Selection ◽  
Sensory Neuron ◽  
Copy Number ◽  
Odorant Receptor ◽  
Chemosensory Receptor ◽  
Large Gene ◽  
Neuron Populations ◽  
Copy Number Changes ◽  
Species Specific

Animals sample their chemical environment using sensory neurons that express diverse chemosensory receptors, which trigger responses when they bind environmental molecules. In addition to modifications in the ligand binding properties of receptors, chemosensory receptor evolution is characterized by copy number changes, often resulting in large gene family size differences between species. Though chemosensory receptor expansions and contractions are frequently described, it is unknown how this is accompanied by changes in the neural circuitry in which they are expressed. Among Drosophila's chemosensory receptor families, the Odorant receptors (Ors) are ideal for addressing this question because, other than an essential co-receptor (Orco), a large majority of Ors are uniquely expressed in single olfactory sensory neuron (OSN) populations. Between-species changes in Or copy number, therefore, may indicate diversification or reduction of peripheral sensory neuron populations. To test this possibility, we focused on a rapidly duplicated/deleted Or subfamily - named Or67a - within Drosophila melanogaster and its most closely-related sister species (D. simulans, D. sechellia, and D. mauritiana). Evolutionary genetic analyses and in vivo physiological assays demonstrate that the common ancestor of these four species possessed three Or67a paralogs that had already diverged adaptively in their odor-evoked responses. Following the group's speciation events, two Or67a paralogs were independently lost in D. melanogaster and D. sechellia, with positive selection continuing to act on the intact genes. Instead of the expected singular expression of each of the functionally diverged Ors in different neurons, we found that the three D. simulans Or67a paralogs are co-expressed in the same cells. Thus, while neuroanatomy is conserved between these species, independent selection on co-expressed receptors has contributed to species-specific peripheral coding of olfactory information. This work reveals a model of adaptive change previously not considered for olfactory evolution and raises the possibility that similar processes may be operating among the largely uninvestigated cases of Or co-expression.

scholarly journals Cause and Effectors: Whole-Genome Comparisons Reveal Shared but Rapidly Evolving Effector Sets among Host-Specific Plant-Castrating Fungi

mBio ◽  
2019 ◽  
Vol 10 (6) ◽  
Author(s):  
William C. Beckerson ◽  
Ricardo C. Rodríguez de la Vega ◽  
Fanny E. Hartmann ◽  
Marine Duhamel ◽  
Tatiana Giraud ◽  
...  
Keyword(s):  
Positive Selection ◽  
Plant Pathogens ◽  
Pfam Domain ◽  
Rapid Evolution ◽  
Host Specialization ◽  
Secreted Proteins ◽  
Smut Fungi ◽  
Core Proteins ◽  
Genes Encoding ◽  
Species Specific

ABSTRACT Plant pathogens utilize a portfolio of secreted effectors to successfully infect and manipulate their hosts. It is, however, still unclear whether changes in secretomes leading to host specialization involve mostly effector gene gains/losses or changes in their sequences. To test these hypotheses, we compared the secretomes of three host-specific castrating anther smut fungi (Microbotryum), two being sister species. To address within-species evolution, which might involve coevolution and local adaptation, we compared the secretomes of strains from differentiated populations. We experimentally validated a subset of signal peptides. Secretomes ranged from 321 to 445 predicted secreted proteins (SPs), including a few species-specific proteins (42 to 75), and limited copy number variation, i.e., little gene family expansion or reduction. Between 52% and 68% of the SPs did not match any Pfam domain, a percentage that reached 80% for the small secreted proteins, indicating rapid evolution. In comparison to background genes, we indeed found SPs to be more differentiated among species and strains, more often under positive selection, and highly expressed in planta; repeat-induced point mutations (RIPs) had no role in effector diversification, as SPs were not closer to transposable elements than background genes and were not more RIP affected. Our study thus identified both conserved core proteins, likely required for the pathogenic life cycle of all Microbotryum species, and proteins that were species specific or evolving under positive selection; these proteins may be involved in host specialization and/or coevolution. Most changes among closely related host-specific pathogens, however, involved rapid changes in sequences rather than gene gains/losses. IMPORTANCE Plant pathogens use molecular weapons to successfully infect their hosts, secreting a large portfolio of various proteins and enzymes. Different plant species are often parasitized by host-specific pathogens; however, it is still unclear whether the molecular basis of such host specialization involves species-specific weapons or different variants of the same weapons. We therefore compared the genes encoding secreted proteins in three plant-castrating pathogens parasitizing different host plants, producing their spores in plant anthers by replacing pollen. We validated our predictions for secretion signals for some genes and checked that our predicted secreted proteins were often highly expressed during plant infection. While we found few species-specific secreted proteins, numerous genes encoding secreted proteins showed signs of rapid evolution and of natural selection. Our study thus found that most changes among closely related host-specific pathogens involved rapid adaptive changes in shared molecular weapons rather than innovations for new weapons.

scholarly journals Evolution of species-specific major seminal fluid proteins in placental mammals by gene death and positive selection

2015 ◽  
Vol 84 (3) ◽  
pp. 217-235 ◽  
Author(s):  
Camille Meslin ◽  
Michel Laurin ◽  
Isabelle Callebaut ◽  
Xavier Druart ◽  
Philippe Monget
Keyword(s):  
Amino Acids ◽  
Positive Selection ◽  
Statistical Power ◽  
Animal Species ◽  
Seminal Fluid ◽  
Domestic Animal ◽  
Secreted Proteins ◽  
Seminal Fluid Proteins ◽  
Species Specific ◽  
Complex Substance

The seminal fluid is a complex substance composed of a variety of secreted proteins and has been shown to play an important role in the fertilisation process in mammals and also in Drosophila. Several genes under positive selection have been documented in some rodents and primates. Our study documents this phenomenon in several other mammalian taxa. We study the evolution of genes that encode for 20 proteins that are quantitatively predominant in the seminal fluid of at least one out of seven domestic animal species. We analyse the amino acid composition of these proteins for positive selection and for the presence of pseudogenes. Genes that disappeared through pseudogenisation include KLK2 in cattle, horse and mice. Traces of positive selection are found in seven genes. The identified amino acids are located in regions exposed to the protein surface, suggesting a role in the interaction of gametes, with possible impact on the process of speciation. Moreover, we found no evidence that the predominance of proteins in seminal fluid and their mode of evolution are correlated, and the uncoupled patterns of change suggest that this result is not due solely to lack of statistical power.

scholarly journals Variation in selection constraints on teleost TLRs with emphasis on their repertoire in the Walking catfish, Clarias batrachus

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Manisha Priyam ◽  
Sanjay K. Gupta ◽  
Biplab Sarkar ◽  
T. R. Sharma ◽  
A. Pattanayak
Keyword(s):  
Phylogenetic Analysis ◽  
Positive Selection ◽  
Strong Evidence ◽  
Selection Pressure ◽  
Arms Race ◽  
Clarias Batrachus ◽  
Toll Like Receptors ◽  
Specific Variation ◽  
Species Specific ◽  
High Degree

AbstractThe high degree of conservation of toll-like receptors (TLRs), and yet their subtle variations for better adaptation of species in the host–pathogen arms race make them worthy candidates for understanding evolution. We have attempted to track the trend of TLR evolution in the most diverse vertebrate group—teleosts, where Clarias batrachus was given emphasis, considering its traits for terrestrial adaptation. Eleven C. batrachus TLRs (TLR1, 2, 3, 5, 7, 8 9, 13, 22, 25, 26) were identified in this study which clustered in proximity to its Siluriformes relative orthologues in the phylogenetic analysis of 228 TLRs from 25 teleosts. Ten TLRs (TLR1, 2, 3, 5, 7, 8 9, 13, 21, 22) with at least 15 member orthologues for each alignment were processed for selection pressure and coevolutionary analysis. TLR1, 7, 8 and 9 were found to be under positive selection in the alignment-wide test. TLR1 also showed maximum episodic diversification in its clades while the teleost group Eupercaria showed the maximum divergence in their TLR repertoire. Episodic diversification was evident in C. batrachus TLR1 and 7 alignments. These results present a strong evidence of a divergent TLR repertoire in teleosts which may be contributing towards species-specific variation in TLR functions.

Phylogenetic evidence for independent origins of GDF1 and GDF3 genes in amphibians and mammals

2018 ◽  
Author(s):  
Juan C. Opazo ◽  
Kattina Zavala
Keyword(s):  
Growth Factor ◽  
Early Development ◽  
Evolutionary History ◽  
Transforming Growth Factor ◽  
Ancestral Gene ◽  
Differentiation Factors ◽  
Duplication Events ◽  
Independent Duplication ◽  
History Of ◽  
Early Developmental

AbstractGrowth differentiation factors 1 (GDF1) and 3 (GDF3) are members of the transforming growth factor superfamily (TGF-β) that is involved in fundamental early-developmental processes that are conserved across vertebrates. The evolutionary history of these genes is still under debate due to ambiguous definitions of homologous relationships among vertebrates. Thus, the goal of this study was to unravel the evolution of the GDF1 and GDF3 genes of vertebrates, emphasizing the understanding of homologous relationships and their evolutionary origin. Surprisingly, our results revealed that the GDF1 and GDF3 genes found in amphibians and mammals are the products of independent duplication events of an ancestral gene in the ancestor of each of these lineages. The main implication of this result is that the GDF1 and GDF3 genes of amphibians and mammals are not 1:1 orthologs. In other words, genes that participate in fundamental processes during early development have been reinvented two independent times during the evolutionary history of tetrapods.

Comparative genomic analysis of a mammalian β-defensin gene cluster

2007 ◽  
Vol 30 (3) ◽  
pp. 213-222 ◽  
Author(s):  
Yashwanth Radhakrishnan ◽  
Mario A. Fares ◽  
Frank S. French ◽  
Susan H. Hall
Keyword(s):  
Positive Selection ◽  
Gene Cluster ◽  
Genomic Analysis ◽  
Urogenital Tract ◽  
Comparative Genomic ◽  
Evolutionary Analysis ◽  
Defensin Gene ◽  
Duplication Events ◽  
Molecular Evolutionary Analysis

Comparative genomic analyses have yielded valuable insights into conserved and divergent aspects of gene function, regulation, and evolution. Herein, we describe the characterization of a mouse β-defensin gene cluster locus on chromosome 2F6. In addition, we present the evolutionary analysis of this cluster and its human, rhesus, and rat orthologs. Expression analysis in mouse revealed the occurrence of defensin cluster transcripts in multiple tissues, with the highest abundance in the urogenital tract. Molecular evolutionary analysis suggests that this cluster originated by a series of duplication events, and by positive selection occurring even after the rodent-primate split. In addition, the constraints analysis showed higher positive selection in rodents than in primates, especially distal to the six-cysteine array. Positive selection in the evolution of these defensins may relate not only to the evolving enhancement of ancestral host defense but also to functional innovations in reproduction. The multiplicity of defensins and their preferential overexpression in the urogenital tract indicate that defensins function in the protection and maintenance of fertility.

scholarly journals Morphogenesis of Bacillus Spore Surfaces

2003 ◽  
Vol 185 (21) ◽  
pp. 6255-6261 ◽  
Author(s):  
Venkata G. R. Chada ◽  
Erik A. Sanstad ◽  
Rong Wang ◽  
Adam Driks
Keyword(s):  
Surface Morphology ◽  
Bacillus Anthracis ◽  
Dynamic Structure ◽  
Coat Proteins ◽  
Force Microscopy ◽  
Bacillus Spore ◽  
Atomic Force ◽  
Ridge Pattern ◽  
Direct Formation ◽  
Species Specific

ABSTRACT Spores produced by bacilli are encased in a proteinaceous multilayered coat and, in some species (including Bacillus anthracis), further surrounded by a glycoprotein-containing exosporium. To characterize bacillus spore surface morphology and to identify proteins that direct formation of coat surface features, we used atomic-force microscopy (AFM) to image the surfaces of wild-type and mutant spores of Bacillus subtilis, as well as the spore surfaces of Bacillus cereus 569 and the Sterne strain of Bacillus anthracis. This analysis revealed that the coat surfaces in these strains are populated by a series of bumps ranging between 7 and 40 nm in diameter, depending on the species. Furthermore, a series of ridges encircled the spore, most of which were oriented along the long axis of the spore. The structures of these ridges differ sufficiently between species to permit species-specific identification. We propose that ridges are formed early in spore formation, when the spore volume likely decreases, and that when the spore swells during germination the ridges unfold. AFM analysis of a set of B. subtilis coat protein gene mutants revealed three coat proteins with roles in coat surface morphology: CotA, CotB, and CotE. Our data indicate novel roles for CotA and CotB in ridge pattern formation. Taken together, these results are consistent with the view that the coat is not inert. Rather, the coat is a dynamic structure that accommodates changes in spore volume.

scholarly journals GeneSeqToFamily: the Ensembl Compara GeneTrees pipeline as a Galaxy workflow

2016 ◽  
Author(s):  
Anil S. Thanki ◽  
Nicola Soranzo ◽  
Wilfried Haerty ◽  
Robert P. Davey
Keyword(s):  
Gene Duplication ◽  
Structural Changes ◽  
Gene Families ◽  
Vital Role ◽  
Software Project ◽  
Command Line ◽  
Gene Trees ◽  
Ancestral Gene ◽  
The Galaxy ◽  
Duplication Events

AbstractBackgroundGene duplication is a major factor contributing to evolutionary novelty, and the contraction or expansion of gene families has often been associated with morphological, physiological and environmental adaptations. The study of homologous genes helps us to understand the evolution of gene families. It plays a vital role in finding ancestral gene duplication events as well as identifying genes that have diverged from a common ancestor under positive selection. There are various tools available, such as MSOAR, OrthoMCL and HomoloGene, to identify gene families and visualise syntenic information between species, providing an overview of syntenic regions evolution at the family level. Unfortunately, none of them provide information about structural changes within genes, such as the conservation of ancestral exon boundaries amongst multiple genomes. The Ensembl GeneTrees computational pipeline generates gene trees based on coding sequences and provides details about exon conservation, and is used in the Ensembl Compara project to discover gene families.FindingsA certain amount of expertise is required to configure and run the Ensembl Compara GeneTrees pipeline via command line. Therefore, we have converted the command line Ensembl Compara GeneTrees pipeline into a Galaxy workflow, called GeneSeqToFamily, and provided additional functionality. This workflow uses existing tools from the Galaxy ToolShed, as well as providing additional wrappers and tools that are required to run the workflow.ConclusionsGeneSeqToFamily represents the Ensembl Compara pipeline as a set of interconnected Galaxy tools, so they can be run interactively within the Galaxy’s user-friendly workflow environment while still providing the flexibility to tailor the analysis by changing configurations and tools if necessary. Additional tools allow users to subsequently visualise the gene families produced by the workflow, using the Aequatus.js interactive tool, which has been developed as part of the Aequatus software project.

scholarly journals Heightened virulence of Yersinia is associated with decreased function of the YopJ protein

2021 ◽  
Author(s):  
Chris A Mares ◽  
Fernando P Lugo ◽  
Mohammad Albataineh ◽  
Beth Goins ◽  
Irene Newton ◽  
...  
Keyword(s):  
Positive Selection ◽  
Sequence Divergence ◽  
Bacterial Pathogenesis ◽  
Effector Protein ◽  
Evolutionary Analysis ◽  
Yersinia Species ◽  
Macrophage Cytotoxicity ◽  
A Minor ◽  
Pathogenic Yersinia

Despite the maintenance of YopP/J alleles throughout the human-pathogenic Yersinia lineage, the benefit of YopP/J-induced phagocyte death for Yersinia pathogenesis in animals is not obvious. To determine how sequence divergence of YopP/J has impacted Yersinia virulence, we examined protein polymorphisms in this Type III secreted effector protein across 17 Yersinia species, and tested the consequences of polymorphism in a murine model of sub-acute systemic yersiniosis. Our evolutionary analysis revealed that codon 177 has been subjected to positive selection - the Y. enterocolitica residue had been altered from a leucine to a phenylalanine in nearly all Y. pseudotuberculosis and Y. pestis strains examined. Despite being a minor change, as both leucine and phenylalanine have hydrophobic side chains, reversion of YopJF177 to the ancestral YopJL177 variant yielded a Y. pseudotuberculosis strain with enhanced cytotoxicity towards macrophages, consistent with previous findings. Surprisingly, expression of YopJF177L in the mildly attenuated ksgA- background rendered the strain completely avirulent in mice. Consistent with this hypothesis that YopJ activity indirectly relates to Yersinia pathogenesis in vivo, ksgA- strains lacking functional YopJ failed to kill macrophages but actually regained virulence in animals. Also, treatment with the anti-apoptosis drug suramin prevented YopJ-mediated macrophage cytotoxicity and enhanced Y. pseudotuberculosis virulence in vivo. Our results demonstrate that Yersinia-induced cell death is detrimental for bacterial pathogenesis in this animal model of illness, and indicate that positive selection has driven YopJ/P and Yersinia evolution towards diminished cytotoxicity and increased virulence, respectively.

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