scholarly journals Recruitment of toxin-like proteins with ancestral venom function supports endoparasitic lifestyles of Myxozoa

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e11208
Author(s):  
Ashlie Hartigan ◽  
Adrian Jaimes-Becerra ◽  
Beth Okamura ◽  
Liam B. Doonan ◽  
Malcolm Ward ◽  
...  
Keyword(s):  
Prey Capture ◽  
Phylogenetic Analyses ◽  
Specific Gene ◽  
Gene Duplications ◽  
Free Living ◽  
Venom Toxin ◽  
Venomous Animals ◽  
Kunitz Type ◽  
Polypodium Hydriforme ◽  
Lineage Specific Gene

Cnidarians are the oldest lineage of venomous animals and use nematocysts to discharge toxins. Whether venom toxins have been recruited to support parasitic lifestyles in the Endocnidozoa (Myxozoa + Polypodium) is, however, unknown. To examine this issue we variously employed transcriptomic, proteomic, associated molecular phylogenies, and localisation studies on representative primitive and derived myxozoans (Malacosporea and Myxosporea, respectively), Polypodium hydriforme, and the free-living staurozoan Calvadosia cruxmelitensis. Our transcriptomics and proteomics analyses provide evidence for expression and translation of venom toxin homologs in myxozoans. Phylogenetic placement of Kunitz type serine protease inhibitors and phospholipase A2 enzymes reveals modification of toxins inherited from ancestral free-living cnidarian toxins, and that venom diversity is reduced in myxozoans concordant with their reduced genome sizes. Various phylogenetic analyses of the Kunitz-type toxin family in Endocnidozoa suggested lineage-specific gene duplications, which offers a possible mechanism for enhancing toxin diversification. Toxin localisation in the malacosporean Buddenbrockia plumatellae substantiates toxin translation and thus illustrates a repurposing of toxin function for endoparasite development and interactions with hosts, rather than for prey capture or defence. Whether myxozoan venom candidates are expressed in transmission stages (e.g. in nematocysts or secretory vesicles) requires further investigation.

scholarly journals Mitochondrial copper and phosphate transporter specificity was defined early in the evolution of eukaryotes

2020 ◽  
Author(s):  
Xinyu Zhu ◽  
Aren Boulet ◽  
Katherine M. Buckley ◽  
Casey B. Phillips ◽  
Micah G. Gammon ◽  
...  
Keyword(s):  
Protein Function ◽  
Phylogenetic Signal ◽  
Phylogenetic Analyses ◽  
Phosphate Transport ◽  
Site Directed Mutagenesis ◽  
Specific Gene ◽  
Ancestral State ◽  
Gene Duplications ◽  
Substrate Selection ◽  
Mitochondrial Carrier Family

AbstractMitochondrial carrier family (MCF/SLC25) proteins are selective transporters that maintain the mitochondrial metabolome. Here we combine computational, biochemical and phenotypic approaches to understand substrate selectivity of SLC25A3. In mammals, SLC25A3 transports both copper and phosphate, yet in Saccharomyces cerevisiae the transport of these substrates is partitioned across two paralogs: PIC2, which transports copper, and MIR1, which transports phosphate. To understand whether the ancestral state of this transporter was a single promiscuous transporter that duplicated and gained selectivity, we explored the evolutionary relationships of PIC2 and MIR1 orthologs across the eukaryotic tree of life. Phylogenetic analyses reveal that PIC2-like and MIR1-like orthologs are present in all major eukaryotic supergroups, indicating that the gene duplication that created these paralogs occurred early in eukaryotic evolution. Frequent lineage-specific gene duplications and losses suggest that substrate specificity may be evolutionarily labile. To link this phylogenetic signal to protein function and resolve the residues involved in substrate selection, we used structural modelling and site-directed mutagenesis to identify PIC2 residues involved in copper and phosphate transport activities. Based on these analyses, we generated a Leu175Ala variant of mouse SLC25A3 that retains the ability to transport copper, but not phosphate, and rescues the cytochrome c oxidase defect in SLC25A3 knockout cells. Taken together, this work uses an evolutionary framework to uncover amino acids involved in substrate recognition by MCF proteins responsible for copper and phosphate transport.

scholarly journals The myxozoan minicollagen gene repertoire was not simplified by the parasitic lifestyle: computational identification of a novel myxozoan minicollagen gene

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Jiří Kyslík ◽  
Anush Kosakyan ◽  
Serafim Nenarokov ◽  
Astrid S. Holzer ◽  
Ivan Fiala
Keyword(s):  
Evolutionary History ◽  
Evolutionary Dynamics ◽  
Driving Forces ◽  
Phylogenetic Analyses ◽  
Specific Gene ◽  
Gene Repertoire ◽  
Large Gene ◽  
Close Relationship ◽  
Simple Body ◽  
Polypodium Hydriforme

Abstract Background Lineage-specific gene expansions represent one of the driving forces in the evolutionary dynamics of unique phylum traits. Myxozoa, a cnidarian subphylum of obligate parasites, are evolutionarily altered and highly reduced organisms with a simple body plan including cnidarian-specific organelles and polar capsules (a type of nematocyst). Minicollagens, a group of structural proteins, are prominent constituents of nematocysts linking Myxozoa and Cnidaria. Despite recent advances in the identification of minicollagens in Myxozoa, the evolutionary history and diversity of minicollagens in Myxozoa and Cnidaria remain elusive. Results We generated new transcriptomes of two myxozoan species using a novel pipeline for filtering of closely related contaminant species in RNA-seq data. Mining of our transcriptomes and published omics data confirmed the existence of myxozoan Ncol-4, reported only once previously, and revealed a novel noncanonical minicollagen, Ncol-5, which is exclusive to Myxozoa. Phylogenetic analyses support a close relationship between myxozoan Ncol-1–3 with minicollagens of Polypodium hydriforme, but suggest independent evolution in the case of the myxozoan minicollagens Ncol-4 and Ncol-5. Additional genome- and transcriptome-wide searches of cnidarian minicollagens expanded the dataset to better clarify the evolutionary trajectories of minicollagen. Conclusions The development of a new approach for the handling of next-generation data contaminated by closely related species represents a useful tool for future applications beyond the field of myxozoan research. This data processing pipeline allowed us to expand the dataset and study the evolution and diversity of minicollagen genes in Myxozoa and Cnidaria. We identified a novel type of minicollagen in Myxozoa (Ncol-5). We suggest that the large number of minicollagen paralogs in some cnidarians is a result of several recent large gene multiplication events. We revealed close juxtaposition of minicollagens Ncol-1 and Ncol-4 in myxozoan genomes, suggesting their common evolutionary history. The unique gene structure of myxozoan Ncol-5 suggests a specific function in the myxozoan polar capsule or tubule. Despite the fact that myxozoans possess only one type of nematocyst, their gene repertoire is similar to those of other cnidarians.

scholarly journals Myxozoan Minicollagen Gene Repertoire Is Not Simplified By The Parasitic Lifestyle: Computational Identification Of Novel Myxozoan Minicollagen Gene 

2020 ◽  
Author(s):  
Jiří Kyslík ◽  
Anush Kosakyan ◽  
Serafim Nenarokov ◽  
Astrid S. Holzer ◽  
Ivan Fiala
Keyword(s):  
Evolutionary History ◽  
Evolutionary Dynamics ◽  
Driving Forces ◽  
Phylogenetic Analyses ◽  
Specific Gene ◽  
Gene Repertoire ◽  
Large Gene ◽  
Close Relationship ◽  
Parasitic Lifestyle ◽  
Polypodium Hydriforme

Abstract BackgroundLineage-specific gene expansions represent one of the driving forces in the evolutionary dynamics of unique phylum traits. The obligate parasitic group of Cnidaria, Myxozoa, are evolutionarily altered and highly reduced organisms with a simple body plan including cnidarian-specific organelles, polar capsules (a type of nematocyst). A prominent constituent of nematocysts, linking Myxozoa and Cnidaria, represents a group of structural proteins, minicollagens. Despite recent advances in the identification of minicollagens in Myxozoa, the evolutionary history and diversity of minicollagens in Myxozoa and Cnidaria remain elusive. ResultsWe present newly generated transcriptomes of two myxozoan species with a novel pipeline for filtering of closely related contaminant species in RNA-seq data. Mining of the set of our transcriptomes and published -omics data confirmed the existence of myxozoan Ncol-4, once only reported, and we discovered a novel non-canonical type of minicollagen, Ncol-5, which is exclusive to Myxozoa. Phylogenetic analyses support a close relationship of myxozoan Ncol-1,2,3 with minicollagens of Polypodium hydriforme, however, suggest rather independent evolution in the case of two myxozoan minicollagens Ncol-4 and Ncol-5. Additional genome- and transcriptome-wide searches of cnidarian minicollagens expand the dataset to clarify better minicollagen evolutionary trajectories. ConclusionsThe development of a new approach for the handling of contaminated next-generation data by closely related species represents a useful tool for future applications not only in the field of myxozoan research. This pipeline of data processing allowed us to expand the dataset and study the evolution and diversity of minicollagen gene family in Myxozoa and Cnidaria. We identified a novel type of minicollagen in Myxozoa (Ncol-5). We suggest that a high number of minicollagen paralogs in some cnidarians is a result of several recent large gene multiplication events. We revealed a close localization of minicollagens Ncol-1 and Ncol-4 in myxozoan genomes suggesting their common evolutionary history. The unique gene structure of myxozoan Ncol-5 may indicate a putative specific function in the myxozoan polar capsule or tubule. The range of myxozoan minicollagens proves that the myxozoan minicollagen gene repertoire is similar to other cnidarians and is not simplified by the parasitic lifestyle.

scholarly journals Single cell transcriptomics, mega-phylogeny and the genetic basis of morphological innovations in Rhizaria

2016 ◽  
Author(s):  
Anders K. Krabberød ◽  
Russell J. S. Orr ◽  
Jon Bråte ◽  
Tom Kristensen ◽  
Kjell R. Bjørklund ◽  
...  
Keyword(s):  
Single Cell ◽  
Intracellular Transport ◽  
Gene Evolution ◽  
Morphological Evolution ◽  
Specific Gene ◽  
Gene Duplications ◽  
Genetic Components ◽  
The Relationship ◽  
Protist Species ◽  
Lineage Specific Gene

AbstractThe innovation of the eukaryote cytoskeleton enabled phagocytosis, intracellular transport and cytokinesis, and is responsible for diverse eukaryotic morphologies. Still, the relationship between phenotypic innovations in the cytoskeleton and their underlying genotype is poorly understood. To explore the genetic mechanism of morphological evolution of the eukaryotic cytoskeleton we provide the first single cell transcriptomes from uncultivable, free-living unicellular eukaryotes: the radiolarian speciesLithomelissa setosaandSticholonche zanclea. Analysis of the genetic components of the cytoskeleton and mapping of the evolution of these to a revised phylogeny of Rhizaria reveals lineage-specific gene duplications and neo-functionalization of α and β tubulin in Retaria, actin in Retaria and Endomyxa, and Arp2/3 complex genes in Chlorarachniophyta. We show how genetic innovations have shaped cytoskeletal structures in Rhizaria, and how single cell transcriptomics can be applied for resolving deep phylogenies and studying gene evolution of uncultivable protist species.

scholarly journals The UDP-Glycosyltransferase Family in Drosophila melanogaster: Nomenclature Update, Gene Expression and Phylogenetic Analysis

2021 ◽  
Vol 12 ◽  
Author(s):  
Seung-Joon Ahn ◽  
Steven J. Marygold
Keyword(s):  
Gene Expression ◽  
Phylogenetic Analysis ◽  
Drosophila Melanogaster ◽  
Expression Patterns ◽  
Specific Gene ◽  
Uridine Diphosphate ◽  
Gene Duplications ◽  
Lipophilic Compounds ◽  
High Degree ◽  
Lineage Specific Gene

UDP-glycosyltransferases (UGTs) are important conjugation enzymes found in all kingdoms of life, catalyzing a sugar conjugation with small lipophilic compounds and playing a crucial role in detoxification and homeostasis. The UGT gene family is defined by a signature motif in the C-terminal domain where the uridine diphosphate (UDP)-sugar donor binds. UGTs have been identified in a number of insect genomes over the last decade and much progress has been achieved in characterizing their expression patterns and molecular functions. Here, we present an update of the complete repertoire of UGT genes in Drosophila melanogaster and provide a brief overview of the latest research in this model insect. A total of 35 UGT genes are found in the D. melanogaster genome, localized to chromosomes 2 and 3 with a high degree of gene duplications on the chromosome arm 3R. All D. melanogaster UGT genes have now been named in FlyBase according to the unified UGT nomenclature guidelines. A phylogenetic analysis of UGT genes shows lineage-specific gene duplications. Analysis of anatomical and induced gene expression patterns demonstrate that some UGT genes are differentially expressed in various tissues or after environmental treatments. Extended searches of UGT orthologs from 18 additional Drosophila species reveal a diversity of UGT gene numbers and composition. The roles of Drosophila UGTs identified to date are briefly reviewed, and include xenobiotic metabolism, nicotine resistance, olfaction, cold tolerance, sclerotization, pigmentation, and immunity. Together, the updated genomic information and research overview provided herein will aid further research in this developing field.

A Variant Noncoding Region Regulates Prrx1 and Predisposes to Atrial Arrhythmias

2021 ◽  
Author(s):  
Fernanda M Bosada ◽  
Mathilde R Rivaud ◽  
Jae-Sun Uhm ◽  
Sander Verheule ◽  
Karel van Duijvenboden ◽  
...  
Keyword(s):  
Sodium Current ◽  
Association Studies ◽  
Noncoding Region ◽  
Specific Gene ◽  
Genome Wide Association Studies ◽  
Enhancer Activity ◽  
Atrial Cardiomyocytes ◽  
The Impact ◽  
Lineage Specific Gene

Rationale: Atrial Fibrillation (AF) is the most common cardiac arrhythmia diagnosed in clinical practice. Genome-wide association studies have identified AF-associated common variants across 100+ genomic loci, but the mechanism underlying the impact of these variant loci on AF susceptibility in vivo has remained largely undefined. One such variant region, highly associated with AF, is found at 1q24, close to PRRX1, encoding the Paired Related Homeobox 1 transcription factor. Objective: To identify the mechanistic link between the variant region at 1q24 and AF predisposition. Methods and Results: The mouse orthologue of the noncoding variant genomic region (R1A) at 1q24 was deleted using CRISPR genome editing. Among the genes sharing the topologically associated domain with the deleted R1A region (Kifap3, Prrx1, Fmo2, Prrc2c), only the broadly expressed gene Prrx1 was downregulated in mutants, and only in cardiomyocytes. Expression and epigenetic profiling revealed that a cardiomyocyte lineage-specific gene program (Mhrt, Myh6, Rbm20, Tnnt2, Ttn, Ckm) was upregulated in R1A-/- atrial cardiomyocytes, and that Mef2 binding motifs were significantly enriched at differentially accessible chromatin sites. Consistently, Prrx1 suppressed Mef2-activated enhancer activity in HL-1 cells. Mice heterozygous or homozygous for the R1A deletion were susceptible to atrial arrhythmia induction, had atrial conduction slowing and more irregular RR intervals. Isolated R1A-/- mouse left atrial cardiomyocytes showed lower action potential upstroke velocities and sodium current, as well as increased systolic and diastolic calcium concentrations compared to controls. Conclusions: The noncoding AF variant region at 1q24 modulates Prrx1 expression in cardiomyocytes. Cardiomyocyte-specific reduction of Prrx1 expression upon deletion of the noncoding region leads to a profound induction of a cardiac lineage-specific gene program and to propensity for AF. These data indicate that AF-associated variants in humans may exert AF predisposition through reduced PRRX1 expression in cardiomyocytes.

scholarly journals A Screen for Gene Paralogies Delineating Evolutionary Branching Order of Early Metazoa

2019 ◽  
Vol 10 (2) ◽  
pp. 811-826 ◽  
Author(s):  
Albert Erives ◽  
Bernd Fritzsch
Keyword(s):  
Phylogenetic Analyses ◽  
Gene Families ◽  
Single Copy ◽  
Gene Duplications ◽  
Nervous Systems ◽  
Evolutionary Diversification ◽  
Transmembrane Channel ◽  
Sensory Epithelia ◽  
Protein X ◽  
Ancient Gene

The evolutionary diversification of animals is one of Earth’s greatest marvels, yet its earliest steps are shrouded in mystery. Animals, the monophyletic clade known as Metazoa, evolved wildly divergent multicellular life strategies featuring ciliated sensory epithelia. In many lineages epithelial sensoria became coupled to increasingly complex nervous systems. Currently, different phylogenetic analyses of single-copy genes support mutually-exclusive possibilities that either Porifera or Ctenophora is sister to all other animals. Resolving this dilemma would advance the ecological and evolutionary understanding of the first animals and the evolution of nervous systems. Here we describe a comparative phylogenetic approach based on gene duplications. We computationally identify and analyze gene families with early metazoan duplications using an approach that mitigates apparent gene loss resulting from the miscalling of paralogs. In the transmembrane channel-like (TMC) family of mechano-transducing channels, we find ancient duplications that define separate clades for Eumetazoa (Placozoa + Cnidaria + Bilateria) vs. Ctenophora, and one duplication that is shared only by Eumetazoa and Porifera. In the Max-like protein X (MLX and MLXIP) family of bHLH-ZIP regulators of metabolism, we find that all major lineages from Eumetazoa and Porifera (sponges) share a duplicated gene pair that is sister to the single-copy gene maintained in Ctenophora. These results suggest a new avenue for deducing deep phylogeny by choosing rather than avoiding ancient gene paralogies.

scholarly journals Network-based microsynteny analysis identifies major differences and genomic outliers in mammalian and angiosperm genomes

2019 ◽  
Vol 116 (6) ◽  
pp. 2165-2174 ◽  
Author(s):  
Tao Zhao ◽  
M. Eric Schranz
Keyword(s):  
Gene Families ◽  
Single Copy ◽  
Specific Gene ◽  
Phylogenetic Groups ◽  
History Of ◽  
Mammalian Genomes ◽  
Syntenic Conservation ◽  
Genome Assemblies ◽  
Lineage Specific Gene ◽  
Relative Gene

A comprehensive analysis of relative gene order, or microsynteny, can provide valuable information for understanding the evolutionary history of genes and genomes, and ultimately traits and species, across broad phylogenetic groups and divergence times. We have used our network-based phylogenomic synteny analysis pipeline to first analyze the overall patterns and major differences between 87 mammalian and 107 angiosperm genomes. These two important groups have both evolved and radiated over the last ∼170 MYR. Secondly, we identified the genomic outliers or “rebel genes” within each clade. We theorize that rebel genes potentially have influenced trait and lineage evolution. Microsynteny networks use genes as nodes and syntenic relationships between genes as edges. Networks were decomposed into clusters using the Infomap algorithm, followed by phylogenomic copy-number profiling of each cluster. The differences in syntenic properties of all annotated gene families, including BUSCO genes, between the two clades are striking: most genes are single copy and syntenic across mammalian genomes, whereas most genes are multicopy and/or have lineage-specific distributions for angiosperms. We propose microsynteny scores as an alternative and complementary metric to BUSCO for assessing genome assemblies. We further found that the rebel genes are different between the two groups: lineage-specific gene transpositions are unusual in mammals, whereas single-copy highly syntenic genes are rare for flowering plants. We illustrate several examples of mammalian transpositions, such as brain-development genes in primates, and syntenic conservation across angiosperms, such as single-copy genes related to photosynthesis. Future experimental work can test if these are indeed rebels with a cause.

Phylogenetic analyses of potentially free-living Symbiodinium spp. isolated from coral reef sand in Okinawa, Japan

2008 ◽  
Vol 155 (1) ◽  
pp. 105-112 ◽  
Author(s):  
Mamiko Hirose ◽  
James D. Reimer ◽  
Michio Hidaka ◽  
Shoichiro Suda
Keyword(s):  
Coral Reef ◽  
Phylogenetic Analyses ◽  
Free Living
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