scholarly journals Expansion, retention and loss in the Acyl-CoA Synthetase “Bubblegum” (Acsbg) gene family in vertebrate history

2018 ◽  
Author(s):  
Mónica Lopes-Marques ◽  
André M. Machado ◽  
Raquel Ruivo ◽  
Elza Fonseca ◽  
Estela Carvalho ◽  
...  
Keyword(s):  
Gene Family ◽  
Metabolic Pathways ◽  
Evolutionary History ◽  
Gene Families ◽  
Gene Repertoire ◽  
Physiological Processes ◽  
Complex Lipid ◽  
History Of ◽  
Enzyme Families ◽  
Rate Limiting

AbstractFatty acids (FAs) constitute a considerable fraction of all lipid molecules with a fundamental role in numerous physiological processes. In animals, the majority of complex lipid molecules are derived from the transformation of FAs through several biochemical pathways. Yet, for FAs to enroll in these pathways they require an activation step. FA activation is catalyzed by the rate limiting action of Acyl-CoA synthases. Several Acyl-CoA enzyme families have been previously described and classified according to the chain length of FA they process. Here, we address the evolutionary history of the ACSBG gene family which activates, FA with more than 16 carbons. Currently, two different ACSBG gene families, ACSBG1 and ACSBG2, are recognized in vertebrates. We provide evidence that a wider and unequal ACSBG gene repertoire is present in vertebrate lineages. We identify a novel ACSBG-like gene lineage which occurs specifically in amphibians, ray finned fish, coelacanths and chondrichthyes named ACSBG3. Also, we show that the ACSBG2 gene lineage duplicated in the Theria ancestor. Our findings, thus offer a far richer understanding on FA activation in vertebrates and provide key insights into the relevance of comparative and functional analysis to perceive physiological differences, namely those related with lipid metabolic pathways.

scholarly journals Evolutionary history of dimethylsulfoniopropionate (DMSP) demethylation enzyme DmdA in marine bacteria

2019 ◽  
Author(s):  
Laura Hernández ◽  
Alberto Vicens ◽  
Luis Enrique Eguiarte ◽  
Valeria Souza ◽  
Valerie De Anda ◽  
...  
Keyword(s):  
Gene Family ◽  
Evolutionary History ◽  
Common Ancestor ◽  
Functional Divergence ◽  
Gene Families ◽  
Recent Common Ancestor ◽  
Common Ancestry ◽  
Demethylation Pathway ◽  
History Of ◽  
New Gene

ABSTRACTDimethylsulfoniopropionate (DMSP), an osmolyte produced by oceanic phytoplankton, is predominantly degraded by bacteria belonging to the Roseobacter lineage and other marine Alphaproteobacteria via DMSP-dependent demethylase A protein (DmdA). To date, the evolutionary history of DmdA gene family is unclear. Some studies indicate a common ancestry between DmdA and GcvT gene families and a co-evolution between Roseobacter and the DMSP-producing-phytoplankton around 250 million years ago (Mya). In this work, we analyzed the evolution of DmdA under three possible evolutionary scenarios: 1) a recent common ancestor of DmdA and GcvT, 2) a coevolution between Roseobacter and the DMSP-producing-phytoplankton, and 3) pre-adapted enzymes to DMSP prior to Roseobacter origin. Our analyses indicate that DmdA is a new gene family originated from GcvT genes by duplication and functional divergence driven by positive selection before a coevolution between Roseobacter and phytoplankton. Our data suggest that Roseobacter acquired dmdA by horizontal gene transfer prior to exposition to an environment with higher DMSP. Here, we propose that the ancestor that carried the DMSP demethylation pathway genes evolved in the Archean, and was exposed to a higher concentration of DMSP in a sulfur rich atmosphere and anoxic ocean, compared to recent Roseobacter ecoparalogs (copies performing the same function under different conditions), which should be adapted to lower concentrations of DMSP.

scholarly journals Evolutionary history of dimethylsulfoniopropionate (DMSP) demethylation enzyme DmdA in marine bacteria

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9861
Author(s):  
Laura Hernández ◽  
Alberto Vicens ◽  
Luis E. Eguiarte ◽  
Valeria Souza ◽  
Valerie De Anda ◽  
...  
Keyword(s):  
Gene Family ◽  
Marine Bacteria ◽  
Evolutionary History ◽  
Functional Divergence ◽  
Gene Families ◽  
Recent Common Ancestor ◽  
Demethylation Pathway ◽  
History Of ◽  
New Gene ◽  
Enzymatic Adaptation

Dimethylsulfoniopropionate (DMSP), an osmolyte produced by oceanic phytoplankton and bacteria, is primarily degraded by bacteria belonging to the Roseobacter lineage and other marine Alphaproteobacteria via DMSP-dependent demethylase A protein (DmdA). To date, the evolutionary history of DmdA gene family is unclear. Some studies indicate a common ancestry between DmdA and GcvT gene families and a co-evolution between Roseobacter and the DMSP-producing-phytoplankton around 250 million years ago (Mya). In this work, we analyzed the evolution of DmdA under three possible evolutionary scenarios: (1) a recent common ancestor of DmdA and GcvT, (2) a coevolution between Roseobacter and the DMSP-producing-phytoplankton, and (3) an enzymatic adaptation for utilizing DMSP in marine bacteria prior to Roseobacter origin. Our analyses indicate that DmdA is a new gene family originated from GcvT genes by duplication and functional divergence driven by positive selection before a coevolution between Roseobacter and phytoplankton. Our data suggest that Roseobacter acquired dmdA by horizontal gene transfer prior to an environment with higher DMSP. Here, we propose that the ancestor that carried the DMSP demethylation pathway genes evolved in the Archean, and was exposed to a higher concentration of DMSP in a sulfur-rich atmosphere and anoxic ocean, compared to recent Roseobacter eco-orthologs (orthologs performing the same function under different conditions), which should be adapted to lower concentrations of DMSP.

scholarly journals Evolution of the FGF Gene Family

2012 ◽  
Vol 2012 ◽  
pp. 1-12 ◽  
Author(s):  
Silvan Oulion ◽  
Stephanie Bertrand ◽  
Hector Escriva
Keyword(s):  
Gene Family ◽  
Evolutionary History ◽  
Tyrosine Kinase Receptors ◽  
Cell Behavior ◽  
New Classification ◽  
Physiological Processes ◽  
Small Proteins ◽  
Synteny Conservation ◽  
History Of

Fibroblast Growth Factors (FGFs) are small proteins generally secreted, acting through binding to transmembrane tyrosine kinase receptors (FGFRs). Activation of FGFRs triggers several cytoplasmic cascades leading to the modification of cell behavior. FGFs play critical roles in a variety of developmental and physiological processes. Since their discovery in mammals, FGFs have been found in many metazoans and some arthropod viruses. Efforts have been previously made to decipher the evolutionary history of this family but conclusions were limited due to a poor taxonomic coverage. We took advantage of the availability of many new sequences from diverse metazoan lineages to further explore the possible evolutionary scenarios explaining the diversity of the FGF gene family. Our analyses, based on phylogenetics and synteny conservation approaches, allow us to propose a new classification of FGF genes into eight subfamilies, and to draw hypotheses for the evolutionary events leading to the present diversity of this gene family.

scholarly journals Phylogenetic diversification of sirtuin genes with a description of a new family member

2020 ◽  
Author(s):  
Juan C. Opazo ◽  
Kattina Zavala ◽  
Michael W. Vandewege ◽  
Federico G. Hoffmann
Keyword(s):  
Gene Family ◽  
Family Member ◽  
Gene Families ◽  
Last Common Ancestor ◽  
Gene Repertoire ◽  
Origin And Evolution ◽  
New Family ◽  
Wide Range ◽  
Evolutionary Context ◽  
History Of

AbstractStudying the evolutionary history of gene families is a challenging and exciting task with a wide range of implications. In addition to exploring fundamental questions about the origin and evolution of genes, disentangling their evolution is also critical to those who do functional/structural work, as the correct interpretation of their results needs to be done in a robust evolutionary context. The sirtuin gene family is a group of genes that are involved in a variety of biological functions mostly related to aging. Their duplicative history is an open question, as well as the definition of the repertoire of sirtuin genes among vertebrates. Our goal is to take advantage of the genomic data available in public databases to advance our understanding of how sirtuin genes are related to each other, and to characterize the gene repertoire in species representative of all the main groups of vertebrates. Our results show a well-resolved phylogeny that represents a significant improvement in our understanding of the duplicative history of the sirtuin gene family. We identified a new sirtuin family member (SIRT3-like) that was apparently lost in amniotes, but retained in all other groups of jawed vertebrates. Our results indicate that there are at least eight sirtuin paralogs among vertebrates and that all of them can be traced back to the last common ancestor of the group that existed between 676 and 615 millions of years ago.

scholarly journals Structure and evolutionary history of a large family of NLR proteins in the zebrafish

2015 ◽  
Author(s):  
Kerstin Howe ◽  
Philipp H Schiffer ◽  
Julia Zielinski ◽  
Thomas Wiehe ◽  
Gavin K Laird ◽  
...  
Keyword(s):  
Gene Family ◽  
Evolutionary History ◽  
Large Family ◽  
Gene Families ◽  
Immune Recognition ◽  
Chromosome 4 ◽  
New Family ◽  
History Of ◽  
Evolutionary Trajectories ◽  
B30.2 Domain

NACHT- and Leucine-Rich-Repeat-containing domain (NLR) proteins act as cytoplasmic sensors for pathogen- and danger-associated molecular patterns and are found throughout the plant and animal kingdoms. In addition to having a small set of conserved NLRs, the genomes in some animal lineages contain massive expansions of this gene family. One of these arose in fishes, after the creation of a gene fusion that combined the core NLR domains with another domain used for immune recognition, the PRY/SPRY or B30.2 domain. We have analysed the expanded NLR gene family in zebrafish, which contains 368 genes, and studied its evolutionary history. The encoded proteins share a defining overall structure, but individual domains show different evolutionary trajectories. Our results suggest gene conversion homogenizes NACHT and B30.2 domain sequences among different gene subfamilies, however, the functional implications of its action remains unclear. The majority of the genes are located on the long arm of chromosome 4, interspersed with several other large multi-gene families, including a new family encoding proteins with multiple tandem arrays of Zinc fingers. This suggests that chromosome 4 may be a hotspot for rapid evolutionary change in zebrafish.

scholarly journals iHam and pyHam: visualizing and processing hierarchical orthologous groups

2018 ◽  
Vol 35 (14) ◽  
pp. 2504-2506 ◽  
Author(s):  
Clément-Marie Train ◽  
Miguel Pignatelli ◽  
Adrian Altenhoff ◽  
Christophe Dessimoz
Keyword(s):  
Gene Family ◽  
Evolutionary History ◽  
Gene Families ◽  
Comparative Genomic ◽  
Last Common Ancestor ◽  
Analysis Method ◽  
Ancestral Gene ◽  
Genomic Analyses ◽  
History Of ◽  
Multiple Species

Abstract Summary The evolutionary history of gene families can be complex due to duplications and losses. This complexity is compounded by the large number of genomes simultaneously considered in contemporary comparative genomic analyses. As provided by several orthology databases, hierarchical orthologous groups (HOGs) are sets of genes that are inferred to have descended from a common ancestral gene within a species clade. This implies that the set of HOGs defined for a particular clade correspond to the ancestral genes found in its last common ancestor. Furthermore, by keeping track of HOG composition along the species tree, it is possible to infer the emergence, duplications and losses of genes within a gene family of interest. However, the lack of tools to manipulate and analyse HOGs has made it difficult to extract, display and interpret this type of information. To address this, we introduce interactive HOG analysis method, an interactive JavaScript widget to visualize and explore gene family history encoded in HOGs and python HOG analysis method, a python library for programmatic processing of genes families. These complementary open source tools greatly ease adoption of HOGs as a scalable and interpretable concept to relate genes across multiple species. Availability and implementation iHam’s code is available at https://github.com/DessimozLab/iHam or can be loaded dynamically. pyHam’s code is available at https://github.com/DessimozLab/pyHam and or via the pip package ‘pyham’.

scholarly journals Evolution of the α2-adrenoreceptors in vertebrates: ADRA2D is absent in mammals and crocodiles

2017 ◽  
Author(s):  
Héctor A. Céspedes ◽  
Kattina Zavala ◽  
Juan C. Opazo
Keyword(s):  
Gene Family ◽  
Evolutionary History ◽  
Genetic Basis ◽  
G Protein Coupled Receptors ◽  
Physiological Processes ◽  
Alternative Variant ◽  
History Of ◽  
G Protein Coupled ◽  
Fourth Member ◽  
Lamprey Species

AbstractEvolutionary studies of genes that have been functionally characterized and whose variation has been associated with pathological conditions represent an opportunity to understand the genetic basis of pathologies. α2-adrenoreceptors (ADRA2) are a class of G protein-coupled receptors that regulate several physiological processes including blood pressure, platelet aggregation, insulin secretion, lipolysis, and neurotransmitter release. This gene family has been extensively studied from a molecular/physiological perspective, yet much less is known about its evolutionary history. Accordingly, the goal of this study was to investigate the evolutionary history of α2-adrenoreceptors (ADRA2) in vertebrates. Our results show that in addition to the three well-recognized α2-adrenoreceptor genes (ADRA2A, ADRA2B and ADRA2C), we recovered a clade that corresponds to the fourth member of the α2-adrenoreceptor gene family (ADRA2D). We also recovered a clade that possesses two ADRA2 sequences found in two lamprey species. Furthermore, our results show that mammals and crocodiles are characterized by possessing three α2-adrenoreceptor genes, whereas all other vertebrate groups possess the full repertoire of α2-adrenoreceptor genes. Among vertebrates ADRA2D seems to be a dispensable gene, as it was lost two independent times during the evolutionary history of the group. Additionally, we found that most examined species possess the most common alleles described for humans; however, there are cases in which non-human mammals possess the alternative variant.

scholarly journals Nephromyces represents a diverse and novel lineage of the Apicomplexa that has retained apicoplasts

2019 ◽  
Author(s):  
Sergio A Muñoz-Gómez ◽  
Keira Durnin ◽  
Laura Eme ◽  
Christopher Paight ◽  
Christopher E Lane ◽  
...  
Keyword(s):  
Life Style ◽  
Metabolic Pathways ◽  
Evolutionary History ◽  
Phylogenetic Analyses ◽  
Phylogenetic Position ◽  
Biosynthetic Pathways ◽  
History Of ◽  
Sea Squirts ◽  
Shed Light ◽  
Apicoplast Genome

Abstract A most interesting exception within the parasitic Apicomplexa is Nephromyces, an extracellular, probably mutualistic, endosymbiont found living inside molgulid ascidian tunicates (i.e., sea squirts). Even though Nephromyces is now known to be an apicomplexan, many other questions about its nature remain unanswered. To gain further insights into the biology and evolutionary history of this unusual apicomplexan, we aimed to (1) find the precise phylogenetic position of Nephromyces within the Apicomplexa, (2) search for the apicoplast genome of Nephromyces, and (3) infer the major metabolic pathways in the apicoplast of Nephromyces. To do this, we sequenced a metagenome and a metatranscriptome from the molgulid renal sac, the specialized habitat where Nephromyces thrives. Our phylogenetic analyses of conserved nucleus-encoded genes robustly suggest that Nephromyces is a novel lineage sister to the Hematozoa, which comprises both the Haemosporidia (e.g., Plasmodium) and the Piroplasmida (e.g., Babesia and Theileria). Furthermore, a survey of the renal sac metagenome revealed 13 small contigs that closely resemble the genomes of the non-photosynthetic reduced plastids, or apicoplasts, of other apicomplexans. We show that these apicoplast genomes correspond to a diverse set of most closely related but genetically divergent Nephromyces lineages that co-inhabit a single tunicate host. In addition, the apicoplast of Nephromyces appears to have retained all biosynthetic pathways inferred to have been ancestral to parasitic apicomplexans. Our results shed light on the evolutionary history of the only probably mutualistic apicomplexan known, Nephromyces, and provide context for a better understanding of its life style and intricate symbiosis.

scholarly journals The hard clam genome reveals massive expansion and diversification of inhibitors of apoptosis in Bivalvia

BMC Biology ◽  
2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Hao Song ◽  
Ximing Guo ◽  
Lina Sun ◽  
Qianghui Wang ◽  
Fengming Han ◽  
...  
Keyword(s):  
Gene Family ◽  
Stress Responses ◽  
Tandem Duplication ◽  
Expression Patterns ◽  
Hard Clam ◽  
Gene Repertoire ◽  
Single Chromosome ◽  
Inhibitors Of Apoptosis ◽  
History Of ◽  
Evolutionary Success

Abstract Background Inhibitors of apoptosis (IAPs) are critical regulators of programmed cell death that are essential for development, oncogenesis, and immune and stress responses. However, available knowledge regarding IAP is largely biased toward humans and model species, while the distribution, function, and evolutionary novelties of this gene family remain poorly understood in many taxa, including Mollusca, the second most speciose phylum of Metazoa. Results Here, we present a chromosome-level genome assembly of an economically significant bivalve, the hard clam Mercenaria mercenaria, which reveals an unexpected and dramatic expansion of the IAP gene family to 159 members, the largest IAP gene repertoire observed in any metazoan. Comparative genome analysis reveals that this massive expansion is characteristic of bivalves more generally. Reconstruction of the evolutionary history of molluscan IAP genes indicates that most originated in early metazoans and greatly expanded in Bivalvia through both lineage-specific tandem duplication and retroposition, with 37.1% of hard clam IAPs located on a single chromosome. The expanded IAPs have been subjected to frequent domain shuffling, which has in turn shaped their architectural diversity. Further, we observed that extant IAPs exhibit dynamic and orchestrated expression patterns among tissues and in response to different environmental stressors. Conclusions Our results suggest that sophisticated regulation of apoptosis enabled by the massive expansion and diversification of IAPs has been crucial for the evolutionary success of hard clam and other molluscan lineages, allowing them to cope with local environmental stresses. This study broadens our understanding of IAP proteins and expression diversity and provides novel resources for studying molluscan biology and IAP function and evolution.

scholarly journals Gene family innovation, conservation and loss on the animal stem lineage

eLife ◽  
2018 ◽  
Vol 7 ◽  
Author(s):  
Daniel J Richter ◽  
Parinaz Fozouni ◽  
Michael B Eisen ◽  
Nicole King
Keyword(s):  
Gene Family ◽  
Gene Families ◽  
Gene Content ◽  
Gene Repertoire ◽  
Toll Like Receptor ◽  
Stem Lineage ◽  
Gains And Losses ◽  
Core Features

Choanoflagellates, the closest living relatives of animals, can provide unique insights into the changes in gene content that preceded the origin of animals. However, only two choanoflagellate genomes are currently available, providing poor coverage of their diversity. We sequenced transcriptomes of 19 additional choanoflagellate species to produce a comprehensive reconstruction of the gains and losses that shaped the ancestral animal gene repertoire. We identified ~1944 gene families that originated on the animal stem lineage, of which only 39 are conserved across all animals in our study. In addition, ~372 gene families previously thought to be animal-specific, including Notch, Delta, and homologs of the animal Toll-like receptor genes, instead evolved prior to the animal-choanoflagellate divergence. Our findings contribute to an increasingly detailed portrait of the gene families that defined the biology of the Urmetazoan and that may underpin core features of extant animals.

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