scholarly journals Replacement and Parallel Simplification of Nonhomologous Proteinases Maintain Venom Phenotypes in Rear-Fanged Snakes

2020 ◽  
Vol 37 (12) ◽  
pp. 3563-3575 ◽  
Author(s):  
Juan David Bayona-Serrano ◽  
Vincent Louis Viala ◽  
Rhett M Rautsaw ◽  
Tristan D Schramer ◽  
Gesiele A Barros-Carvalho ◽  
...  
Keyword(s):  
Snake Venom ◽  
Evolutionary History ◽  
Phenotypic Traits ◽  
Gene Duplications ◽  
Snake Venoms ◽  
Venom Component ◽  
History Of ◽  
Biochemical Components ◽  
Functional Analyses ◽  
Specific Sequences

Abstract Novel phenotypes are commonly associated with gene duplications and neofunctionalization, less documented are the cases of phenotypic maintenance through the recruitment of novel genes. Proteolysis is the primary toxic character of many snake venoms, and ADAM metalloproteinases, named snake venom metalloproteinases (SVMPs), are largely recognized as the major effectors of this phenotype. However, by investigating original transcriptomes from 58 species of advanced snakes (Caenophidia) across their phylogeny, we discovered that a different enzyme, matrix metalloproteinase (MMP), is actually the dominant venom component in three tribes (Tachymenini, Xenodontini, and Conophiini) of rear-fanged snakes (Dipsadidae). Proteomic and functional analyses of these venoms further indicate that MMPs are likely playing an “SVMP-like” function in the proteolytic phenotype. A detailed look into the venom-specific sequences revealed a new highly expressed MMP subtype, named snake venom MMP (svMMP), which originated independently on at least three occasions from an endogenous MMP-9. We further show that by losing ancillary noncatalytic domains present in its ancestors, svMMPs followed an evolutionary path toward a simplified structure during their expansion in the genomes, thus paralleling what has been proposed for the evolution of their Viperidae counterparts, the SVMPs. Moreover, we inferred an inverse relationship between the expression of svMMPs and SVMPs along the evolutionary history of Xenodontinae, pointing out that one type of enzyme may be substituting for the other, whereas the general (metallo)proteolytic phenotype is maintained. These results provide rare evidence on how relevant phenotypic traits can be optimized via natural selection on nonhomologous genes, yielding alternate biochemical components.

scholarly journals Evolutionary history of the human multigene families reveals widespread gene duplications throughout the history of animals

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Nashaiman Pervaiz ◽  
Nazia Shakeel ◽  
Ayesha Qasim ◽  
Rabail Zehra ◽  
Saneela Anwar ◽  
...  
Keyword(s):  
Evolutionary History ◽  
Multigene Families ◽  
Gene Duplications ◽  
History Of

scholarly journals Sensing soluble uric acid by Naip1-Nlrp3 platform

2021 ◽  
Vol 12 (2) ◽  
Author(s):  
Tarcio Teodoro Braga ◽  
Mariana Rodrigues Davanso ◽  
Davi Mendes ◽  
Tiago Antonio de Souza ◽  
Anderson Fernandes de Brito ◽  
...  
Keyword(s):  
Uric Acid ◽  
Evolutionary History ◽  
Evolutionary Process ◽  
Soluble Form ◽  
Purine Nucleotide ◽  
Fatty Acid Production ◽  
History Of ◽  
Related Response ◽  
Nucleotide Degradation ◽  
Functional Analyses

AbstractUric acid (UA), a product of purine nucleotide degradation able to initiate an immune response, represents a breakpoint in the evolutionary history of humans, when uricase, the enzyme required for UA cleavage, was lost. Despite being inert in human cells, UA in its soluble form (sUA) can increase the level of interleukin-1β (IL-1β) in murine macrophages. We, therefore, hypothesized that the recognition of sUA is achieved by the Naip1-Nlrp3 inflammasome platform. Through structural modelling predictions and transcriptome and functional analyses, we found that murine Naip1 expression in human macrophages induces IL-1β expression, fatty acid production and an inflammation-related response upon sUA stimulation, a process reversed by the pharmacological and genetic inhibition of Nlrp3. Moreover, molecular interaction experiments showed that Naip1 directly recognizes sUA. Accordingly, Naip may be the sUA receptor lost through the human evolutionary process, and a better understanding of its recognition may lead to novel anti-hyperuricaemia therapies.

scholarly journals Functional analyses of the horizontally acquired Phytophaga glycoside hydrolase family 45 (GH45) proteins reveal distinct functional characteristics

2018 ◽  
Author(s):  
André Busch ◽  
Etienne G.J. Danchin ◽  
Yannick Pauchet
Keyword(s):  
Glycoside Hydrolase ◽  
Evolutionary History ◽  
Plant Cell Wall ◽  
Glycoside Hydrolase Family ◽  
Last Common Ancestor ◽  
Gene Encoding ◽  
Amorphous Cellulose ◽  
History Of ◽  
Functional Analyses ◽  
Hydrolase Family

AbstractCellulose, a major polysaccharide of the plant cell wall, consists of β-1,4-linked glucose moieties forming a molecular network recalcitrant to enzymatic breakdown. Although cellulose is potentially a rich source of energy, the ability to degrade it is rare in animals and was believed to be present only in cellulolytic microbes. Recently, it has become clear that some animals encode endogenous cellulases belonging to several glycoside hydrolase families (GHs), including GH45. GH45s are distributed patchily among the Metazoa and, in insects, are encoded only by the genomes of Phytophaga beetles. This study aims to understand both the enzymatic properties and the evolutionary history of GH45s in these beetles. To this end, we tested the enzymatic abilities of 37 GH45s derived from five species of Phytophaga beetles and learned that beetle-derived GH45s degrade three different substrates: amorphous cellulose, xyloglucan and glucomannan. Our phylogenetic and gene structure analyses indicate that at least one gene encoding a putative cellulolytic GH45 was present in the last common ancestor of the Phytophaga, and that GH45 xyloglucanases evolved several times independently in these beetles. The most closely related clade to Phytophaga GH45s contained fungal sequences, suggesting this GH family was acquired by horizontal gene transfer from fungi. Other than in insects, arthropod GH45s do not share a common origin and appear to have emerged at least three times independently.

scholarly journals Molecular palaeontology illuminates the evolution of ecdysozoan vision

2018 ◽  
Vol 285 (1892) ◽  
pp. 20182180 ◽  
Author(s):  
James F. Fleming ◽  
Reinhardt Møbjerg Kristensen ◽  
Martin Vinther Sørensen ◽  
Tae-Yoon S. Park ◽  
Kazuharu Arakawa ◽  
...  
Keyword(s):  
Colour Vision ◽  
Evolutionary History ◽  
Large Scale ◽  
Molecular Level ◽  
Visual Pigments ◽  
Gene Duplications ◽  
Opsin Genes ◽  
Integrative Study ◽  
Velvet Worms ◽  
History Of

Colour vision is known to have arisen only twice—once in Vertebrata and once within the Ecdysozoa, in Arthropoda. However, the evolutionary history of ecdysozoan vision is unclear. At the molecular level, visual pigments, composed of a chromophore and a protein belonging to the opsin family, have different spectral sensitivities and these mediate colour vision. At the morphological level, ecdysozoan vision is conveyed by eyes of variable levels of complexity; from the simple ocelli observed in the velvet worms (phylum Onychophora) to the marvellously complex eyes of insects, spiders, and crustaceans. Here, we explore the evolution of ecdysozoan vision at both the molecular and morphological level; combining analysis of a large-scale opsin dataset that includes previously unknown ecdysozoan opsins with morphological analyses of key Cambrian fossils with preserved eye structures. We found that while several non-arthropod ecdysozoan lineages have multiple opsins, arthropod multi-opsin vision evolved through a series of gene duplications that were fixed in a period of 35–71 million years (Ma) along the stem arthropod lineage. Our integrative study of the fossil and molecular record of vision indicates that fossils with more complex eyes were likely to have possessed a larger complement of opsin genes.

scholarly journals The expansion and diversity of the CYP75 gene family in Vitaceae

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e12174
Author(s):  
Yang Xiao ◽  
Jun Wen ◽  
Ran Meng ◽  
Ying Meng ◽  
Qiang Zhou ◽  
...  
Keyword(s):  
Gene Family ◽  
Protein Sequence ◽  
Evolutionary History ◽  
Protein Sequences ◽  
Flavonoid Biosynthesis ◽  
The Other ◽  
Gene Duplications ◽  
Middle Region ◽  
Transcriptome Data ◽  
History Of

The CYP75 gene family plays an important role in flavonoid biosynthesis in plants. Little is known about the evolution of the gene family within the grape family. Here, we extracted the CYP75 genes from transcriptome data of 15 grape species and 36 representative genomes from other plants to explore the evolutionary history of the CYP75 gene family in Vitaceae. The structure of the CYP75 protein sequences is highly conserved with the variation mainly occurring in the N terminal and the middle region. The evolutionary analyses suggested classifying the CYP75 gene family into three groups in Vitaceae, namely Vitaceae A1, Vitaceae A2 and Vitaceae B. The Vitaceae A1 and A2 belong to the CYP75A subfamily and the Vitaceae B belongs to the CYP75B subfamily. Within the Vitaceae A1, most Vitaceae taxa present only one copy of the CYP75A protein sequence except for Vitis vinifera with a high number of sequences, which might have originated through recent gene duplications after its split from the other species. Vitaceae A2 contain only CYP75A sequences from Vitaceae sister to one from Camellia sinensis, probably representing a relict lineage. The CYP75B proteins were found to be dominated in Vitaceae and other angiosperms. Our results provide important insights into understanding the evolutionary history of the CYP75 gene family in Vitaceae and other angiosperms.

scholarly journals Multiple ancestral and a plethora of recent gene duplications during the evolution of the green sensitive opsin genes (RH2) in teleost fishes

2021 ◽  
Author(s):  
Zuzana Musilova ◽  
Fabio Cortesi
Keyword(s):  
Evolutionary History ◽  
Gene Families ◽  
Gene Duplications ◽  
Teleost Fishes ◽  
Cone Opsin ◽  
Genomic Tools ◽  
Genome Duplications ◽  
History Of ◽  
Modern Genomic ◽  
Almost All

Vertebrates have four visual cone opsin classes that, together with a light-sensitive chromophore, provide sensitivity from the ultraviolet to the red wavelengths of light. The rhodopsin-like 2 (RH2) opsin is sensitive to the centre blue-green part of the spectrum, which is the most prevalent light underwater. While various vertebrate groups such as mammals and sharks have lost the RH2 gene, in teleost fishes this opsin has continued to proliferate. By investigating the genomes of 115 teleost species, we find that RH2 shows an extremely dynamic evolutionary history with repeated gene duplications, gene losses and gene conversion affecting entire orders, families and species. At least four ancestral duplications provided the substrate for todays RH2 diversity with duplications occurring in the common ancestors of Clupeocephala, Neoteleostei, and Acanthopterygii. Following these events, RH2 has continued to duplicate both in tandem and during lineage specific genome duplications. However, it has also been lost many times over so that in the genomes of extant teleosts, we find between zero to eight RH2 copies. Using retinal transcriptomes in a phylogenetic representative dataset of 30 species, we show that RH2 is expressed as the dominant green-sensitive opsin in almost all fish lineages. The exceptions are the Osteoglossomorpha (bony tongues and mooneyes) and several characin species that have lost RH2, and tarpons, other characins and gobies which do not or only lowly express the gene. These fishes instead express a green-shifted long-wavelength-sensitive LWS opsin. Our study highlights the strength of using modern genomic tools within a comparative framework to elucidate the detailed evolutionary history of gene families.

Mosaic evolution in the middle Miocene planktonic foraminifera Fohsella lineage

Paleobiology ◽  
2018 ◽  
Vol 44 (2) ◽  
pp. 263-272
Author(s):  
Weimin Si ◽  
William A. Berggren ◽  
Marie-Pierre Aubry
Keyword(s):  
Evolutionary History ◽  
Middle Miocene ◽  
Planktonic Foraminifera ◽  
Phenotypic Traits ◽  
Geographic Ranges ◽  
History Of ◽  
Morphologic Evolution ◽  
Coiling Direction ◽  
Directional Trend ◽  
Selection Of

AbstractRecent studies have shown that modes of evolution, namely directional trend, random walk, and stasis, vary across morphologic traits and over the geographic range of a taxon. If so, is it possible that our interpretation of evolutionary modes is actually driven by our selection of traits in a study? In an attempt to answer this question, we have restudied the middle Miocene planktonic foraminifera Fohsella lineage, an iconic example of gradual morphologic evolution. In contrast to previous studies that have focused on the gross morphology as embodied by the edge view of tests, we analyze here multiple phenotypic traits chosen because their biologic and ecologic significance is well understood in living populations. We find that traits in the lineage did not evolve in concert. The timing and geographic pattern of changes in shape, coiling direction, size, and ecology were different. The evolution of this lineage is a mosaic combination of different evolutionary modes for different traits. We suggest that overemphasis on the evolution of some single trait, such as the edge-view outline, from narrow geographic ranges has significantly underestimated the dynamic evolutionary history of this group.

scholarly journals Comment on “A promiscuous intermediate underlies the evolution of LEAFY DNA binding specificity”

Science ◽  
2015 ◽  
Vol 347 (6222) ◽  
pp. 621.2-621 ◽  
Author(s):  
Jacob O. Brunkard ◽  
Anne M. Runkel ◽  
Patricia C. Zambryski
Keyword(s):  
Transcription Factors ◽  
Dna Binding ◽  
Gene Duplication ◽  
Evolutionary History ◽  
Binding Specificity ◽  
Gene Duplications ◽  
Data Set ◽  
New Model ◽  
Dna Binding Specificity ◽  
History Of

Sayou et al. (Reports, 7 February 2014, p. 645) proposed a new model for evolution of transcription factors without gene duplication, using LEAFY as an archetype. Their proposal contradicts the evolutionary history of plants and ignores evidence that LEAFY evolves through gene duplications. Within their data set, we identified a moss with multiple LEAFY orthologs, which contests their model and supports that LEAFY evolves through duplications.

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