scholarly journals Evolutionary Plasticity in Detoxification Gene Modules: The Preservation and Loss of the Pregnane X Receptor in Chondrichthyes Lineages

2019 ◽  
Vol 20 (9) ◽  
pp. 2331 ◽  
Author(s):  
Elza S. S. Fonseca ◽  
Raquel Ruivo ◽  
André M. Machado ◽  
Francisca Conrado ◽  
Boon-Hui Tay ◽  
...  
Keyword(s):  
Functional Characterization ◽  
Constitutive Androstane Receptor ◽  
Pregnane X Receptor ◽  
Gene Families ◽  
Critical Question ◽  
Group I ◽  
Activation Profile ◽  
Gene Duplication And Loss ◽  
Molecular Landscape ◽  
Gene Orthologs

To appraise how evolutionary processes, such as gene duplication and loss, influence an organism’s xenobiotic sensitivity is a critical question in toxicology. Of particular importance are gene families involved in the mediation of detoxification responses, such as members of the nuclear receptor subfamily 1 group I (NR1I), the pregnane X receptor (PXR), and the constitutive androstane receptor (CAR). While documented in multiple vertebrate genomes, PXR and CAR display an intriguing gene distribution. PXR is absent in birds and reptiles, while CAR shows a tetrapod-specific occurrence. More elusive is the presence of PXR and CAR gene orthologs in early branching and ecologically-important Chondrichthyes (chimaeras, sharks and rays). Therefore, we investigated various genome projects and use them to provide the first identification and functional characterization of a Chondrichthyan PXR from the chimaera elephant shark (Callorhinchus milii, Holocephali). Additionally, we substantiate the targeted PXR gene loss in Elasmobranchii (sharks and rays). Compared to other vertebrate groups, the chimaera PXR ortholog displays a diverse expression pattern (skin and gills) and a unique activation profile by classical xenobiotic ligands. Our findings provide insights into the molecular landscape of detoxification mechanisms and suggest lineage-specific adaptations in response to xenobiotics in gnathostome evolution.

scholarly journals Evolutionary History and Functional Characterization of the Amphibian Xenosensor CAR

2012 ◽  
Vol 26 (1) ◽  
pp. 14-26 ◽  
Author(s):  
Marianne Mathäs ◽  
Oliver Burk ◽  
Huan Qiu ◽  
Christian Nußhag ◽  
Ute Gödtel-Armbrust ◽  
...  
Keyword(s):  
Evolutionary History ◽  
Functional Characterization ◽  
Constitutive Androstane Receptor ◽  
Pregnane X Receptor ◽  
Constitutive Activity ◽  
Whole Genome Duplications ◽  
Genome Duplications ◽  
History Of ◽  
Land Vertebrates

Abstract The xenosensing constitutive androstane receptor (CAR) is widely considered to have arisen in early mammals via duplication of the pregnane X receptor (PXR). We report that CAR emerged together with PXR and the vitamin D receptor from an ancestral NR1I gene already in early vertebrates, as a result of whole-genome duplications. CAR genes were subsequently lost from the fish lineage, but they are conserved in all taxa of land vertebrates. This contrasts with PXR, which is found in most fish species, whereas it is lost from Sauropsida (reptiles and birds) and plays a role unrelated to xenosensing in Xenopus. This role is fulfilled in Xenopus by CAR, which exhibits low basal activity and pronounced responsiveness to activators such as drugs and steroids, altogether resembling mammalian PXR. The constitutive activity typical for mammalian CAR emerged first in Sauropsida, and it is thus common to all fully terrestrial land vertebrates (Amniota). The constitutive activity can be achieved by humanizing just two amino acids of the Xenopus CAR. Taken together, our results provide a comprehensive reconstruction of the evolutionary history of the NR1I subfamily of nuclear receptors. They identify CAR as the more conserved and remarkably plastic NR1I xenosensor in land vertebrates. Nonmammalian CAR should help to dissect the specific functions of PXR and CAR in the metabolism of xeno- and endobiotics in humans. Xenopus CAR is a first reported amphibian xenosensor, which opens the way to toxicogenomic and bioaugmentation studies in this critically endangered taxon of land vertebrates.

scholarly journals Phylogenetic Identification and Functional Characterization of Orthologs and Paralogs across Human, Mouse, Fly, and Worm

2014 ◽  
Author(s):  
Yi-Chieh Wu ◽  
Mukul S Bansal ◽  
Matthew D Rasmussen ◽  
Javier Herrero ◽  
Manolis Kellis
Keyword(s):  
Incomplete Lineage Sorting ◽  
Phylogenetic Signal ◽  
Functional Characterization ◽  
Gene Tree ◽  
Gene Families ◽  
Medical Community ◽  
Model Organisms ◽  
Yeast Genome ◽  
Lineage Sorting ◽  
Gene Duplication And Loss

Model organisms can serve the biological and medical community by enabling the study of conserved gene families and pathways in experimentally-tractable systems. Their use, however, hinges on the ability to reliably identify evolutionary orthologs and paralogs with high accuracy, which can be a great challenge at both small and large evolutionary distances. Here, we present a phylogenomics-based approach for the identification of orthologous and paralogous genes in human, mouse, fly, and worm, which forms the foundation of the comparative analyses of the modENCODE and mouse ENCODE projects. We study a median of 16,101 genes across 2 mammalian genomes (human, mouse), 12 Drosophila genomes, 5 Caenorhabditis genomes, and an outgroup yeast genome, and demonstrate that accurate inference of evolutionary relationships and events across these species must account for frequent gene-tree topology errors due to both incomplete lineage sorting and insufficient phylogenetic signal. Furthermore, we show that integration of two separate phylogenomic pipelines yields increased accuracy, suggesting that their sources of error are independent, and finally, we leverage the resulting annotation of homologous genes to study the functional impact of gene duplication and loss in the context of rich gene expression and functional genomic datasets of the modENCODE, mouse ENCODE, and human ENCODE projects.

scholarly journals Functional characterization of a full length pregnane X receptor, expression in vivo, and identification of PXR alleles, in Zebrafish (Danio rerio)

2013 ◽  
Vol 142-143 ◽  
pp. 447-457 ◽  
Author(s):  
Afonso C.D. Bainy ◽  
Akira Kubota ◽  
Jared V. Goldstone ◽  
Roger Lille-Langøy ◽  
Sibel I. Karchner ◽  
...  
Keyword(s):  
Danio Rerio ◽  
Functional Characterization ◽  
Pregnane X Receptor ◽  
Full Length ◽  
Receptor Expression

Regulatory Cross-Talk between Drug Metabolism and Lipid Homeostasis: Constitutive Androstane Receptor and Pregnane X Receptor Increase Insig-1 Expression

2008 ◽  
Vol 73 (4) ◽  
pp. 1282-1289 ◽  
Author(s):  
Adrian Roth ◽  
Renate Looser ◽  
Michel Kaufmann ◽  
Sharon M. Blättler ◽  
Franck Rencurel ◽  
...  
Keyword(s):  
Drug Metabolism ◽  
Cross Talk ◽  
Constitutive Androstane Receptor ◽  
Pregnane X Receptor ◽  
Lipid Homeostasis

scholarly journals Constitutive androstane receptor and pregnane X receptor cooperatively ameliorate DSS-induced colitis

2019 ◽  
Vol 51 (2) ◽  
pp. 226-235 ◽  
Author(s):  
Daisuke Uehara ◽  
Hiroki Tojima ◽  
Satoru Kakizaki ◽  
Yuichi Yamazaki ◽  
Norio Horiguchi ◽  
...  
Keyword(s):  
Constitutive Androstane Receptor ◽  
Pregnane X Receptor

scholarly journals Global Survey and Expressions of the Phosphate Transporter Gene Families in Brassica napus and Their Roles in Phosphorus Response

2020 ◽  
Vol 21 (5) ◽  
pp. 1752 ◽  
Author(s):  
Jin Yang ◽  
Jie Zhou ◽  
Hong-Jun Zhou ◽  
Mang-Mang Wang ◽  
Ming-Ming Liu ◽  
...  
Keyword(s):  
Brassica Napus ◽  
Expression Profiles ◽  
Phylogenetic Analyses ◽  
Functional Divergence ◽  
Gene Families ◽  
Small Scale ◽  
Transporter Gene ◽  
Promoter Regions ◽  
Network Analyses ◽  
Group I

Phosphate (Pi) transporters play critical roles in Pi acquisition and homeostasis. However, currently little is known about these genes in oil crops. In this study, we aimed to characterize the five Pi transporter gene families (PHT1-5) in allotetraploid Brassica napus. We identified and characterized 81 putative PHT genes in B. napus (BnaPHTs), including 45 genes in PHT1 family (BnaPHT1s), four BnaPHT2s, 10 BnaPHT3s, 13 BnaPHT4s and nine BnaPHT5s. Phylogenetic analyses showed that the largest PHT1 family could be divided into two groups (Group I and II), while PHT4 may be classified into five, Groups I-V. Gene structure analysis revealed that the exon-intron pattern was conservative within the same family or group. The sequence characteristics of these five families were quite different, which may contribute to their functional divergence. Transcription factor (TF) binding network analyses identified many potential TF binding sites in the promoter regions of candidates, implying their possible regulating patterns. Collinearity analysis demonstrated that most BnaPHTs were derived from an allopolyploidization event (~40.7%) between Brassica rapa and Brassica oleracea ancestors, and small-scale segmental duplication events (~39.5%) in the descendant. RNA-Seq analyses proved that many BnaPHTs were preferentially expressed in leaf and flower tissues. The expression profiles of most colinearity-pairs in B. napus are highly correlated, implying functional redundancy, while a few pairs may have undergone neo-functionalization or sub-functionalization during evolution. The expression levels of many BnaPHTs tend to be up-regulated by different hormones inductions, especially for IAA, ABA and 6-BA treatments. qRT-PCR assay demonstrated that six BnaPHT1s (BnaPHT1.11, BnaPHT1.14, BnaPHT1.20, BnaPHT1.35, BnaPHT1.41, BnaPHT1.44) were significantly up-regulated under low- and/or rich- Pi conditions in B. napus roots. This work analyzes the evolution and expression of the PHT family in Brassica napus, which will help further research on their role in Pi transport.

scholarly journals Vitis OneGenE: A Causality-Based Approach to Generate Gene Networks in Vitis vinifera Sheds Light on the Laccase and Dirigent Gene Families

Biomolecules ◽  
2021 ◽  
Vol 11 (12) ◽  
pp. 1744
Author(s):  
Stefania Pilati ◽  
Giulia Malacarne ◽  
David Navarro-Payá ◽  
Gabriele Tomè ◽  
Laura Riscica ◽  
...  
Keyword(s):  
Gene Networks ◽  
Functional Characterization ◽  
Gene Families ◽  
Stilbene Synthase ◽  
Breeding Programs ◽  
Transcriptomic Data ◽  
Network Analyses ◽  
Manual Curation ◽  
Inference Methods

The abundance of transcriptomic data and the development of causal inference methods have paved the way for gene network analyses in grapevine. Vitis OneGenE is a transcriptomic data mining tool that finds direct correlations between genes, thus producing association networks. As a proof of concept, the stilbene synthase gene regulatory network obtained with OneGenE has been compared with published co-expression analysis and experimental data, including cistrome data for MYB stilbenoid regulators. As a case study, the two secondary metabolism pathways of stilbenoids and lignin synthesis were explored. Several isoforms of laccase, peroxidase, and dirigent protein genes, putatively involved in the final oxidative oligomerization steps, were identified as specifically belonging to either one of these pathways. Manual curation of the predicted sequences exploiting the last available genome assembly, and the integration of phylogenetic and OneGenE analyses, identified a group of laccases exclusively present in grapevine and related to stilbenoids. Here we show how network analysis by OneGenE can accelerate knowledge discovery by suggesting new candidates for functional characterization and application in breeding programs.

scholarly journals Phylogenomic and Microsynteny Analysis Provides Evidence of Genome Arrangements of High-Affinity Nitrate Transporter Gene Families of Plants

2021 ◽  
Vol 22 (23) ◽  
pp. 13036
Author(s):  
Normig M. Zoghbi-Rodríguez ◽  
Samuel David Gamboa-Tuz ◽  
Alejandro Pereira-Santana ◽  
Luis C. Rodríguez-Zapata ◽  
Lorenzo Felipe Sánchez-Teyer ◽  
...  
Keyword(s):  
Functional Characterization ◽  
Nitrate Assimilation ◽  
Gene Families ◽  
Land Plants ◽  
Nitrate Transport ◽  
Phylogenomic Analysis ◽  
Evolutionary Constraint ◽  
N Availability ◽  
Nitrate Transporter ◽  
High Affinity

Nitrate transporter 2 (NRT2) and NRT3 or nitrate-assimilation-related 2 (NAR2) proteins families form a two-component, high-affinity nitrate transport system, which is essential for the acquisition of nitrate from soils with low N availability. An extensive phylogenomic analysis across land plants for these families has not been performed. In this study, we performed a microsynteny and orthology analysis on the NRT2 and NRT3 genes families across 132 plants (Sensu lato) to decipher their evolutionary history. We identified significant differences in the number of sequences per taxonomic group and different genomic contexts within the NRT2 family that might have contributed to N acquisition by the plants. We hypothesized that the greater losses of NRT2 sequences correlate with specialized ecological adaptations, such as aquatic, epiphytic, and carnivory lifestyles. We also detected expansion on the NRT2 family in specific lineages that could be a source of key innovations for colonizing contrasting niches in N availability. Microsyntenic analysis on NRT3 family showed a deep conservation on land plants, suggesting a high evolutionary constraint to preserve their function. Our study provides novel information that could be used as guide for functional characterization of these gene families across plant lineages.

Fructosyltransferase and invertase genes evolved by gene duplication and rearrangements: rice, perennial ryegrass, and wheat gene families

Genome ◽  
2006 ◽  
Vol 49 (9) ◽  
pp. 1081-1091 ◽  
Author(s):  
Michael G. Francki ◽  
Esther Walker ◽  
John W. Forster ◽  
German Spangenberg ◽  
Rudi Appels
Keyword(s):  
Perennial Ryegrass ◽  
Abiotic Stress Tolerance ◽  
Gene Families ◽  
Amino Acid Similarity ◽  
Gene Variation ◽  
Wheat Gene ◽  
Multiple Copies ◽  
Duplication Events ◽  
Invertase Gene ◽  
Gene Orthologs

The invertase enzyme family is responsible for carbohydrate metabolism in rice, perennial ryegrass, and wheat. Fructan molecules accumulate in cell vacuoles of perennial ryegrass and wheat and are associated with abiotic stress tolerance. High levels of amino acid similarity between the fructosyltransferases responsible for fructan accumulation indicates that they may have evolved from invertase-like ancestral genes. In this study, we have applied comparative genomics to determine the mechanisms that lead to the evolution of fructosytransferase and invertase genes in rice, perennial ryegrass, and wheat. Duplications and rearrangements have been inferred to generate variant forms of the rice invertases since divergence from a common grass progenitor. The occurrence of multiple copies of fructosyltransferase genes indicated that duplication events continued during evolution of the wheat and perennial ryegrass lineages. Further gene rearrangements were evident in perennial ryegrass genes, albeit at a reduced level compared with the rice invertases. Gene orthologs were largely static after duplication during evolution of the wheat lineage. This study details evolutionary events that contribute to fructosyltransferase and invertase gene variation in grasses.

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