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Wang X, Hu J, Song L, Rong E, Yang C, Chen X, Pu J, Sun H, Gao C, Burt DW, Liu J, Li N, Huang Y. Functional divergence of oligoadenylate synthetase 1 (OAS1) proteins in Tetrapods. SCIENCE CHINA. LIFE SCIENCES 2022; 65:1395-1412. [PMID: 34826092 DOI: 10.1007/s11427-021-2002-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Accepted: 08/25/2021] [Indexed: 06/13/2023]
Abstract
OASs play critical roles in immune response against virus infection by polymerizing ATP into 2-5As, which initiate the classical OAS/RNase L pathway and induce degradation of viral RNA. OAS members are functionally diverged in four known innate immune pathways (OAS/RNase L, OASL/IRF7, OASL/RIG-I, and OASL/cGAS), but how they functionally diverged is unclear. Here, we focus on evolutionary patterns and explore the link between evolutionary processes and functional divergence of Tetrapod OAS1. We show that Palaeognathae and Primate OAS1 genes are conserved in genomic and protein structures but differ in function. The former (i.e., ostrich) efficiently synthesized long 2-5A and activated RNase L, while the latter (i.e., human) synthesized short 2-5A and did not activate RNase L. We predicted and verified that two in-frame indels and one positively selected site in the active site pocket contributed to the functional divergence of Palaeognathae and Primate OAS1. Moreover, we discovered and validated that an in-frame indel in the C-terminus of Palaeognathae OAS1 affected the binding affinity of dsRNA and enzymatic activity, and contributed to the functional divergence of Palaeognathae OAS1 proteins. Our findings unravel the molecular mechanism for functional divergence and give insights into the emergence of novel functions in Tetrapod OAS1.
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Affiliation(s)
- Xiaoxue Wang
- State Key Laboratory for Agrobiotechnology, College of Biology Sciences, China Agricultural University, Beijing, 100193, China
| | - Jiaxiang Hu
- State Key Laboratory for Agrobiotechnology, College of Biology Sciences, China Agricultural University, Beijing, 100193, China
| | - Linfei Song
- State Key Laboratory for Agrobiotechnology, College of Biology Sciences, China Agricultural University, Beijing, 100193, China
| | - Enguang Rong
- State Key Laboratory for Agrobiotechnology, College of Biology Sciences, China Agricultural University, Beijing, 100193, China
| | - Chenghuai Yang
- China Institute of Veterinary Drug Control, Beijing, 100081, China
| | - Xiaoyun Chen
- China Institute of Veterinary Drug Control, Beijing, 100081, China
| | - Juan Pu
- Key Laboratory of Animal Epidemiology and Zoonosis, Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, 100083, China
| | - Honglei Sun
- Key Laboratory of Animal Epidemiology and Zoonosis, Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, 100083, China
| | - Chuze Gao
- State Key Laboratory for Agrobiotechnology, College of Biology Sciences, China Agricultural University, Beijing, 100193, China
| | - David W Burt
- University of Queensland, St. Lucia, Brisbane, QLD, 4072, Australia
| | - Jinhua Liu
- Key Laboratory of Animal Epidemiology and Zoonosis, Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, 100083, China
| | - Ning Li
- State Key Laboratory for Agrobiotechnology, College of Biology Sciences, China Agricultural University, Beijing, 100193, China
| | - Yinhua Huang
- State Key Laboratory for Agrobiotechnology, College of Biology Sciences, China Agricultural University, Beijing, 100193, China.
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2
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Lian J, Nelson R, Lehner R. Carboxylesterases in lipid metabolism: from mouse to human. Protein Cell 2017; 9:178-195. [PMID: 28677105 PMCID: PMC5818367 DOI: 10.1007/s13238-017-0437-z] [Citation(s) in RCA: 155] [Impact Index Per Article: 22.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Accepted: 05/31/2017] [Indexed: 12/12/2022] Open
Abstract
Mammalian carboxylesterases hydrolyze a wide range of xenobiotic and endogenous compounds, including lipid esters. Physiological functions of carboxylesterases in lipid metabolism and energy homeostasis in vivo have been demonstrated by genetic manipulations and chemical inhibition in mice, and in vitro through (over)expression, knockdown of expression, and chemical inhibition in a variety of cells. Recent research advances have revealed the relevance of carboxylesterases to metabolic diseases such as obesity and fatty liver disease, suggesting these enzymes might be potential targets for treatment of metabolic disorders. In order to translate pre-clinical studies in cellular and mouse models to humans, differences and similarities of carboxylesterases between mice and human need to be elucidated. This review presents and discusses the research progress in structure and function of mouse and human carboxylesterases, and the role of these enzymes in lipid metabolism and metabolic disorders.
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Affiliation(s)
- Jihong Lian
- Group on Molecular and Cell Biology of Lipids, University of Alberta, Edmonton, Alberta, Canada. .,Department of Pediatrics, University of Alberta, Edmonton, Alberta, Canada.
| | - Randal Nelson
- Group on Molecular and Cell Biology of Lipids, University of Alberta, Edmonton, Alberta, Canada.,Department of Pediatrics, University of Alberta, Edmonton, Alberta, Canada
| | - Richard Lehner
- Group on Molecular and Cell Biology of Lipids, University of Alberta, Edmonton, Alberta, Canada.,Department of Pediatrics, University of Alberta, Edmonton, Alberta, Canada.,Department of Cell Biology, University of Alberta, Edmonton, Alberta, Canada
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3
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Li G, Davis BW, Eizirik E, Murphy WJ. Phylogenomic evidence for ancient hybridization in the genomes of living cats (Felidae). Genome Res 2016; 26:1-11. [PMID: 26518481 PMCID: PMC4691742 DOI: 10.1101/gr.186668.114] [Citation(s) in RCA: 156] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Accepted: 10/13/2015] [Indexed: 12/27/2022]
Abstract
Inter-species hybridization has been recently recognized as potentially common in wild animals, but the extent to which it shapes modern genomes is still poorly understood. Distinguishing historical hybridization events from other processes leading to phylogenetic discordance among different markers requires a well-resolved species tree that considers all modes of inheritance and overcomes systematic problems due to rapid lineage diversification by sampling large genomic character sets. Here, we assessed genome-wide phylogenetic variation across a diverse mammalian family, Felidae (cats). We combined genotypes from a genome-wide SNP array with additional autosomal, X- and Y-linked variants to sample ∼150 kb of nuclear sequence, in addition to complete mitochondrial genomes generated using light-coverage Illumina sequencing. We present the first robust felid time tree that accounts for unique maternal, paternal, and biparental evolutionary histories. Signatures of phylogenetic discordance were abundant in the genomes of modern cats, in many cases indicating hybridization as the most likely cause. Comparison of big cat whole-genome sequences revealed a substantial reduction of X-linked divergence times across several large recombination cold spots, which were highly enriched for signatures of selection-driven post-divergence hybridization between the ancestors of the snow leopard and lion lineages. These results highlight the mosaic origin of modern felid genomes and the influence of sex chromosomes and sex-biased dispersal in post-speciation gene flow. A complete resolution of the tree of life will require comprehensive genomic sampling of biparental and sex-limited genetic variation to identify and control for phylogenetic conflict caused by ancient admixture and sex-biased differences in genomic transmission.
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Affiliation(s)
- Gang Li
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas 77843, USA
| | - Brian W Davis
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas 77843, USA; Interdisciplinary Program in Genetics, Texas A&M University, College Station, Texas 77843, USA
| | - Eduardo Eizirik
- Faculdade de Biociências, PUCRS, Porto Alegre, RS 90619-900, Brazil
| | - William J Murphy
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas 77843, USA; Interdisciplinary Program in Genetics, Texas A&M University, College Station, Texas 77843, USA
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Ru YF, Xue HM, Ni ZM, Xia D, Zhou YC, Zhang YL. An epididymis-specific carboxyl esterase CES5A is required for sperm capacitation and male fertility in the rat. Asian J Androl 2015; 17:292-7. [PMID: 25475668 PMCID: PMC4650488 DOI: 10.4103/1008-682x.143314] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Despite the fact that the phenomenon of capacitation was discovered over half century ago and much progress has been made in identifying sperm events involved in capacitation, few specific molecules of epididymal origin have been identified as being directly involved in this process in vivo. Previously, our group cloned and characterized a carboxyl esterase gene Ces5a in the rat epididymis. The CES5A protein is mainly expressed in the corpus and cauda epididymidis and secreted into the corresponding lumens. Here, we report the function of CES5A in sperm maturation. By local injection of Lentivirus-mediated siRNA in the CES5A-expressing region of the rat epididymis, Ces5a-knockdown animal models were created. These animals exhibited an inhibited sperm capacitation and a reduction in male fertility. These results suggest that CES5A plays an important role in sperm maturation and male fertility.
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Affiliation(s)
| | | | | | | | - Yu-Chuan Zhou
- Shanghai Key Laboratory of Molecular Andrology, State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yong-Lian Zhang
- Shanghai Key Laboratory of Molecular Andrology, State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences; Shanghai Institute of Planned Parenthood Research, Shanghai, China
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5
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Montague MJ, Li G, Gandolfi B, Khan R, Aken BL, Searle SMJ, Minx P, Hillier LW, Koboldt DC, Davis BW, Driscoll CA, Barr CS, Blackistone K, Quilez J, Lorente-Galdos B, Marques-Bonet T, Alkan C, Thomas GWC, Hahn MW, Menotti-Raymond M, O'Brien SJ, Wilson RK, Lyons LA, Murphy WJ, Warren WC. Comparative analysis of the domestic cat genome reveals genetic signatures underlying feline biology and domestication. Proc Natl Acad Sci U S A 2014; 111:17230-5. [PMID: 25385592 PMCID: PMC4260561 DOI: 10.1073/pnas.1410083111] [Citation(s) in RCA: 198] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Little is known about the genetic changes that distinguish domestic cat populations from their wild progenitors. Here we describe a high-quality domestic cat reference genome assembly and comparative inferences made with other cat breeds, wildcats, and other mammals. Based upon these comparisons, we identified positively selected genes enriched for genes involved in lipid metabolism that underpin adaptations to a hypercarnivorous diet. We also found positive selection signals within genes underlying sensory processes, especially those affecting vision and hearing in the carnivore lineage. We observed an evolutionary tradeoff between functional olfactory and vomeronasal receptor gene repertoires in the cat and dog genomes, with an expansion of the feline chemosensory system for detecting pheromones at the expense of odorant detection. Genomic regions harboring signatures of natural selection that distinguish domestic cats from their wild congeners are enriched in neural crest-related genes associated with behavior and reward in mouse models, as predicted by the domestication syndrome hypothesis. Our description of a previously unidentified allele for the gloving pigmentation pattern found in the Birman breed supports the hypothesis that cat breeds experienced strong selection on specific mutations drawn from random bred populations. Collectively, these findings provide insight into how the process of domestication altered the ancestral wildcat genome and build a resource for future disease mapping and phylogenomic studies across all members of the Felidae.
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Affiliation(s)
- Michael J Montague
- The Genome Institute, Washington University School of Medicine, St. Louis, MO 63108
| | - Gang Li
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine, Texas A&M University, College Station, TX 77843
| | - Barbara Gandolfi
- Department of Veterinary Medicine & Surgery, College of Veterinary Medicine, University of Missouri, Columbia, MO 65201
| | - Razib Khan
- Population Health & Reproduction, School of Veterinary Medicine, University of California, Davis, CA 95616
| | - Bronwen L Aken
- Wellcome Trust Sanger Institute, Hinxton CB10 1SA, United Kingdom
| | | | - Patrick Minx
- The Genome Institute, Washington University School of Medicine, St. Louis, MO 63108
| | - LaDeana W Hillier
- The Genome Institute, Washington University School of Medicine, St. Louis, MO 63108
| | - Daniel C Koboldt
- The Genome Institute, Washington University School of Medicine, St. Louis, MO 63108
| | - Brian W Davis
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine, Texas A&M University, College Station, TX 77843
| | - Carlos A Driscoll
- National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD 20886
| | - Christina S Barr
- National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD 20886
| | - Kevin Blackistone
- National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD 20886
| | - Javier Quilez
- Catalan Institution for Research and Advanced Studies, Institute of Evolutionary Biology, Pompeu Fabra University, 08003 Barcelona, Spain
| | - Belen Lorente-Galdos
- Catalan Institution for Research and Advanced Studies, Institute of Evolutionary Biology, Pompeu Fabra University, 08003 Barcelona, Spain
| | - Tomas Marques-Bonet
- Catalan Institution for Research and Advanced Studies, Institute of Evolutionary Biology, Pompeu Fabra University, 08003 Barcelona, Spain; Centro de Analisis Genomico 08028, Barcelona, Spain
| | - Can Alkan
- Department of Computer Engineering, Bilkent University, Ankara 06800, Turkey
| | - Gregg W C Thomas
- Department of Biology, Indiana University, Bloomington, IN 47405
| | - Matthew W Hahn
- Department of Biology, Indiana University, Bloomington, IN 47405
| | | | - Stephen J O'Brien
- Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg 199178, Russia; and Oceanographic Center, Nova Southeastern University, Fort Lauderdale, FL 33314
| | - Richard K Wilson
- The Genome Institute, Washington University School of Medicine, St. Louis, MO 63108
| | - Leslie A Lyons
- Department of Veterinary Medicine & Surgery, College of Veterinary Medicine, University of Missouri, Columbia, MO 65201;
| | - William J Murphy
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine, Texas A&M University, College Station, TX 77843;
| | - Wesley C Warren
- The Genome Institute, Washington University School of Medicine, St. Louis, MO 63108;
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Apps P, Mmualefe L, Jordan NR, Golabek KA, McNutt JW. The “tomcat compound” 3-mercapto-3-methylbutanol occurs in the urine of free-ranging leopards but not in African lions or cheetahs. BIOCHEM SYST ECOL 2014. [DOI: 10.1016/j.bse.2013.12.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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7
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Cheng N, Mao Y, Shi Y, Tao S. Coevolution in RNA molecules driven by selective constraints: evidence from 5S rRNA. PLoS One 2012; 7:e44376. [PMID: 22973441 PMCID: PMC3433437 DOI: 10.1371/journal.pone.0044376] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2011] [Accepted: 08/06/2012] [Indexed: 11/20/2022] Open
Abstract
Understanding intra-molecular coevolution helps to elucidate various structural and functional constraints acting on molecules and might have practical applications in predicting molecular structure and interactions. In this study, we used 5S rRNA as a template to investigate how selective constraints have shaped the RNA evolution. We have observed the nonrandom occurrence of paired differences along the phylogenetic trees, the high rate of compensatory evolution, and the high TIR scores (the ratio of the numbers of terminal to intermediate states), all of which indicate that significant positive selection has driven the evolution of 5S rRNA. We found three mechanisms of compensatory evolution: Watson-Crick interaction (the primary one), complex interactions between multiple sites within a stem, and interplay of stems and loops. Coevolutionary interactions between sites were observed to be highly dependent on the structural and functional environment in which they occurred. Coevolution occurred mostly in those sites closest to loops or bulges within structurally or functionally important helices, which may be under weaker selective constraints than other stem positions. Breaking these pairs would directly increase the size of the adjoining loop or bulge, causing a partial or total structural rearrangement. In conclusion, our results indicate that sequence coevolution is a direct result of maintaining optimal structural and functional integrity.
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Affiliation(s)
- Nan Cheng
- StateKey Laboratory of Crop Stress Biology in Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, People’s Republic of China
- Bioinformatics Center, Northwest A&F University, Yangling, People’s Republic of China
| | - Yuanhui Mao
- StateKey Laboratory of Crop Stress Biology in Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, People’s Republic of China
| | - Youyi Shi
- College of Science, Northwest A&F University, Yangling, People’s Republic of China
| | - Shiheng Tao
- StateKey Laboratory of Crop Stress Biology in Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, People’s Republic of China
- Bioinformatics Center, Northwest A&F University, Yangling, People’s Republic of China
- * E-mail:
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Kalyana-Sundaram S, Kumar-Sinha C, Shankar S, Robinson DR, Wu YM, Cao X, Asangani IA, Kothari V, Prensner JR, Lonigro RJ, Iyer MK, Barrette T, Shanmugam A, Dhanasekaran SM, Palanisamy N, Chinnaiyan AM. Expressed pseudogenes in the transcriptional landscape of human cancers. Cell 2012; 149:1622-34. [PMID: 22726445 DOI: 10.1016/j.cell.2012.04.041] [Citation(s) in RCA: 217] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2011] [Revised: 01/10/2012] [Accepted: 04/26/2012] [Indexed: 12/12/2022]
Abstract
Pseudogene transcripts can provide a novel tier of gene regulation through generation of endogenous siRNAs or miRNA-binding sites. Characterization of pseudogene expression, however, has remained confined to anecdotal observations due to analytical challenges posed by the extremely close sequence similarity with their counterpart coding genes. Here, we describe a systematic analysis of pseudogene "transcription" from an RNA-Seq resource of 293 samples, representing 13 cancer and normal tissue types, and observe a surprisingly prevalent, genome-wide expression of pseudogenes that could be categorized as ubiquitously expressed or lineage and/or cancer specific. Further, we explore disease subtype specificity and functions of selected expressed pseudogenes. Taken together, we provide evidence that transcribed pseudogenes are a significant contributor to the transcriptional landscape of cells and are positioned to play significant roles in cellular differentiation and cancer progression, especially in light of the recently described ceRNA networks. Our work provides a transcriptome resource that enables high-throughput analyses of pseudogene expression.
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