201
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Ahrens JB, Nunez-Castilla J, Siltberg-Liberles J. Evolution of intrinsic disorder in eukaryotic proteins. Cell Mol Life Sci 2017; 74:3163-3174. [PMID: 28597295 PMCID: PMC11107722 DOI: 10.1007/s00018-017-2559-0] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 06/01/2017] [Indexed: 12/23/2022]
Abstract
Conformational flexibility conferred though regions of intrinsic structural disorder allows proteins to behave as dynamic molecules. While it is well-known that intrinsically disordered regions can undergo disorder-to-order transitions in real-time as part of their function, we also are beginning to learn more about the dynamics of disorder-to-order transitions along evolutionary time-scales. Intrinsically disordered regions endow proteins with functional promiscuity, which is further enhanced by the ability of some of these regions to undergo real-time disorder-to-order transitions. Disorder content affects gene retention after whole genome duplication, but it is not necessarily conserved. Altered patterns of disorder resulting from evolutionary disorder-to-order transitions indicate that disorder evolves to modify function through refining stability, regulation, and interactions. Here, we review the evolution of intrinsically disordered regions in eukaryotic proteins. We discuss the interplay between secondary structure and disorder on evolutionary time-scales, the importance of disorder for eukaryotic proteome expansion and functional divergence, and the evolutionary dynamics of disorder.
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Affiliation(s)
- Joseph B Ahrens
- Department of Biological Sciences, Biomolecular Sciences Institute, Florida International University, 11200 SW 8th St, Miami, FL, 33199, USA
| | - Janelle Nunez-Castilla
- Department of Biological Sciences, Biomolecular Sciences Institute, Florida International University, 11200 SW 8th St, Miami, FL, 33199, USA
| | - Jessica Siltberg-Liberles
- Department of Biological Sciences, Biomolecular Sciences Institute, Florida International University, 11200 SW 8th St, Miami, FL, 33199, USA.
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202
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Céspedes HA, Zavala K, Vandewege MW, Opazo JC. Evolution of the α 2-adrenoreceptors in vertebrates: ADRA2D is absent in mammals and crocodiles. Gen Comp Endocrinol 2017. [PMID: 28622977 DOI: 10.1016/j.ygcen.2017.06.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Evolutionary 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. Finally, transcript abundance profiles revealed that during the early evolutionary history of gnathostomes, the expression of ADRA2D in different taxonomic groups became specialized to different tissues, but in the ancestor of sarcopterygians this specialization would have been lost.
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Affiliation(s)
- Héctor A Céspedes
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
| | - Kattina Zavala
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
| | - Michael W Vandewege
- Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409, USA
| | - Juan C Opazo
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile; David Rockefeller Center For Latin American Studies, Harvard University, Cambridge, MA 02138, USA.
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203
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Timoshevskiy VA, Lampman RT, Hess JE, Porter LL, Smith JJ. Deep ancestry of programmed genome rearrangement in lampreys. Dev Biol 2017; 429:31-34. [PMID: 28669817 PMCID: PMC5554715 DOI: 10.1016/j.ydbio.2017.06.032] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Revised: 05/16/2017] [Accepted: 06/28/2017] [Indexed: 11/27/2022]
Abstract
In most multicellular organisms, the structure and content of the genome is rigorously maintained over the course of development. However some species have evolved genome biologies that permit, or require, developmentally regulated changes in the physical structure and content of the genome (programmed genome rearrangement: PGR). Relatively few vertebrates are known to undergo PGR, although all agnathans surveyed to date (several hagfish and one lamprey: Petromyzon marinus) show evidence of large scale PGR. To further resolve the ancestry of PGR within vertebrates, we developed probes that allow simultaneous tracking of nearly all sequences eliminated by PGR in P. marinus and a second lamprey species (Entosphenus tridentatus). These comparative analyses reveal conserved subcellular structures (lagging chromatin and micronuclei) associated with PGR and provide the first comparative embryological evidence in support of the idea that PGR represents an ancient and evolutionarily stable strategy for regulating inherent developmental/genetic conflicts between germline and soma.
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Affiliation(s)
| | - Ralph T Lampman
- Yakama Nation Fisheries Resource Management Program, Toppenish, WA 98948, USA
| | - Jon E Hess
- Columbia River Inter-Tribal Fish Commission, Portland, OR 97232, USA
| | - Laurie L Porter
- Columbia River Inter-Tribal Fish Commission, Portland, OR 97232, USA
| | - Jeramiah J Smith
- University of Kentucky, Department of Biology, Lexington, KY 40506, USA.
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204
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Wei X, Xu Z, Wang G, Hou J, Ma X, Liu H, Liu J, Chen B, Luo M, Xie B, Li R, Ruan J, Liu X. pBACode: a random-barcode-based high-throughput approach for BAC paired-end sequencing and physical clone mapping. Nucleic Acids Res 2017; 45:e52. [PMID: 27980066 PMCID: PMC5397170 DOI: 10.1093/nar/gkw1261] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Accepted: 12/09/2016] [Indexed: 12/14/2022] Open
Abstract
Applications that use Bacterial Artificial Chromosome (BAC) libraries often require paired-end sequences and knowledge of the physical location of each clone in plates. To facilitate obtaining this information in high-throughput, we generated pBACode vectors: a pool of BAC cloning vectors, each with a pair of random barcodes flanking its cloning site. In a pBACode BAC library, the BAC ends and their linked barcodes can be sequenced in bulk. Barcode pairs are determined by sequencing the empty pBACode vectors, which allows BAC ends to be paired according to their barcodes. For physical clone mapping, the barcodes are used as unique markers for their linked genomic sequence. After multi-dimensional pooling of BAC clones, the barcodes are sequenced and deconvoluted to locate each clone. We generated a pBACode library of 94,464 clones for the flounder Paralichthys olivaceus and obtained paired-end sequence from 95.4% of the clones. Incorporating BAC paired-ends into the genome preassembly improved its continuity by over 10-fold. Furthermore, we were able to use the barcodes to map the physical locations of each clone in just 50 pools, with up to 11 808 clones per pool. Our physical clone mapping located 90.2% of BAC clones, enabling targeted characterization of chromosomal rearrangements.
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Affiliation(s)
- Xiaolin Wei
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China.,PTN (Peking University-Tsinghua University-National Institute of Biological Sciences) Joint Graduate Program, Beijing 100084, China.,School of Life Sciences, Peking University, Beijing 100084, China
| | - Zhichao Xu
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China.,PTN (Peking University-Tsinghua University-National Institute of Biological Sciences) Joint Graduate Program, Beijing 100084, China
| | - Guixing Wang
- Beidaihe Central Experiment Station, Chinese Academy of Fishery Sciences, Qinhuangdao 066100, China
| | - Jilun Hou
- Beidaihe Central Experiment Station, Chinese Academy of Fishery Sciences, Qinhuangdao 066100, China
| | - Xiaopeng Ma
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China.,PTN (Peking University-Tsinghua University-National Institute of Biological Sciences) Joint Graduate Program, Beijing 100084, China
| | - Haijin Liu
- Beidaihe Central Experiment Station, Chinese Academy of Fishery Sciences, Qinhuangdao 066100, China
| | - Jiadong Liu
- National Key Laboratory of Crop Genetic Improvement and College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Bo Chen
- National Key Laboratory of Crop Genetic Improvement and College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Meizhong Luo
- National Key Laboratory of Crop Genetic Improvement and College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Bingyan Xie
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Ruiqiang Li
- Novogene Bioinformatics Institute, Beijing 100083, China
| | - Jue Ruan
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China
| | - Xiao Liu
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
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205
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Parker HJ, Krumlauf R. Segmental arithmetic: summing up the Hox gene regulatory network for hindbrain development in chordates. WILEY INTERDISCIPLINARY REVIEWS-DEVELOPMENTAL BIOLOGY 2017; 6. [PMID: 28771970 DOI: 10.1002/wdev.286] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2017] [Revised: 06/13/2017] [Accepted: 06/15/2017] [Indexed: 11/10/2022]
Abstract
Organization and development of the early vertebrate hindbrain are controlled by a cascade of regulatory interactions that govern the process of segmentation and patterning along the anterior-posterior axis via Hox genes. These interactions can be assembled into a gene regulatory network that provides a framework to interpret experimental data, generate hypotheses, and identify gaps in our understanding of the progressive process of hindbrain segmentation. The network can be broadly separated into a series of interconnected programs that govern early signaling, segmental subdivision, secondary signaling, segmentation, and ultimately specification of segmental identity. Hox genes play crucial roles in multiple programs within this network. Furthermore, the network reveals properties and principles that are likely to be general to other complex developmental systems. Data from vertebrate and invertebrate chordate models are shedding light on the origin and diversification of the network. Comprehensive cis-regulatory analyses of vertebrate Hox gene regulation have enabled powerful cross-species gene regulatory comparisons. Such an approach in the sea lamprey has revealed that the network mediating segmental Hox expression was present in ancestral vertebrates and has been maintained across diverse vertebrate lineages. Invertebrate chordates lack hindbrain segmentation but exhibit conservation of some aspects of the network, such as a role for retinoic acid in establishing nested Hox expression domains. These comparisons lead to a model in which early vertebrates underwent an elaboration of the network between anterior-posterior patterning and Hox gene expression, leading to the gene-regulatory programs for segmental subdivision and rhombomeric segmentation. WIREs Dev Biol 2017, 6:e286. doi: 10.1002/wdev.286 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Hugo J Parker
- Stowers Institute for Medical Research, Kansas City, MO, USA
| | - Robb Krumlauf
- Stowers Institute for Medical Research, Kansas City, MO, USA.,Department of Anatomy and Cell Biology, Kansas University Medical Center, Kansas City, Kansas 66160, USA
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206
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Müller V, de Boer RJ, Bonhoeffer S, Szathmáry E. An evolutionary perspective on the systems of adaptive immunity. Biol Rev Camb Philos Soc 2017; 93:505-528. [PMID: 28745003 DOI: 10.1111/brv.12355] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Revised: 06/28/2017] [Accepted: 06/30/2017] [Indexed: 12/22/2022]
Abstract
We propose an evolutionary perspective to classify and characterize the diverse systems of adaptive immunity that have been discovered across all major domains of life. We put forward a new function-based classification according to the way information is acquired by the immune systems: Darwinian immunity (currently known from, but not necessarily limited to, vertebrates) relies on the Darwinian process of clonal selection to 'learn' by cumulative trial-and-error feedback; Lamarckian immunity uses templated targeting (guided adaptation) to internalize heritable information on potential threats; finally, shotgun immunity operates through somatic mechanisms of variable targeting without feedback. We argue that the origin of Darwinian (but not Lamarckian or shotgun) immunity represents a radical innovation in the evolution of individuality and complexity, and propose to add it to the list of major evolutionary transitions. While transitions to higher-level units entail the suppression of selection at lower levels, Darwinian immunity re-opens cell-level selection within the multicellular organism, under the control of mechanisms that direct, rather than suppress, cell-level evolution for the benefit of the individual. From a conceptual point of view, the origin of Darwinian immunity can be regarded as the most radical transition in the history of life, in which evolution by natural selection has literally re-invented itself. Furthermore, the combination of clonal selection and somatic receptor diversity enabled a transition from limited to practically unlimited capacity to store information about the antigenic environment. The origin of Darwinian immunity therefore comprises both a transition in individuality and the emergence of a new information system - the two hallmarks of major evolutionary transitions. Finally, we present an evolutionary scenario for the origin of Darwinian immunity in vertebrates. We propose a revival of the concept of the 'Big Bang' of vertebrate immunity, arguing that its origin involved a 'difficult' (i.e. low-probability) evolutionary transition that might have occurred only once, in a common ancestor of all vertebrates. In contrast to the original concept, we argue that the limiting innovation was not the generation of somatic diversity, but the regulatory circuitry needed for the safe operation of amplifiable immune responses with somatically acquired targeting. Regulatory complexity increased abruptly by genomic duplications at the root of the vertebrate lineage, creating a rare opportunity to establish such circuitry. We discuss the selection forces that might have acted at the origin of the transition, and in the subsequent stepwise evolution leading to the modern immune systems of extant vertebrates.
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Affiliation(s)
- Viktor Müller
- Parmenides Center for the Conceptual Foundations of Science, 82049 Pullach/Munich, Germany.,Department of Plant Systematics, Ecology and Theoretical Biology, Institute of Biology, Eötvös Loránd University, 1117 Budapest, Hungary.,Evolutionary Systems Research Group, MTA Centre for Ecological Research, 8237 Tihany, Hungary
| | - Rob J de Boer
- Theoretical Biology, Department of Biology, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - Sebastian Bonhoeffer
- Institute of Integrative Biology, Department of Environmental Systems Science, ETH Zurich, 8092 Zurich, Switzerland
| | - Eörs Szathmáry
- Parmenides Center for the Conceptual Foundations of Science, 82049 Pullach/Munich, Germany.,Department of Plant Systematics, Ecology and Theoretical Biology, Institute of Biology, Eötvös Loránd University, 1117 Budapest, Hungary.,Evolutionary Systems Research Group, MTA Centre for Ecological Research, 8237 Tihany, Hungary
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207
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Evolution of the cAMP-dependent protein kinase (PKA) catalytic subunit isoforms. PLoS One 2017; 12:e0181091. [PMID: 28742821 PMCID: PMC5526564 DOI: 10.1371/journal.pone.0181091] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Accepted: 06/25/2017] [Indexed: 01/16/2023] Open
Abstract
The 3’,5’-cyclic adenosine monophosphate (cAMP)-dependent protein kinase, or protein kinase A (PKA), pathway is one of the most versatile and best studied signaling pathways in eukaryotic cells. The two paralogous PKA catalytic subunits Cα and Cβ, encoded by the genes PRKACA and PRKACB, respectively, are among the best understood model kinases in signal transduction research. In this work, we explore and elucidate the evolution of the alternative 5’ exons and the splicing pattern giving rise to the numerous PKA catalytic subunit isoforms. In addition to the universally conserved Cα1/Cβ1 isoforms, we find kinase variants with short N-termini in all main vertebrate classes, including the sperm-specific Cα2 isoform found to be conserved in all mammals. We also describe, for the first time, a PKA Cα isoform with a long N-terminus, paralogous to the PKA Cβ2 N-terminus. An analysis of isoform-specific variation highlights residues and motifs that are likely to be of functional importance.
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208
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Bayramov AV, Ermakova GV, Eroshkin FM, Kucheryavyy AV, Martynova NY, Zaraisky AG. Presence of homeobox gene of Anf class in Pacific lamprey Lethenteron camtschaticum confirms the hypothesis about the importance of emergence of Anf genes for the origin of telencephalon in vertebrate evolution. Russ J Dev Biol 2017. [DOI: 10.1134/s1062360417040026] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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209
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Read TD, Petit RA, Joseph SJ, Alam MT, Weil MR, Ahmad M, Bhimani R, Vuong JS, Haase CP, Webb DH, Tan M, Dove ADM. Draft sequencing and assembly of the genome of the world's largest fish, the whale shark: Rhincodon typus Smith 1828. BMC Genomics 2017; 18:532. [PMID: 28709399 PMCID: PMC5513125 DOI: 10.1186/s12864-017-3926-9] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 07/06/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The whale shark (Rhincodon typus) has by far the largest body size of any elasmobranch (shark or ray) species. Therefore, it is also the largest extant species of the paraphyletic assemblage commonly referred to as fishes. As both a phenotypic extreme and a member of the group Chondrichthyes - the sister group to the remaining gnathostomes, which includes all tetrapods and therefore also humans - its genome is of substantial comparative interest. Whale sharks are also listed as an endangered species on the International Union for Conservation of Nature's Red List of threatened species and are of growing popularity as both a target of ecotourism and as a charismatic conservation ambassador for the pelagic ecosystem. A genome map for this species would aid in defining effective conservation units and understanding global population structure. RESULTS We characterised the nuclear genome of the whale shark using next generation sequencing (454, Illumina) and de novo assembly and annotation methods, based on material collected from the Georgia Aquarium. The data set consisted of 878,654,233 reads, which yielded a draft assembly of 1,213,200 contigs and 997,976 scaffolds. The estimated genome size was 3.44Gb. As expected, the proteome of the whale shark was most closely related to the only other complete genome of a cartilaginous fish, the holocephalan elephant shark. The whale shark contained a novel Toll-like-receptor (TLR) protein with sequence similarity to both the TLR4 and TLR13 proteins of mammals and TLR21 of teleosts. The data are publicly available on GenBank, FigShare, and from the NCBI Short Read Archive under accession number SRP044374. CONCLUSIONS This represents the first shotgun elasmobranch genome and will aid studies of molecular systematics, biogeography, genetic differentiation, and conservation genetics in this and other shark species, as well as providing comparative data for studies of evolutionary biology and immunology across the jawed vertebrate lineages.
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Affiliation(s)
- Timothy D Read
- Department of Medicine, Division of Infectious Diseases, Emory University School of Medicine, 1760 Haygood Drive, Atlanta, GA, 30322, USA.,Department of Human Genetics, Emory University School of Medicine, 1760 Haygood Drive, Atlanta, GA, 30322, USA
| | - Robert A Petit
- Department of Medicine, Division of Infectious Diseases, Emory University School of Medicine, 1760 Haygood Drive, Atlanta, GA, 30322, USA.,Department of Human Genetics, Emory University School of Medicine, 1760 Haygood Drive, Atlanta, GA, 30322, USA
| | - Sandeep J Joseph
- Department of Medicine, Division of Infectious Diseases, Emory University School of Medicine, 1760 Haygood Drive, Atlanta, GA, 30322, USA.,Department of Human Genetics, Emory University School of Medicine, 1760 Haygood Drive, Atlanta, GA, 30322, USA
| | - Md Tauqeer Alam
- Department of Medicine, Division of Infectious Diseases, Emory University School of Medicine, 1760 Haygood Drive, Atlanta, GA, 30322, USA.,Department of Human Genetics, Emory University School of Medicine, 1760 Haygood Drive, Atlanta, GA, 30322, USA
| | - M Ryan Weil
- Department of Medicine, Division of Infectious Diseases, Emory University School of Medicine, 1760 Haygood Drive, Atlanta, GA, 30322, USA.,Department of Human Genetics, Emory University School of Medicine, 1760 Haygood Drive, Atlanta, GA, 30322, USA
| | - Maida Ahmad
- Department of Medicine, Division of Infectious Diseases, Emory University School of Medicine, 1760 Haygood Drive, Atlanta, GA, 30322, USA.,Department of Human Genetics, Emory University School of Medicine, 1760 Haygood Drive, Atlanta, GA, 30322, USA
| | - Ravila Bhimani
- Department of Medicine, Division of Infectious Diseases, Emory University School of Medicine, 1760 Haygood Drive, Atlanta, GA, 30322, USA.,Department of Human Genetics, Emory University School of Medicine, 1760 Haygood Drive, Atlanta, GA, 30322, USA
| | - Jocelyn S Vuong
- Department of Medicine, Division of Infectious Diseases, Emory University School of Medicine, 1760 Haygood Drive, Atlanta, GA, 30322, USA.,Department of Human Genetics, Emory University School of Medicine, 1760 Haygood Drive, Atlanta, GA, 30322, USA
| | - Chad P Haase
- Department of Medicine, Division of Infectious Diseases, Emory University School of Medicine, 1760 Haygood Drive, Atlanta, GA, 30322, USA.,Department of Human Genetics, Emory University School of Medicine, 1760 Haygood Drive, Atlanta, GA, 30322, USA
| | - D Harry Webb
- , Georgia Aquarium, 225 Baker Street, Atlanta, GA, 30313, USA
| | - Milton Tan
- Department of Medicine, Division of Infectious Diseases, Emory University School of Medicine, 1760 Haygood Drive, Atlanta, GA, 30322, USA. .,Department of Human Genetics, Emory University School of Medicine, 1760 Haygood Drive, Atlanta, GA, 30322, USA.
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210
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CTCF binding landscape in jawless fish with reference to Hox cluster evolution. Sci Rep 2017; 7:4957. [PMID: 28694486 PMCID: PMC5504073 DOI: 10.1038/s41598-017-04506-x] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Accepted: 05/17/2017] [Indexed: 11/25/2022] Open
Abstract
The nuclear protein CCCTC-binding factor (CTCF) contributes as an insulator to chromatin organization in animal genomes. Currently, our knowledge of its binding property is confined mainly to mammals. In this study, we identified CTCF homologs in extant jawless fishes and performed ChIP-seq for the CTCF protein in the Arctic lamprey. Our phylogenetic analysis suggests that the lamprey lineage experienced gene duplication that gave rise to its unique paralog, designated CTCF2, which is independent from the previously recognized duplication between CTCF and CTCFL. The ChIP-seq analysis detected comparable numbers of CTCF binding sites between lamprey, chicken, and human, and revealed that the lamprey CTCF protein binds to the two-part motif, consisting of core and upstream motifs previously reported for mammals. These findings suggest that this mode of CTCF binding was established in the last common ancestor of extant vertebrates (more than 500 million years ago). We analyzed CTCF binding inside Hox clusters, which revealed a reinforcement of CTCF binding in the region spanning Hox1-4 genes that is unique to lamprey. Our study provides not only biological insights into the antiquity of CTCF-based epigenomic regulation known in mammals but also a technical basis for comparative epigenomic studies encompassing the whole taxon Vertebrata.
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211
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Indrischek H, Prohaska SJ, Gurevich VV, Gurevich EV, Stadler PF. Uncovering missing pieces: duplication and deletion history of arrestins in deuterostomes. BMC Evol Biol 2017; 17:163. [PMID: 28683816 PMCID: PMC5501109 DOI: 10.1186/s12862-017-1001-4] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Accepted: 06/19/2017] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND The cytosolic arrestin proteins mediate desensitization of activated G protein-coupled receptors (GPCRs) via competition with G proteins for the active phosphorylated receptors. Arrestins in active, including receptor-bound, conformation are also transducers of signaling. Therefore, this protein family is an attractive therapeutic target. The signaling outcome is believed to be a result of structural and sequence-dependent interactions of arrestins with GPCRs and other protein partners. Here we elucidated the detailed evolution of arrestins in deuterostomes. RESULTS Identity and number of arrestin paralogs were determined searching deuterostome genomes and gene expression data. In contrast to standard gene prediction methods, our strategy first detects exons situated on different scaffolds and then solves the problem of assigning them to the correct gene. This increases both the completeness and the accuracy of the annotation in comparison to conventional database search strategies applied by the community. The employed strategy enabled us to map in detail the duplication- and deletion history of arrestin paralogs including tandem duplications, pseudogenizations and the formation of retrogenes. The two rounds of whole genome duplications in the vertebrate stem lineage gave rise to four arrestin paralogs. Surprisingly, visual arrestin ARR3 was lost in the mammalian clades Afrotheria and Xenarthra. Duplications in specific clades, on the other hand, must have given rise to new paralogs that show signatures of diversification in functional elements important for receptor binding and phosphate sensing. CONCLUSION The current study traces the functional evolution of deuterostome arrestins in unprecedented detail. Based on a precise re-annotation of the exon-intron structure at nucleotide resolution, we infer the gain and loss of paralogs and patterns of conservation, co-variation and selection.
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Affiliation(s)
- Henrike Indrischek
- Computational EvoDevo Group, Department of Computer Science, Universität Leipzig, Härtelstraße 16-18, Leipzig, D-04107, Germany.
- Bioinformatics Group, Department of Computer Science, Universität Leipzig, Härtelstraße 16-18, Leipzig, D-04107, Germany.
- Interdisciplinary Center for Bioinformatics, Universität Leipzig, Härtelstraße 16-18, Leipzig, D-04107, Germany.
| | - Sonja J Prohaska
- Computational EvoDevo Group, Department of Computer Science, Universität Leipzig, Härtelstraße 16-18, Leipzig, D-04107, Germany
- Interdisciplinary Center for Bioinformatics, Universität Leipzig, Härtelstraße 16-18, Leipzig, D-04107, Germany
| | - Vsevolod V Gurevich
- Department of Pharmacology, Vanderbilt University, 2200 Pierce Ave, Nashville, TN 37232, USA
| | - Eugenia V Gurevich
- Department of Pharmacology, Vanderbilt University, 2200 Pierce Ave, Nashville, TN 37232, USA
| | - Peter F Stadler
- Bioinformatics Group, Department of Computer Science, Universität Leipzig, Härtelstraße 16-18, Leipzig, D-04107, Germany
- Interdisciplinary Center for Bioinformatics, Universität Leipzig, Härtelstraße 16-18, Leipzig, D-04107, Germany
- Max Planck Institute for Mathematics in the Sciences, Inselstraße 22, Leipzig, D-04103, Germany
- Fraunhofer Institute for Cell Therapy and Immunology, Perlickstraße 1, Leipzig, D-04103, Germany
- Department of Theoretical Chemistry, University of Vienna, Währinger Straße 17, Vienna, A-1090, Austria
- Center for non-coding RNA in Technology and Health, Grønegårdsvej 3, Frederiksberg C, DK-1870, Denmark
- Santa Fe Institute, 1399 Hyde Park Rd., Santa Fe, NM 87501, USA
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212
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Igarashi K, Kurosaki T, Roychoudhuri R. BACH transcription factors in innate and adaptive immunity. Nat Rev Immunol 2017; 17:437-450. [PMID: 28461702 DOI: 10.1038/nri.2017.26] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
BTB and CNC homology (BACH) proteins are transcriptional repressors of the basic region leucine zipper (bZIP) transcription factor family. Recent studies indicate widespread roles of BACH proteins in controlling the development and function of the innate and adaptive immune systems, including the differentiation of effector and memory cells of the B and T cell lineages, CD4+ regulatory T cells and macrophages. Here, we emphasize similarities at a molecular level in the cell-type-specific activities of BACH factors, proposing that competitive interactions of BACH proteins with transcriptional activators of the bZIP family form a common mechanistic theme underlying their diverse actions. The findings contribute to a general understanding of how transcriptional repressors shape lineage commitment and cell-type-specific functions through repression of alternative lineage programmes.
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Affiliation(s)
- Kazuhiko Igarashi
- Department of Biochemistry, Center for Regulatory Epigenome and Diseases, Tohoku University Graduate School of Medicine, Sendai 980-8575, Japan
| | - Tomohiro Kurosaki
- Laboratory for Lymphocyte Differentiation, WPI Immunology Frontier Research Center, Osaka University, Suita 565-0871, Japan
- Laboratory for Lymphocyte Differentiation, RIKEN Center for Integrative Medical Sciences (IMS), Tsurumi-ku, Yokohama 230-0045, Japan
| | - Rahul Roychoudhuri
- Laboratory of Lymphocyte Signalling and Development, The Babraham Institute, Cambridge CB22 3AT, UK
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213
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Al-Salam A, Irwin DM. Evolution of the vertebrate insulin receptor substrate (Irs) gene family. BMC Evol Biol 2017; 17:148. [PMID: 28645244 PMCID: PMC5482937 DOI: 10.1186/s12862-017-0994-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Accepted: 06/07/2017] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Insulin receptor substrate (Irs) proteins are essential for insulin signaling as they allow downstream effectors to dock with, and be activated by, the insulin receptor. A family of four Irs proteins have been identified in mice, however the gene for one of these, IRS3, has been pseudogenized in humans. While it is known that the Irs gene family originated in vertebrates, it is not known when it originated and which members are most closely related to each other. A better understanding of the evolution of Irs genes and proteins should provide insight into the regulation of metabolism by insulin. RESULTS Multiple genes for Irs proteins were identified in a wide variety of vertebrate species. Phylogenetic and genomic neighborhood analyses indicate that this gene family originated very early in vertebrae evolution. Most Irs genes were duplicated and retained in fish after the fish-specific genome duplication. Irs genes have been lost of various lineages, including Irs3 in primates and birds and Irs1 in most fish. Irs3 and Irs4 experienced an episode of more rapid protein sequence evolution on the ancestral mammalian lineage. Comparisons of the conservation of the proteins sequences among Irs paralogs show that domains involved in binding to the plasma membrane and insulin receptors are most strongly conserved, while divergence has occurred in sequences involved in interacting with downstream effector proteins. CONCLUSIONS The Irs gene family originated very early in vertebrate evolution, likely through genome duplications, and in parallel with duplications of other components of the insulin signaling pathway, including insulin and the insulin receptor. While the N-terminal sequences of these proteins are conserved among the paralogs, changes in the C-terminal sequences likely allowed changes in biological function.
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Affiliation(s)
- Ahmad Al-Salam
- Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, 1 King's College Circle, Toronto, ON, M5S 1A8, Canada
| | - David M Irwin
- Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, 1 King's College Circle, Toronto, ON, M5S 1A8, Canada.
- Banting and Best Diabetes Centre, University of Toronto, Toronto, ON, Canada.
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214
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Kawasaki K, Mikami M, Nakatomi M, Braasch I, Batzel P, H Postlethwait J, Sato A, Sasagawa I, Ishiyama M. SCPP Genes and Their Relatives in Gar: Rapid Expansion of Mineralization Genes in Osteichthyans. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2017. [PMID: 28643450 DOI: 10.1002/jez.b.22755] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Gar is an actinopterygian that has bone, dentin, enameloid, and ganoin (enamel) in teeth and/or scales. Mineralization of these tissues involves genes encoding various secretory calcium-binding phosphoproteins (SCPPs) in osteichthyans, but no SCPP genes have been identified in chondrichthyans to date. In the gar genome, we identified 38 SCPP genes, seven of which encode "acidic-residue-rich" proteins and 31 encode "Pro/Gln (P/Q) rich" proteins. These gar SCPP genes constitute the largest known repertoire, including many newly identified P/Q-rich genes expressed in teeth and/or scales. Among gar SCPP genes, six acidic and three P/Q-rich genes were identified as orthologs of sarcopterygian genes. The sarcopterygian orthologs of most of these acidic genes are involved in bone and/or dentin formation, and sarcopterygian orthologs of all three P/Q-rich genes participate in enamel formation. The finding of these genes in gar suggests that an elaborate SCPP gene-based genetic system for tissue mineralization was already present in stem osteichthyans. While SCPP genes have been thought to originate from ancient SPARCL1, SPARCL1L1 appears to be more closely related to these genes, because it established a structure similar to acidic SCPP genes probably in stem gnathostomes, perhaps at about the same time with the origin of tissue mineralization. Assuming enamel evolved in stem osteichthyans, all P/Q-rich SCPP genes likely arose within the osteichthyan lineage. Furthermore, the absence of acidic SCPP genes in chondrichthyans might be explained by the secondary loss of earliest acidic genes. It appears that many SCPP genes expanded rapidly in stem osteichthyans and in basal actinopterygians.
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Affiliation(s)
- Kazuhiko Kawasaki
- Department of Anthropology, Pennsylvania State University, University Park, Pennsylvania
| | - Masato Mikami
- Department of Microbiology, School of Life Dentistry at Niigata, The Nippon Dental University, Niigata, Japan
| | | | - Ingo Braasch
- Department of Integrative Biology and Program in Ecology, Evolutionary Biology, and Behavior, Michigan State University, East Lansing, Michigan
| | - Peter Batzel
- Institute of Neuroscience, University of Oregon, Eugene, Oregon
| | | | - Akie Sato
- Department of Anatomy and Histology, School of Dental Medicine, Tsurumi University, Yokohama, Japan
| | - Ichiro Sasagawa
- Advanced Research Center, School of Life Dentistry at Niigata, The Nippon Dental University, Niigata, Japan
| | - Mikio Ishiyama
- Department of Histology, School of Life Dentistry at Niigata, The Nippon Dental University, Niigata, Japan
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215
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York JR, Yuan T, Zehnder K, McCauley DW. Lamprey neural crest migration is Snail-dependent and occurs without a differential shift in cadherin expression. Dev Biol 2017. [PMID: 28624345 DOI: 10.1016/j.ydbio.2017.06.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
The acquisition of neural crest cells was a key step in the origin of the vertebrate body plan. An outstanding question is how neural crest cells acquired their ability to undergo an epithelial-mesenchymal transition (EMT) and migrate extensively throughout the vertebrate embryo. We tested if differential regulation of classical cadherins-a highly conserved feature of neural crest EMT and migration in jawed vertebrates-mediates these cellular behaviors in lamprey, a basal jawless vertebrate. Lamprey has single copies of the type I and type II classical cadherins (CadIA and CadIIA). CadIIA is expressed in premigratory neural crest, and requires the transcription factor Snail for proper expression, yet CadIA is never expressed in the neural tube during neural crest development, suggesting that differential regulation of classical cadherin expression is not required to initiate neural crest migration in basal vertebrates. We hypothesize that neural crest cells evolved by retention of regulatory programs linking distinct mesenchymal and multipotency properties, and emigrated from the neural tube without differentially regulating type I/type II cadherins. Our results point to the coupling of mesenchymal state and multipotency as a key event facilitating the origin of migratory neural crest cells.
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Affiliation(s)
- Joshua R York
- Department of Biology, University of Oklahoma, 730 Van Vleet Oval, Norman, OK 73019, USA
| | - Tian Yuan
- Department of Biology, University of Oklahoma, 730 Van Vleet Oval, Norman, OK 73019, USA
| | - Kevin Zehnder
- Department of Biology, University of Oklahoma, 730 Van Vleet Oval, Norman, OK 73019, USA
| | - David W McCauley
- Department of Biology, University of Oklahoma, 730 Van Vleet Oval, Norman, OK 73019, USA.
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216
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Robertson FM, Gundappa MK, Grammes F, Hvidsten TR, Redmond AK, Lien S, Martin SAM, Holland PWH, Sandve SR, Macqueen DJ. Lineage-specific rediploidization is a mechanism to explain time-lags between genome duplication and evolutionary diversification. Genome Biol 2017; 18:111. [PMID: 28615063 PMCID: PMC5470254 DOI: 10.1186/s13059-017-1241-z] [Citation(s) in RCA: 104] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 05/19/2017] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND The functional divergence of duplicate genes (ohnologues) retained from whole genome duplication (WGD) is thought to promote evolutionary diversification. However, species radiation and phenotypic diversification are often temporally separated from WGD. Salmonid fish, whose ancestor underwent WGD by autotetraploidization ~95 million years ago, fit such a 'time-lag' model of post-WGD radiation, which occurred alongside a major delay in the rediploidization process. Here we propose a model, 'lineage-specific ohnologue resolution' (LORe), to address the consequences of delayed rediploidization. Under LORe, speciation precedes rediploidization, allowing independent ohnologue divergence in sister lineages sharing an ancestral WGD event. RESULTS Using cross-species sequence capture, phylogenomics and genome-wide analyses of ohnologue expression divergence, we demonstrate the major impact of LORe on salmonid evolution. One-quarter of each salmonid genome, harbouring at least 4550 ohnologues, has evolved under LORe, with rediploidization and functional divergence occurring on multiple independent occasions >50 million years post-WGD. We demonstrate the existence and regulatory divergence of many LORe ohnologues with functions in lineage-specific physiological adaptations that potentially facilitated salmonid species radiation. We show that LORe ohnologues are enriched for different functions than 'older' ohnologues that began diverging in the salmonid ancestor. CONCLUSIONS LORe has unappreciated significance as a nested component of post-WGD divergence that impacts the functional properties of genes, whilst providing ohnologues available solely for lineage-specific adaptation. Under LORe, which is predicted following many WGD events, the functional outcomes of WGD need not appear 'explosively', but can arise gradually over tens of millions of years, promoting lineage-specific diversification regimes under prevailing ecological pressures.
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Affiliation(s)
- Fiona M Robertson
- Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen, AB24 2TZ, UK
| | - Manu Kumar Gundappa
- Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen, AB24 2TZ, UK
| | - Fabian Grammes
- Centre for Integrative Genetics (CIGENE), Faculty of Biosciences, Norwegian University of Life Sciences, Ås, NO-1432, Norway
| | - Torgeir R Hvidsten
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, 1432, Ås, Norway.,Umeå Plant Science Centre, Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, SE-90187, Umeå, Sweden
| | - Anthony K Redmond
- Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen, AB24 2TZ, UK.,Centre for Genome-Enabled Biology & Medicine, University of Aberdeen, Aberdeen, AB24 2TZ, UK
| | - Sigbjørn Lien
- Centre for Integrative Genetics (CIGENE), Faculty of Biosciences, Norwegian University of Life Sciences, Ås, NO-1432, Norway
| | - Samuel A M Martin
- Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen, AB24 2TZ, UK
| | - Peter W H Holland
- Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK
| | - Simen R Sandve
- Centre for Integrative Genetics (CIGENE), Faculty of Biosciences, Norwegian University of Life Sciences, Ås, NO-1432, Norway
| | - Daniel J Macqueen
- Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen, AB24 2TZ, UK.
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217
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Holzer G, Laudet V. New Insights into Vertebrate Thyroid Hormone Receptor Evolution. NUCLEAR RECEPTOR RESEARCH 2017. [DOI: 10.11131/2017/101287] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Guillaume Holzer
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Université Claude Bernard Lyon 1, UMR CNRS 5242, Ecole Normale Supérieure de Lyon, 46 Allée d'Italie, 69364 Lyon Cedex 07, France
| | - Vincent Laudet
- Observatoire Océanologique de Banyuls-sur-Mer, UMR CNRS 7232, Université Pierre et Marie Curie Paris, 1 avenue Pierre Fabre, 66650 Banyuls-sur-Mer, France
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218
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Pasquali CC, Islam Z, Adamoski D, Ferreira IM, Righeto RD, Bettini J, Portugal RV, Yue WWY, Gonzalez A, Dias SMG, Ambrosio ALB. The origin and evolution of human glutaminases and their atypical C-terminal ankyrin repeats. J Biol Chem 2017; 292:11572-11585. [PMID: 28526749 DOI: 10.1074/jbc.m117.787291] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Revised: 05/11/2017] [Indexed: 12/14/2022] Open
Abstract
On the basis of tissue-specific enzyme activity and inhibition by catalytic products, Hans Krebs first demonstrated the existence of multiple glutaminases in mammals. Currently, two human genes are known to encode at least four glutaminase isoforms. However, the phylogeny of these medically relevant enzymes remains unclear, prompting us to investigate their origin and evolution. Using prokaryotic and eukaryotic glutaminase sequences, we built a phylogenetic tree whose topology suggested that the multidomain architecture was inherited from bacterial ancestors, probably simultaneously with the hosting of the proto-mitochondrion endosymbiont. We propose an evolutionary model wherein the appearance of the most active enzyme isoform, glutaminase C (GAC), which is expressed in many cancers, was a late retrotransposition event that occurred in fishes from the Chondrichthyes class. The ankyrin (ANK) repeats in the glutaminases were acquired early in their evolution. To obtain information on ANK folding, we solved two high-resolution structures of the ANK repeat-containing C termini of both kidney-type glutaminase (KGA) and GLS2 isoforms (glutaminase B and liver-type glutaminase). We found that the glutaminase ANK repeats form unique intramolecular contacts through two highly conserved motifs; curiously, this arrangement occludes a region usually involved in ANK-mediated protein-protein interactions. We also solved the crystal structure of full-length KGA and present a small-angle X-ray scattering model for full-length GLS2. These structures explain these proteins' compromised ability to assemble into catalytically active supra-tetrameric filaments, as previously shown for GAC. Collectively, these results provide information about glutaminases that may aid in the design of isoform-specific glutaminase inhibitors.
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Affiliation(s)
- Camila Cristina Pasquali
- From the Laboratório Nacional de Biociências, Centro Nacional de Pesquisa em Energia e Materiais, Campinas, São Paulo 13083-970, Brazil
| | - Zeyaul Islam
- From the Laboratório Nacional de Biociências, Centro Nacional de Pesquisa em Energia e Materiais, Campinas, São Paulo 13083-970, Brazil
| | - Douglas Adamoski
- From the Laboratório Nacional de Biociências, Centro Nacional de Pesquisa em Energia e Materiais, Campinas, São Paulo 13083-970, Brazil
| | - Igor Monteze Ferreira
- From the Laboratório Nacional de Biociências, Centro Nacional de Pesquisa em Energia e Materiais, Campinas, São Paulo 13083-970, Brazil.,the Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, United Kingdom
| | - Ricardo Diogo Righeto
- the Laboratório Nacional de Nanotecnologia, Centro Nacional de Pesquisa em Energia e Materiais, Campinas, São Paulo 13083-970, Brazil.,the School of Electrical and Computer Engineering, University of Campinas, São Paulo 13083-852, Brazil, and
| | - Jefferson Bettini
- the Laboratório Nacional de Nanotecnologia, Centro Nacional de Pesquisa em Energia e Materiais, Campinas, São Paulo 13083-970, Brazil
| | - Rodrigo Villares Portugal
- the Laboratório Nacional de Nanotecnologia, Centro Nacional de Pesquisa em Energia e Materiais, Campinas, São Paulo 13083-970, Brazil
| | - Wyatt Wai-Yin Yue
- the Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, United Kingdom
| | - Ana Gonzalez
- the Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California 94025
| | - Sandra Martha Gomes Dias
- From the Laboratório Nacional de Biociências, Centro Nacional de Pesquisa em Energia e Materiais, Campinas, São Paulo 13083-970, Brazil,
| | - Andre Luis Berteli Ambrosio
- From the Laboratório Nacional de Biociências, Centro Nacional de Pesquisa em Energia e Materiais, Campinas, São Paulo 13083-970, Brazil,
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219
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Ishijima J, Uno Y, Nunome M, Nishida C, Kuraku S, Matsuda Y. Molecular cytogenetic characterization of chromosome site-specific repetitive sequences in the Arctic lamprey (Lethenteron camtschaticum, Petromyzontidae). DNA Res 2017; 24:93-101. [PMID: 28025319 PMCID: PMC5381345 DOI: 10.1093/dnares/dsw053] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2016] [Accepted: 11/02/2016] [Indexed: 12/19/2022] Open
Abstract
All extant lamprey karyotypes are characterized by almost all dot-shaped microchromosomes. To understand the molecular basis of chromosome structure in lampreys, we performed chromosome C-banding and silver staining and chromosome mapping of the 18S–28S and 5S ribosomal RNA (rRNA) genes and telomeric TTAGGG repeats in the Arctic lamprey (Lethenteron camtschaticum). In addition, we cloned chromosome site-specific repetitive DNA sequences and characterized them by nucleotide sequencing, chromosome in situ hybridization, and filter hybridization. Three types of repetitive sequences were detected; a 200-bp AT-rich repetitive sequence, LCA-EcoRIa that co-localized with the 18S–28S rRNA gene clusters of 3 chromosomal pairs; a 364-bp AT-rich LCA-EcoRIb sequence that showed homology to the EcoRI sequence family from the sea lamprey (Petromyzon marinus), which contains short repeats as centromeric motifs; and a GC-rich 702-bp LCA-ApaI sequence that was distributed on nearly all chromosomes and showed significant homology with the integrase-coding region of a Ty3/Gypsy family long terminal repeat (LTR) retrotransposon. All three repetitive sequences are highly conserved within the Petromyzontidae or within Petromyzontidae and Mordaciidae. Molecular cytogenetic characterization of these site-specific repeats showed that they may be correlated with programed genome rearrangement (LCA-EcoRIa), centromere structure and function (LCA-EcoRIb), and site-specific amplification of LTR retroelements through homogenization between non-homologous chromosomes (LCA-ApaI).
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Affiliation(s)
- Junko Ishijima
- Laboratory of Animal Cytogenetics, Department of Biological Sciences, Graduate School of Science, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan
| | - Yoshinobu Uno
- Laboratory of Animal Genetics, Department of Applied Molecular Biosciences, Nagoya University, Nagoya, Aichi 464-8601, Japan
| | - Mitsuo Nunome
- Avian Bioscience Research Center, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Aichi 464-8601, Japan
| | - Chizuko Nishida
- Department of Natural History Sciences, Faculty of Science, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan
| | - Shigehiro Kuraku
- Phyloinformatics Unit, RIKEN Center for Life Science Technologies, Kobe 650-0047, Japan
| | - Yoichi Matsuda
- Laboratory of Animal Genetics, Department of Applied Molecular Biosciences, Nagoya University, Nagoya, Aichi 464-8601, Japan
- Avian Bioscience Research Center, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Aichi 464-8601, Japan
- To whom correspondence should be addressed. Tel. +81 52 789 4100. Fax. +81 52 789 4099.
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220
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Zhou L, Gui J. Natural and artificial polyploids in aquaculture. AQUACULTURE AND FISHERIES 2017. [DOI: 10.1016/j.aaf.2017.04.003] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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221
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Buckley KM, Ho ECH, Hibino T, Schrankel CS, Schuh NW, Wang G, Rast JP. IL17 factors are early regulators in the gut epithelium during inflammatory response to Vibrio in the sea urchin larva. eLife 2017; 6. [PMID: 28447937 PMCID: PMC5457136 DOI: 10.7554/elife.23481] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2016] [Accepted: 04/25/2017] [Indexed: 12/25/2022] Open
Abstract
IL17 cytokines are central mediators of mammalian immunity. In vertebrates, these factors derive from diverse cellular sources. Sea urchins share a molecular heritage with chordates that includes the IL17 system. Here, we characterize the role of epithelial expression of IL17 in the larval gut-associated immune response. The purple sea urchin genome encodes 10 IL17 subfamilies (35 genes) and 2 IL17 receptors. Most of these subfamilies are conserved throughout echinoderms. Two IL17 subfamilies are sequentially strongly upregulated and attenuated in the gut epithelium in response to bacterial disturbance. IL17R1 signal perturbation results in reduced expression of several response genes including an IL17 subtype, indicating a potential feedback. A third IL17 subfamily is activated in adult immune cells indicating that expression in immune cells and epithelia is divided among families. The larva provides a tractable model to investigate the regulation and consequences of gut epithelial IL17 expression across the organism. DOI:http://dx.doi.org/10.7554/eLife.23481.001 To protect themselves from the constant invasion of harmful microbes, animals have evolved complex immune systems. The gut is one of the most active sites of the immune system and plays a key role in regulating immune responses. In mammals, cells lining the gut wall can sense the presence of harmful bacteria and communicate this information to tissues across the body by producing specialized proteins called Interleukin-17 (IL-17). IL-17 proteins are important for regulating inflammation and are thought to activate specific immune cells in an infected area. Some aspects of immune systems are similar between different animal species, which can provide clues of how immunity evolved and how it is regulated. For example, sea urchins, which evolved 400-600 million years ago, begin life as simple larvae consisting of a few thousand cells. As oceans harbor a multitude of bacteria and viruses, sea urchin larvae need an efficient immune system to defend themselves. These larvae can respond to specific types of bacteria within a few hours after the microbes have entered their gut by modifying gene expression in distant cells. As these changes occur in cells that are removed from the bacteria, it is thought that the gut cells that initially sense the bacteria, somehow communicate this information. Now, Buckley et al. exposed sea urchin larvae to a marine bacterium and measured the responses of the cells and their gene expression. The infection affected several types of cells, and in the first 24 hours, a subset of immune cells changed shape and started migrating to the gut wall. In addition, IL-17 gene expression changed significantly in gut cells in the early phases of the larval immune response. Buckley et al. identified three types of IL-17 proteins involved in sea urchin immunity: two that are important for the immune response in the gut during the larval stage, and a third that is only present in adults. These findings suggest that IL-17 signaling is an ancient and central element of gut-associated immune response, which even exists in animals that evolved long before humans. These findings demonstrate that the sea urchin larva represents a unique and ideal experimental model to study immune responses in a living organism that is more closely related to mammals than some other models, like fruit flies or worms. By understanding the fundamental mechanisms that mediate gut health, this work may highlight new drug targets to treat conditions like Crohn’s disease and colon cancer. DOI:http://dx.doi.org/10.7554/eLife.23481.002
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Affiliation(s)
- Katherine M Buckley
- Department of Immunology, University of Toronto, Toronto, Canada.,Sunnybrook Research Institute, Toronto, Canada
| | - Eric Chun Hei Ho
- Sunnybrook Research Institute, Toronto, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Canada
| | - Taku Hibino
- Sunnybrook Research Institute, Toronto, Canada
| | - Catherine S Schrankel
- Department of Immunology, University of Toronto, Toronto, Canada.,Sunnybrook Research Institute, Toronto, Canada
| | - Nicholas W Schuh
- Sunnybrook Research Institute, Toronto, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Canada
| | - Guizhi Wang
- Sunnybrook Research Institute, Toronto, Canada
| | - Jonathan P Rast
- Department of Immunology, University of Toronto, Toronto, Canada.,Sunnybrook Research Institute, Toronto, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Canada
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222
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Fritzsch B, Elliott KL. Evolution and Development of the Inner Ear Efferent System: Transforming a Motor Neuron Population to Connect to the Most Unusual Motor Protein via Ancient Nicotinic Receptors. Front Cell Neurosci 2017; 11:114. [PMID: 28484373 PMCID: PMC5401870 DOI: 10.3389/fncel.2017.00114] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Accepted: 04/05/2017] [Indexed: 02/06/2023] Open
Abstract
All craniate chordates have inner ears with hair cells that receive input from the brain by cholinergic centrifugal fibers, the so-called inner ear efferents (IEEs). Comparative data suggest that IEEs derive from facial branchial motor (FBM) neurons that project to the inner ear instead of facial muscles. Developmental data showed that IEEs develop adjacent to FBMs and segregation from IEEs might depend on few transcription factors uniquely associated with IEEs. Like other cholinergic terminals in the peripheral nervous system (PNS), efferent terminals signal on hair cells through nicotinic acetylcholine channels, likely composed out of alpha 9 and alpha 10 units (Chrna9, Chrna10). Consistent with the evolutionary ancestry of IEEs is the even more conserved ancestry of Chrna9 and 10. The evolutionary appearance of IEEs may reflect access of FBMs to a novel target, possibly related to displacement or loss of mesoderm-derived muscle fibers by the ectoderm-derived ear vesicle. Experimental transplantations mimicking this possible aspect of ear evolution showed that different motor neurons of the spinal cord or brainstem form cholinergic synapses on hair cells when ears replace somites or eyes. Transplantation provides experimental evidence in support of the evolutionary switch of FBM neurons to become IEEs. Mammals uniquely evolved a prestin related motor system to cause shape changes in outer hair cells regulated by the IEEs. In summary, an ancient motor neuron population drives in craniates via signaling through highly conserved Chrna receptors a uniquely derived cellular contractility system that is essential for hearing in mammals.
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223
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Peat JR, Ortega-Recalde O, Kardailsky O, Hore TA. The elephant shark methylome reveals conservation of epigenetic regulation across jawed vertebrates. F1000Res 2017; 6:526. [PMID: 28580133 PMCID: PMC5437953 DOI: 10.12688/f1000research.11281.1] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/12/2017] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Methylation of CG dinucleotides constitutes a critical system of epigenetic memory in bony vertebrates, where it modulates gene expression and suppresses transposon activity. The genomes of studied vertebrates are pervasively hypermethylated, with the exception of regulatory elements such as transcription start sites (TSSs), where the presence of methylation is associated with gene silencing. This system is not found in the sparsely methylated genomes of invertebrates, and establishing how it arose during early vertebrate evolution is impeded by a paucity of epigenetic data from basal vertebrates. METHODS We perform whole-genome bisulfite sequencing to generate the first genome-wide methylation profiles of a cartilaginous fish, the elephant shark Callorhinchus milii. Employing these to determine the elephant shark methylome structure and its relationship with expression, we compare this with higher vertebrates and an invertebrate chordate using published methylation and transcriptome data. Results: Like higher vertebrates, the majority of elephant shark CG sites are highly methylated, and methylation is abundant across the genome rather than patterned in the mosaic configuration of invertebrates. This global hypermethylation includes transposable elements and the bodies of genes at all expression levels. Significantly, we document an inverse relationship between TSS methylation and expression in the elephant shark, supporting the presence of the repressive regulatory architecture shared by higher vertebrates. CONCLUSIONS Our demonstration that methylation patterns in a cartilaginous fish are characteristic of higher vertebrates imply the conservation of this epigenetic modification system across jawed vertebrates separated by 465 million years of evolution. In addition, these findings position the elephant shark as a valuable model to explore the evolutionary history and function of vertebrate methylation.
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Affiliation(s)
- Julian R Peat
- Department of Anatomy, University of Otago, Dunedin, 9016, New Zealand
| | | | - Olga Kardailsky
- Department of Anatomy, University of Otago, Dunedin, 9016, New Zealand
| | - Timothy A Hore
- Department of Anatomy, University of Otago, Dunedin, 9016, New Zealand
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Lamb TD, Hunt DM. Evolution of the vertebrate phototransduction cascade activation steps. Dev Biol 2017; 431:77-92. [PMID: 28347645 DOI: 10.1016/j.ydbio.2017.03.018] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Revised: 02/28/2017] [Accepted: 03/20/2017] [Indexed: 02/06/2023]
Abstract
We examine the molecular phylogeny of the proteins underlying the activation steps of vertebrate phototransduction, for both agnathan and jawed vertebrate taxa. We expand the number of taxa analysed and we update the alignment and tree building methodology from a previous analysis. For each of the four primary components (the G-protein transducin alpha subunit, GαT, the cyclic GMP phosphodiesterase, PDE6, and the alpha and beta subunits of the cGMP-gated ion channel, CNGC), the phylogenies appear consistent with expansion from an ancestral proto-vertebrate cascade during two rounds of whole-genome duplication followed by divergence of the agnathan and jawed vertebrate lineages. In each case, we consider possible scenarios for the underlying gene duplications and losses, and we apply relevant constraints to the tree construction. From tests of the topology of the resulting trees, we obtain a scenario for the expansion of each component during 2R that accurately fits the observations. Similar analysis of the visual opsins indicates that the only expansion to have occurred during 2R was the formation of Rh1 and Rh2. Finally, we propose a hypothetical scenario for the conversion of an ancestral chordate cascade into the proto-vertebrate phototransduction cascade, prior to whole-genome duplication. Together, our models provide a plausible account for the origin and expansion of the vertebrate phototransduction cascade.
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Affiliation(s)
- Trevor D Lamb
- Eccles Institute of Neuroscience, John Curtin School of Medical Research, The Australian National University, ACT 2600, Australia.
| | - David M Hunt
- The Lions Eye Institute, The University of Western Australia, WA 6009, Australia; School of Biological Sciences, The University of Western Australia, WA 6009, Australia
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Vicens A, Andrade‐López K, Cortez D, Gutiérrez RM, Treviño CL. Premammalian origin of the sperm-specific Slo3 channel. FEBS Open Bio 2017; 7:382-390. [PMID: 28286733 PMCID: PMC5337896 DOI: 10.1002/2211-5463.12186] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Revised: 12/01/2016] [Accepted: 12/16/2016] [Indexed: 01/05/2023] Open
Abstract
Slo3 is a sperm-specific potassium (K+) channel essential for male fertility. Slo3 channels have so far been considered to be specific to mammals. Through exploratory genomics, we identified the Slo3 gene in the genome of terrestrial (birds and reptiles) and aquatic (fish) vertebrates. In the case of fish, Slo3 has undergone several episodes of gene loss. Transcriptomic analysis showed that vertebrate Slo3 transcript orthologues are predominantly expressed in testis, in concordance with the mammalian Slo3. We conclude that the Slo3 gene arose during the radiation of early vertebrates, much earlier than previously thought. Our findings add to the growing evidence indicating that the phylogenetic profiles of sperm-specific channels are intermittent throughout metazoan evolution, which probably reflects the adaptation of sperm to different ionic milieus and fertilization environments.
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Affiliation(s)
- Alberto Vicens
- Departamento de Genética del Desarrollo y Fisiología MolecularInstituto de BiotecnologíaUniversidad Nacional Autónoma de MéxicoCuernavaca MorelosMéxico
| | - Karla Andrade‐López
- Departamento de Genética del Desarrollo y Fisiología MolecularInstituto de BiotecnologíaUniversidad Nacional Autónoma de MéxicoCuernavaca MorelosMéxico
| | - Diego Cortez
- Centro de Ciencias GenómicasUniversidad Nacional Autónoma de MéxicoCuernavaca MorelosMéxico
| | - Rosa María Gutiérrez
- Departamento de Microbiología MolecularInstituto de BiotecnologíaUniversidad Nacional Autónoma de MéxicoCuernavaca MorelosMéxico
| | - Claudia L. Treviño
- Departamento de Genética del Desarrollo y Fisiología MolecularInstituto de BiotecnologíaUniversidad Nacional Autónoma de MéxicoCuernavaca MorelosMéxico
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226
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Christensen KA, Davidson WS. Autopolyploidy genome duplication preserves other ancient genome duplications in Atlantic salmon (Salmo salar). PLoS One 2017; 12:e0173053. [PMID: 28241055 PMCID: PMC5328387 DOI: 10.1371/journal.pone.0173053] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 02/14/2017] [Indexed: 11/19/2022] Open
Abstract
Salmonids (e.g. Atlantic salmon, Pacific salmon, and trouts) have a long legacy of genome duplication. In addition to three ancient genome duplications that all teleosts are thought to share, salmonids have had one additional genome duplication. We explored a methodology for untangling these duplications from each other to better understand them in Atlantic salmon. In this methodology, homeologous regions (paralogous/duplicated genomic regions originating from a whole genome duplication) from the most recent genome duplication were assumed to have duplicated genes at greater density and have greater sequence similarity. This assumption was used to differentiate duplicated gene pairs in Atlantic salmon that are either from the most recent genome duplication or from earlier duplications. From a comparison with multiple vertebrate species, it is clear that Atlantic salmon have retained more duplicated genes from ancient genome duplications than other vertebrates--often at higher density in the genome and containing fewer synonymous mutations. It may be that polysomic inheritance is the mechanism responsible for maintaining ancient gene duplicates in salmonids. Polysomic inheritance (when multiple chromosomes pair during meiosis) is thought to be relatively common in salmonids compared to other vertebrate species. These findings illuminate how genome duplications may not only increase the number of duplicated genes, but may also be involved in the maintenance of them from previous genome duplications as well.
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Affiliation(s)
- Kris A. Christensen
- Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - William S. Davidson
- Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
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Abdelrahman H, ElHady M, Alcivar-Warren A, Allen S, Al-Tobasei R, Bao L, Beck B, Blackburn H, Bosworth B, Buchanan J, Chappell J, Daniels W, Dong S, Dunham R, Durland E, Elaswad A, Gomez-Chiarri M, Gosh K, Guo X, Hackett P, Hanson T, Hedgecock D, Howard T, Holland L, Jackson M, Jin Y, Khalil K, Kocher T, Leeds T, Li N, Lindsey L, Liu S, Liu Z, Martin K, Novriadi R, Odin R, Palti Y, Peatman E, Proestou D, Qin G, Reading B, Rexroad C, Roberts S, Salem M, Severin A, Shi H, Shoemaker C, Stiles S, Tan S, Tang KFJ, Thongda W, Tiersch T, Tomasso J, Prabowo WT, Vallejo R, van der Steen H, Vo K, Waldbieser G, Wang H, Wang X, Xiang J, Yang Y, Yant R, Yuan Z, Zeng Q, Zhou T. Aquaculture genomics, genetics and breeding in the United States: current status, challenges, and priorities for future research. BMC Genomics 2017; 18:191. [PMID: 28219347 PMCID: PMC5319170 DOI: 10.1186/s12864-017-3557-1] [Citation(s) in RCA: 112] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Accepted: 02/06/2017] [Indexed: 12/31/2022] Open
Abstract
Advancing the production efficiency and profitability of aquaculture is dependent upon the ability to utilize a diverse array of genetic resources. The ultimate goals of aquaculture genomics, genetics and breeding research are to enhance aquaculture production efficiency, sustainability, product quality, and profitability in support of the commercial sector and for the benefit of consumers. In order to achieve these goals, it is important to understand the genomic structure and organization of aquaculture species, and their genomic and phenomic variations, as well as the genetic basis of traits and their interrelationships. In addition, it is also important to understand the mechanisms of regulation and evolutionary conservation at the levels of genome, transcriptome, proteome, epigenome, and systems biology. With genomic information and information between the genomes and phenomes, technologies for marker/causal mutation-assisted selection, genome selection, and genome editing can be developed for applications in aquaculture. A set of genomic tools and resources must be made available including reference genome sequences and their annotations (including coding and non-coding regulatory elements), genome-wide polymorphic markers, efficient genotyping platforms, high-density and high-resolution linkage maps, and transcriptome resources including non-coding transcripts. Genomic and genetic control of important performance and production traits, such as disease resistance, feed conversion efficiency, growth rate, processing yield, behaviour, reproductive characteristics, and tolerance to environmental stressors like low dissolved oxygen, high or low water temperature and salinity, must be understood. QTL need to be identified, validated across strains, lines and populations, and their mechanisms of control understood. Causal gene(s) need to be identified. Genetic and epigenetic regulation of important aquaculture traits need to be determined, and technologies for marker-assisted selection, causal gene/mutation-assisted selection, genome selection, and genome editing using CRISPR and other technologies must be developed, demonstrated with applicability, and application to aquaculture industries.Major progress has been made in aquaculture genomics for dozens of fish and shellfish species including the development of genetic linkage maps, physical maps, microarrays, single nucleotide polymorphism (SNP) arrays, transcriptome databases and various stages of genome reference sequences. This paper provides a general review of the current status, challenges and future research needs of aquaculture genomics, genetics, and breeding, with a focus on major aquaculture species in the United States: catfish, rainbow trout, Atlantic salmon, tilapia, striped bass, oysters, and shrimp. While the overall research priorities and the practical goals are similar across various aquaculture species, the current status in each species should dictate the next priority areas within the species. This paper is an output of the USDA Workshop for Aquaculture Genomics, Genetics, and Breeding held in late March 2016 in Auburn, Alabama, with participants from all parts of the United States.
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Affiliation(s)
- Hisham Abdelrahman
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Mohamed ElHady
- Department of Biological Sciences, Auburn University, Auburn, AL, 36849, USA
| | | | - Standish Allen
- Aquaculture Genetics & Breeding Technology Center, Virginia Institute of Marine Science, Gloucester Point, VA, 23062, USA
| | - Rafet Al-Tobasei
- Department of Biology, Middle Tennessee State University, Murfreesboro, TN, 37132, USA
| | - Lisui Bao
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Ben Beck
- Aquatic Animal Health Research Unit, USDA-ARS, 990 Wire Road, Auburn, AL, 36832, USA
| | - Harvey Blackburn
- USDA-ARS-NL Wheat & Corn Collections at a Glance GRP, National Animal Germplasm Program, 1111 S. Mason St., Fort Collins, CO, 80521-4500, USA
| | - Brian Bosworth
- USDA-ARS/CGRU, 141 Experimental Station Road, Stoneville, MS, 38701, USA
| | - John Buchanan
- Center for Aquaculture Technologies, 8395 Camino Santa Fe, Suite E, San Diego, CA, 92121, USA
| | - Jesse Chappell
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - William Daniels
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Sheng Dong
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Rex Dunham
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Evan Durland
- Department of Fisheries and Wildlife, Oregon State University, Corvallis, OR, 97331, USA
| | - Ahmed Elaswad
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Marta Gomez-Chiarri
- Department of Fisheries, Animal & Veterinary Science, 134 Woodward Hall, 9 East Alumni Avenue, Kingston, RI, 02881, USA
| | - Kamal Gosh
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Ximing Guo
- Haskin Shellfish Research Laboratory, Department of Marine and Coastal Sciences, Rutgers University, 6959 Miller Avenue, Port Norris, NJ, 08349, USA
| | - Perry Hackett
- Department of Genetics, Cell Biology and Development, 5-108 MCB, 420 Washington Avenue SE, Minneapolis, MN, 55455, USA
| | - Terry Hanson
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Dennis Hedgecock
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089-0371, USA
| | - Tiffany Howard
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Leigh Holland
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Molly Jackson
- Taylor Shellfish Farms, 130 SE Lynch RD, Shelton, WA, 98584, USA
| | - Yulin Jin
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Karim Khalil
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Thomas Kocher
- Department of Biology, University of Maryland, 2132 Biosciences Research Building, College Park, MD, 20742, USA
| | - Tim Leeds
- National Center for Cool and Cold Water Aquaculture, Agricultural Research Service, United States Department of Agriculture, Kearneysville, WV, 25430, USA
| | - Ning Li
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Lauren Lindsey
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Shikai Liu
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Zhanjiang Liu
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA.
| | - Kyle Martin
- Troutlodge, 27090 Us Highway 12, Naches, WA, 98937, USA
| | - Romi Novriadi
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Ramjie Odin
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Yniv Palti
- National Center for Cool and Cold Water Aquaculture, Agricultural Research Service, United States Department of Agriculture, Kearneysville, WV, 25430, USA
| | - Eric Peatman
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Dina Proestou
- USDA ARS NEA NCWMAC Shellfish Genetics at the University Rhode Island, 469 CBLS, 120 Flagg Road, Kingston, RI, 02881, USA
| | - Guyu Qin
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Benjamin Reading
- Department of Applied Ecology, North Carolina State University, Raleigh, NC, 27695-7617, USA
| | - Caird Rexroad
- USDA ARS Office of National Programs, George Washington Carver Center Room 4-2106, 5601 Sunnyside Avenue, Beltsville, MD, 20705, USA
| | - Steven Roberts
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, WA, 98105, USA
| | - Mohamed Salem
- Department of Biology, Middle Tennessee State University, Murfreesboro, TN, 37132, USA
| | - Andrew Severin
- Genome Informatics Facility, Office of Biotechnology, Iowa State University, Ames, IA, 50011, USA
| | - Huitong Shi
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Craig Shoemaker
- Aquatic Animal Health Research Unit, USDA-ARS, 990 Wire Road, Auburn, AL, 36832, USA
| | - Sheila Stiles
- USDOC/NOAA, National Marine Fisheries Service, NEFSC, Milford Laboratory, Milford, Connectcut, 06460, USA
| | - Suxu Tan
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Kathy F J Tang
- School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, AZ, 85721, USA
| | - Wilawan Thongda
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Terrence Tiersch
- Aquatic Germplasm and Genetic Resources Center, School of Renewable Natural Resources, Louisiana State University Agricultural Center, Baton Rouge, LA, 70820, USA
| | - Joseph Tomasso
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Wendy Tri Prabowo
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Roger Vallejo
- National Center for Cool and Cold Water Aquaculture, Agricultural Research Service, United States Department of Agriculture, Kearneysville, WV, 25430, USA
| | | | - Khoi Vo
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Geoff Waldbieser
- USDA-ARS/CGRU, 141 Experimental Station Road, Stoneville, MS, 38701, USA
| | - Hanping Wang
- Aquaculture Genetics and Breeding Laboratory, The Ohio State University South Centers, Piketon, OH, 45661, USA
| | - Xiaozhu Wang
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Jianhai Xiang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Yujia Yang
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Roger Yant
- Hybrid Catfish Company, 1233 Montgomery Drive, Inverness, MS, 38753, USA
| | - Zihao Yuan
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Qifan Zeng
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Tao Zhou
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
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Hahn ME, Karchner SI, Merson RR. Diversity as Opportunity: Insights from 600 Million Years of AHR Evolution. CURRENT OPINION IN TOXICOLOGY 2017; 2:58-71. [PMID: 28286876 DOI: 10.1016/j.cotox.2017.02.003] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
The aryl hydrocarbon receptor (AHR) was for many years of interest only to pharmacologists and toxicologists. However, this protein has fundamental roles in biology that are being revealed through studies in diverse animal species. The AHR is an ancient protein. AHR homologs exist in most major groups of modern bilaterian animals, including deuterostomes (chordates, hemichordates, echinoderms) and the two major clades of protostome invertebrates [ecdysozoans (e.g. arthropods and nematodes) and lophotrochozoans (e.g. molluscs and annelids)]. AHR homologs also have been identified in cnidarians such as the sea anemone Nematostella and in the genome of Trichoplax, a placozoan. Bilaterians, cnidarians, and placozoans form the clade Eumetazoa, whose last common ancestor lived approximately 600 million years ago (MYA). The presence of AHR homologs in modern representatives of all these groups indicates that the original eumetazoan animal possessed an AHR homolog. Studies in invertebrates and vertebrates reveal parallel functions of AHR in the development and function of sensory neural systems, suggesting that these may be ancestral roles. Vertebrate animals are characterized by the expansion and diversification of AHRs, via gene and genome duplications, from the ancestral protoAHR into at least five classes of AHR-like proteins: AHR, AHR1, AHR2, AHR3, and AHRR. The evolution of multiple AHRs in vertebrates coincided with the acquisition of high-affinity binding of halogenated and polynuclear aromatic hydrocarbons and the emergence of adaptive functions involving regulation of xenobiotic-metabolizing enzymes and roles in adaptive immunity. The existence of multiple AHRs may have facilitated subfunction partitioning and specialization of specific AHR types in some taxa. Additional research in diverse model and non-model species will continue to enrich our understanding of AHR and its pleiotropic roles in biology and toxicology.
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Affiliation(s)
- Mark E Hahn
- Biology Department, Woods Hole Oceanographic Institution, MS-32, Woods Hole, MA 02543, USA
| | - Sibel I Karchner
- Biology Department, Woods Hole Oceanographic Institution, MS-32, Woods Hole, MA 02543, USA
| | - Rebeka R Merson
- Biology Department, Rhode Island College, 600 Mt. Pleasant Avenue, 251 Fogarty Life Sciences, Providence, RI 02908
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A SNP Based Linkage Map of the Arctic Charr ( Salvelinus alpinus) Genome Provides Insights into the Diploidization Process After Whole Genome Duplication. G3-GENES GENOMES GENETICS 2017; 7:543-556. [PMID: 27986793 PMCID: PMC5295600 DOI: 10.1534/g3.116.038026] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Diploidization, which follows whole genome duplication events, does not occur evenly across the genome. In salmonid fishes, certain pairs of homeologous chromosomes preserve tetraploid loci in higher frequencies toward the telomeres due to residual tetrasomic inheritance. Research suggests this occurs only in homeologous pairs where one chromosome arm has undergone a fusion event. We present a linkage map for Arctic charr (Salvelinus alpinus), a salmonid species with relatively fewer chromosome fusions. Genotype by sequencing identified 19,418 SNPs, and a linkage map consisting of 4508 markers was constructed from a subset of high quality SNPs and microsatellite markers that were used to anchor the new map to previous versions. Both male- and female-specific linkage maps contained the expected number of 39 linkage groups. The chromosome type associated with each linkage group was determined, and 10 stable metacentric chromosomes were identified, along with a chromosome polymorphism involving the sex chromosome AC04. Two instances of a weak form of pseudolinkage were detected in the telomeric regions of homeologous chromosome arms in both female and male linkage maps. Chromosome arm homologies within the Atlantic salmon (Salmo salar) and rainbow trout (Oncorhynchus mykiss) genomes were determined. Paralogous sequence variants (PSVs) were identified, and their comparative BLASTn hit locations showed that duplicate markers exist in higher numbers on seven pairs of homeologous arms, previously identified as preserving tetrasomy in salmonid species. Homeologous arm pairs where neither arm has been part of a fusion event in Arctic charr had fewer PSVs, suggesting faster diploidization rates in these regions.
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231
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Kolosov D, Bui P, Donini A, Wilkie MP, Kelly SP. A role for tight junction-associated MARVEL proteins in larval sea lamprey (Petromyzon marinus) osmoregulation. J Exp Biol 2017; 220:3657-3670. [DOI: 10.1242/jeb.161562] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Accepted: 08/07/2017] [Indexed: 01/13/2023]
Abstract
This study reports on tight junction-associated MARVEL proteins of larval sea lamprey (Petromyzon marinus) and their potential role in ammocoete osmoregulation. Two Occludin isoforms (designated Ocln and Ocln-a) and a tricellulin (Tric) were identified. Transcripts encoding ocln, ocln-a, and tric were broadly expressed in larval lamprey, with greatest abundance of ocln in gut, liver and kidney, ocln-a in the gill and skin, and tric in the kidney. Ocln and Ocln-a resolved as ∼63 kDa and ∼35 kDa MW proteins respectively while Tric resolved as a ∼50 kDa protein. Ocln immunolocalized to the gill vasculature and in gill mucous cells while Ocln-a localized to the gill pouch and gill epithelium. Both Ocln and Ocln-a localized in the nephron, the epidermis and the luminal side of the gut. In branchial tissue, Tric exhibited punctate localization, consistent with its presence at regions of tricellular contact. Following ion-poor water (IPW) acclimation of ammocoetes, serum [Na+] and [Cl−] reduced, but not [Ca++], and carcass moisture content increased. In association, Ocln abundance increased in skin and kidney, but reduced in gill of IPW-acclimated ammocoetes while Ocln-a abundance reduced in the kidney only. Tric abundance increased in the gill. Region-specific alterations in ocln, ocln-a and tric mRNA abundance was also observed in the gut. Data support a role for Ocln, Ocln-a and Tric in the osmoregulatory strategies of a basal vertebrate.
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Affiliation(s)
- Dennis Kolosov
- Department of Biology, York University, Toronto, ON, Canada M3J 1P3
- Current address: Department of Biology, McMaster University, Hamilton, ON, Canada L8S 4K1
| | - Phuong Bui
- Department of Biology, York University, Toronto, ON, Canada M3J 1P3
| | - Andrew Donini
- Department of Biology, York University, Toronto, ON, Canada M3J 1P3
| | - Mike P. Wilkie
- Department of Biology, Wilfrid Laurier University, Waterloo, ON, Canada N2L 3C5
| | - Scott P. Kelly
- Department of Biology, York University, Toronto, ON, Canada M3J 1P3
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Nishimiya O, Katsu Y, Inagawa H, Hiramatsu N, Todo T, Hara A. Molecular cloning and characterization of hagfish estrogen receptors. J Steroid Biochem Mol Biol 2017; 165:190-201. [PMID: 27287934 DOI: 10.1016/j.jsbmb.2016.06.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Revised: 06/05/2016] [Accepted: 06/06/2016] [Indexed: 11/17/2022]
Abstract
One or more distinct forms of the nuclear estrogen receptor (ER) have been isolated from many vertebrates to date. To better understand the molecular evolution of ERs, we cloned and characterized er cDNAs from the inshore hagfish, Eptatretus burgeri, a modern representative of the most primitive vertebrates, the agnathans. Two er cDNAs, er1 and er2, were isolated from the liver of a reproductive female hagfish. A phylogenetic analysis placed hagfish ER1 into a position prior to the divergence of vertebrate ERs. Conversely, hagfish ER2 was placed at the base of the vertebrate ERβ clade. The tissue distribution patterns of both ER subtype mRNAs appeared to be different, suggesting that each subtype has different physiological roles associated with estrogen actions. An estrogen responsive-luciferase reporter assay using mammalian HEK293 cells was used to functionally characterize these hagfish ERs. Both ER proteins displayed estrogen-dependent activation of transcription. These results clearly demonstrate that the hagfish has two functional ER subtypes.
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Affiliation(s)
- Osamu Nishimiya
- Laboratory of Fish Reproductive Physiology and Biochemistry, Division of Marine Life Sciences, Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Hokkaido, 041-8611, Japan
| | - Yoshinao Katsu
- Laboratory of Reproductive and Developmental Biology, Department of Biological Sciences, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Hiroyuki Inagawa
- Department of Applied Aquabiology, National Fisheries University, Shimonoseki, Yamaguchi 759-6595, Japan
| | - Naoshi Hiramatsu
- Laboratory of Fish Reproductive Physiology and Biochemistry, Division of Marine Life Sciences, Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Hokkaido, 041-8611, Japan
| | - Takashi Todo
- Laboratory of Fish Reproductive Physiology and Biochemistry, Division of Marine Life Sciences, Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Hokkaido, 041-8611, Japan.
| | - Akihiko Hara
- Laboratory of Fish Reproductive Physiology and Biochemistry, Division of Marine Life Sciences, Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Hokkaido, 041-8611, Japan
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233
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Sotero-Caio CG, Platt RN, Suh A, Ray DA. Evolution and Diversity of Transposable Elements in Vertebrate Genomes. Genome Biol Evol 2017; 9:161-177. [PMID: 28158585 PMCID: PMC5381603 DOI: 10.1093/gbe/evw264] [Citation(s) in RCA: 147] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/06/2016] [Indexed: 12/21/2022] Open
Abstract
Transposable elements (TEs) are selfish genetic elements that mobilize in genomes via transposition or retrotransposition and often make up large fractions of vertebrate genomes. Here, we review the current understanding of vertebrate TE diversity and evolution in the context of recent advances in genome sequencing and assembly techniques. TEs make up 4-60% of assembled vertebrate genomes, and deeply branching lineages such as ray-finned fishes and amphibians generally exhibit a higher TE diversity than the more recent radiations of birds and mammals. Furthermore, the list of taxa with exceptional TE landscapes is growing. We emphasize that the current bottleneck in genome analyses lies in the proper annotation of TEs and provide examples where superficial analyses led to misleading conclusions about genome evolution. Finally, recent advances in long-read sequencing will soon permit access to TE-rich genomic regions that previously resisted assembly including the gigantic, TE-rich genomes of salamanders and lungfishes.
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Affiliation(s)
| | - Roy N. Platt
- Department of Biological Sciences, Texas Tech University, Lubbock, TX
| | - Alexander Suh
- Department of Evolutionary Biology (EBC), Uppsala University, Uppsala, Sweden
| | - David A. Ray
- Department of Biological Sciences, Texas Tech University, Lubbock, TX
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234
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Sebé-Pedrós A, Ruiz-Trillo I. Evolution and Classification of the T-Box Transcription Factor Family. Curr Top Dev Biol 2017; 122:1-26. [DOI: 10.1016/bs.ctdb.2016.06.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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235
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Zavala K, Vandewege MW, Hoffmann FG, Opazo JC. Evolution of the β-adrenoreceptors in vertebrates. Gen Comp Endocrinol 2017; 240:129-137. [PMID: 27769631 DOI: 10.1016/j.ygcen.2016.10.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Revised: 10/13/2016] [Accepted: 10/17/2016] [Indexed: 11/19/2022]
Abstract
The study of the evolutionary history of genes related to human disease lies at the interface of evolution and medicine. These studies provide the evolutionary context on which medical researchers should work, and are also useful in providing information to suggest further genetic experiments, especially in model species where genetic manipulations can be made. Here we studied the evolution of the β-adrenoreceptor gene family in vertebrates with the aim of adding an evolutionary framework to the already abundant physiological information. Our results show that in addition to the three already described vertebrate β-adrenoreceptor genes there is an additional group containing cyclostome sequences. We suggest that β-adrenoreceptors diversified as a product of the two whole genome duplications that occurred in the ancestor of vertebrates. Gene expression patterns are in general consistent across species, suggesting that expression dynamics were established early in the evolutionary history of vertebrates, and have been maintained since then. Finally, amino acid polymorphisms that are associated to pathological conditions in humans appear to be common in non-human mammals, suggesting that the phenotypic effects of these mutations depend on epistatic interaction with other positions. The evolutionary analysis of the β-adrenoreceptors delivers new insights about the diversity of these receptors in vertebrates, the evolution of the expression patterns and a comparative perspective regarding the polymorphisms that in humans are linked to pathological conditions.
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Affiliation(s)
- Kattina Zavala
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
| | - Michael W Vandewege
- Department of Biochemistry, Molecular Biology, Entomology, and Plant Pathology, Mississippi State University, MS, USA
| | - Federico G Hoffmann
- Department of Biochemistry, Molecular Biology, Entomology, and Plant Pathology, Mississippi State University, MS, USA; Institute for Genomics, Biocomputing, and Biotechnology, Mississippi State University, MS, USA
| | - Juan C Opazo
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile.
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236
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XU W, CHEN S. Genomics and genetic breeding in aquatic animals: progress and prospects. FRONTIERS OF AGRICULTURAL SCIENCE AND ENGINEERING 2017; 4:305. [DOI: 10.15302/j-fase-2017154] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/30/2023]
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237
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Siefkes MJ. Use of physiological knowledge to control the invasive sea lamprey ( Petromyzon marinus) in the Laurentian Great Lakes. CONSERVATION PHYSIOLOGY 2017; 5:cox031. [PMID: 28580146 PMCID: PMC5448140 DOI: 10.1093/conphys/cox031] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Revised: 04/21/2017] [Accepted: 05/17/2017] [Indexed: 05/14/2023]
Abstract
Sea lamprey (Petromyzon marinus) control in the Laurentian Great Lakes of North America is an example of using physiological knowledge to successfully control an invasive species and rehabilitate an ecosystem and valuable fishery. The parasitic sea lamprey contributed to the devastating collapse of native fish communities after invading the Great Lakes during the 1800s and early 1900s. Economic tragedy ensued with the loss of the fishery and severe impacts to property values and tourism resulting from sea lamprey-induced ecological changes. To control the sea lamprey and rehabilitate the once vibrant Great Lakes ecosystem and economy, the Great Lakes Fishery Commission (Commission) was formed by treaty between Canada and the United States in 1955. The Commission has developed a sea lamprey control programme based on their physiological vulnerabilities, which includes (i) the application of selective pesticides (lampricides), which successfully kill sedentary sea lamprey larvae in their natal streams; (ii) barriers to spawning migrations and associated traps to prevent infestations of upstream habitats and remove adult sea lamprey before they reproduce; and (iii) the release of sterilized males to reduce the reproductive potential of spawning populations in select streams. Since 1958, the application of the sea lamprey control programme has suppressed sea lamprey populations by ~90% from peak abundance. Great Lakes fish populations have rebounded and the economy is now thriving. In hopes of further enhancing the efficacy and selectivity of the sea lamprey control programme, the Commission is exploring the use of (i) sea lamprey chemosensory cues (pheromones and alarm cues) to manipulate behaviours and physiologies, and (ii) genetics to identify and manipulate genes associated with key physiological functions, for control purposes. Overall, the Commission capitalizes on the unique physiology of the sea lamprey and strives to develop a diverse integrated programme to successfully control a once devastating invasive species.
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Affiliation(s)
- Michael J. Siefkes
- Great Lakes Fishery Commission, 2100 Commonwealth Blvd., Suite 100, Ann Arbor, MI 48105, USA
- Corresponding author: Great Lakes Fishery Commission, 2100 Commonwealth Blvd., Suite 100, Ann Arbor, MI 48105, USA. Tel: +1 7346693013; Fax: +1 7347412010;
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238
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Bayramov AV, Ermakova GV, Eroshkin FM, Kucheryavyy AV, Martynova NY, Zaraisky AG. The presence of Anf/Hesx1 homeobox gene in lampreys suggests that it could play an important role in emergence of telencephalon. Sci Rep 2016; 6:39849. [PMID: 28008996 PMCID: PMC5180219 DOI: 10.1038/srep39849] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 11/28/2016] [Indexed: 12/18/2022] Open
Abstract
Accumulated evidence indicates that the core genetic mechanisms regulating early patterning of the brain rudiment in vertebrates are very similar to those operating during development of the anterior region of invertebrate embryos. However, the mechanisms underlying the morphological differences between the elaborate vertebrate brain and its simpler invertebrate counterpart remain poorly understood. Recently, we hypothesized that the emergence of the most anterior unit of the vertebrate brain, the telencephalon, could be related to the appearance in vertebrates’ ancestors of a unique homeobox gene, Anf/Hesx1(further Anf), which is absent from all invertebrates and regulates the earliest steps of telencephalon development in vertebrates. However, the failure of Anf to be detected in one of the most basal extant vertebrate species, the lamprey, seriously compromises this hypothesis. Here, we report the cloning of Anf in three lamprey species and demonstrate that this gene is indeed expressed in embryos in the same pattern as in other vertebrates and executes the same functions by inhibiting the expression of the anterior general regulator Otx2 in favour of the telencephalic regulator FoxG1. These results are consistent with the hypothesis that the Anf homeobox gene may have been important in the evolution of the telencephalon.
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Affiliation(s)
- Andrey V Bayramov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
| | - Galina V Ermakova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
| | - Fedor M Eroshkin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
| | - Alexandr V Kucheryavyy
- Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Moscow, 119071, Russia
| | - Natalia Y Martynova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
| | - Andrey G Zaraisky
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
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239
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Kollitz EM, Zhang G, Hawkins MB, Whitfield GK, Reif DM, Kullman SW. Evolutionary and Functional Diversification of the Vitamin D Receptor-Lithocholic Acid Partnership. PLoS One 2016; 11:e0168278. [PMID: 27942020 PMCID: PMC5152921 DOI: 10.1371/journal.pone.0168278] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Accepted: 11/28/2016] [Indexed: 01/14/2023] Open
Abstract
The evolution, molecular behavior, and physiological function of nuclear receptors are of particular interest given their diverse roles in regulating essential biological processes. The vitamin D receptor (VDR) is well known for its canonical roles in calcium homeostasis and skeletal maintenance. Additionally, VDR has received an increased amount of attention due to the discovery of numerous non-calcemic functions, including the detoxification of lithocholic acid. Lithocholic acid is a toxic metabolite of chenodeoxycholic acid, a primary bile acid. The partnership between the VDR and lithocholic acid has been hypothesized to be a recent adaptation that evolved to mediate the detoxification and elimination of lithocholic acid from the gut. This partnership is speculated to be limited to higher vertebrates (birds and mammals), as lower vertebrates do not synthesize the parent compound of lithocholic acid. However, the molecular functions associated with the observed insensitivity of basal VDRs to lithocholic acid have not been explored. Here we characterize canonical nuclear receptor functions of VDRs from select species representing key nodes in vertebrate evolution and span a range of bile salt phenotypes. Competitive ligand binding assays revealed that the receptor's affinity for lithocholic acid is highly conserved across species, suggesting that lithocholic acid affinity is an ancient and non-adaptive trait. However, transient transactivation assays revealed that lithocholic acid-mediated VDR activation might have evolved more recently, as the non-mammalian receptors did not respond to lithocholic acid unless exogenous coactivator proteins were co-expressed. Subsequent functional assays indicated that differential lithocholic acid-mediated receptor activation is potentially driven by differential protein-protein interactions between VDR and nuclear receptor coregulator proteins. We hypothesize that the vitamin D receptor-lithocholic acid partnership evolved as a by-product of natural selection on the ligand-receptor partnership between the vitamin D receptor and the native VDR ligand: 1α,25-dihydroxyvitamin D3, the biologically active metabolite of vitamin D3.
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Affiliation(s)
- Erin M. Kollitz
- Toxicology Program, Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina, United States of America
- Nicholas School of the Environment, Duke University, Durham, NC, United States of America
| | - Guozhu Zhang
- Bioinformatics Research Center, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Mary Beth Hawkins
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina, United States of America
| | - G. Kerr Whitfield
- Department of Basic Medical Sciences, The University of Arizona College of Medicine, Phoenix, Arizona, United States of America
| | - David M. Reif
- Bioinformatics Research Center, North Carolina State University, Raleigh, North Carolina, United States of America
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Seth W. Kullman
- Toxicology Program, Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina, United States of America
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240
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Romaus-Sanjurjo D, Fernández-López B, Sobrido-Cameán D, Barreiro-Iglesias A, Rodicio MC. Cloning of the GABA B Receptor Subunits B1 and B2 and their Expression in the Central Nervous System of the Adult Sea Lamprey. Front Neuroanat 2016; 10:118. [PMID: 28008311 PMCID: PMC5143684 DOI: 10.3389/fnana.2016.00118] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Accepted: 11/22/2016] [Indexed: 11/25/2022] Open
Abstract
In vertebrates, γ-aminobutyric acid (GABA) is the main inhibitory transmitter in the central nervous system (CNS) acting through ionotropic (GABAA) and metabotropic (GABAB) receptors. The GABAB receptor produces a slow inhibition since it activates second messenger systems through the binding and activation of guanine nucleotide-binding proteins [G-protein-coupled receptors (GPCRs)]. Lampreys are a key reference to understand molecular evolution in vertebrates. The importance of the GABAB receptor for the modulation of the circuits controlling locomotion and other behaviors has been shown in pharmacological/physiological studies in lampreys. However, there is no data about the sequence of the GABAB subunits or their expression in the CNS of lampreys. Our aim was to identify the sea lamprey GABAB1 and GABAB2 transcripts and study their expression in the CNS of adults. We cloned two partial sequences corresponding to the GABAB1 and GABAB2 cDNAs of the sea lamprey as confirmed by sequence analysis and comparison with known GABAB sequences of other vertebrates. In phylogenetic analyses, the sea lamprey GABAB sequences clustered together with GABABs sequences of vertebrates and emerged as an outgroup to all gnathostome sequences. We observed a broad and overlapping expression of both transcripts in the entire CNS. Expression was mainly observed in neuronal somas of the periventricular regions including the identified reticulospinal cells. No expression was observed in identifiable fibers. Comparison of our results with those reported in other vertebrates indicates that a broad and overlapping expression of the GABAB subunits in the CNS is a conserved character shared by agnathans and gnathostomes.
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Affiliation(s)
- Daniel Romaus-Sanjurjo
- Department of Functional Biology, CIBUS, Faculty of Biology, Universidade de Santiago de Compostela Santiago de Compostela, Spain
| | - Blanca Fernández-López
- Department of Functional Biology, CIBUS, Faculty of Biology, Universidade de Santiago de Compostela Santiago de Compostela, Spain
| | - Daniel Sobrido-Cameán
- Department of Functional Biology, CIBUS, Faculty of Biology, Universidade de Santiago de Compostela Santiago de Compostela, Spain
| | - Antón Barreiro-Iglesias
- Department of Functional Biology, CIBUS, Faculty of Biology, Universidade de Santiago de Compostela Santiago de Compostela, Spain
| | - María Celina Rodicio
- Department of Functional Biology, CIBUS, Faculty of Biology, Universidade de Santiago de Compostela Santiago de Compostela, Spain
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241
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Chen L, Wu F, Yuan S, Feng B. Identification and characteristic of three members of the C1q/TNF-related proteins (CTRPs) superfamily in Eudontomyzon morii. FISH & SHELLFISH IMMUNOLOGY 2016; 59:233-240. [PMID: 27771341 DOI: 10.1016/j.fsi.2016.10.034] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Revised: 10/17/2016] [Accepted: 10/18/2016] [Indexed: 06/06/2023]
Abstract
C1q is the target recognition protein of the classical complement pathway and a major connecting link between innate and acquired immunity. C1q and the multifunctional tumor necrosis factor (TNF) ligand family is of similar crystal structures, are designated the C1q/TNF-related proteins (CTRPs) superfamily. They are involved in processes as diverse as host defense, inflammation, apoptosis, autoimmunity, cell differentiation, organogenesis, hibernation and insulinresistant obesity. In this study, three members of the CTRPs superfamily were isolated and characterized in Yalu River lampreys (Eudontomyzon morii), and are respectively named LaC1qC, LaCTRP1, LaCTRP9. The full-length cDNAs of C1qC-like (LaC1qAL), CTRP1-like (LaCTRP1), and CTRP9-like (LaCTRP9) consist of 723, 762 and 825 bp of nucleotide sequence encoding polypeptides of 241, 254 and 275 amino acids, respectively. All-three proteins share three common domains: a signal peptide at the N terminus, a collagenous domain (characteristic Gly-X-Y repeats), and a C-terminal globular domain. In addition, the higher expression level of the three proteins in heart by RT-PCR and real-time PCR tissue profiling implied that they might involve in immune response or injury repair of the heart in lamprey.
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Affiliation(s)
- Liyong Chen
- Guangdong Province Key Laboratory for Medical Molecular Diagnostics, China-America Cancer Research Institute, Dongguan Scientific Research Center, Guangdong Medical University, Dongguan 523808, China.
| | - Fenfang Wu
- State Key Laboratory of Biocontrol, Guangdong Province Key Laboratory for Pharmaceutical Functional Genes, Department of Biochemistry, School of Life Sciences, Sun Yat-Sen (Zhongshan) University, Guangzhou 510275, China
| | - Shengjian Yuan
- State Key Laboratory of Biocontrol, Guangdong Province Key Laboratory for Pharmaceutical Functional Genes, Department of Biochemistry, School of Life Sciences, Sun Yat-Sen (Zhongshan) University, Guangzhou 510275, China
| | - Bo Feng
- State Key Laboratory of Biocontrol, Guangdong Province Key Laboratory for Pharmaceutical Functional Genes, Department of Biochemistry, School of Life Sciences, Sun Yat-Sen (Zhongshan) University, Guangzhou 510275, China
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242
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Clower MK, Holub AS, Smith RT, Wyngaard GA. EMBRYONIC DEVELOPMENT AND A QUANTITATIVE MODEL OF PROGRAMMED DNA ELIMINATION IN MESOCYCLOPS EDAX (S. A. FORBES, 1891) (COPEPODA: CYCLOPOIDA). JOURNAL OF CRUSTACEAN BIOLOGY : A QUARTERLY OF THE CRUSTACEAN SOCIETY FOR THE PUBLICATION OF RESEARCH ON ANY ASPECT OF THE BIOLOGY OF CRUSTACEA 2016; 36:661-674. [PMID: 27857452 PMCID: PMC5110247 DOI: 10.1163/1937240x-00002473] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The highly programmed fragmentation of chromosomes and elimination of large amounts of nuclear DNA from the presomatic cell lineages (i.e., chromatin diminution), occurs in the embryos of the freshwater zooplankton Mesocyclops edax (S. A. Forbes, 1891) (Crustacea: Copepoda). The somatic genome is reorganized and reduced to a size five times smaller even though the germline genome remains intact. We present the first comprehensive, quantitative model of DNA content throughout embryogenesis in a copepod that possesses embryonic DNA elimination. We used densitometric image analysis to measure the DNA content of polar bodies, germline and somatic nuclei, and excised DNA "droplets." We report: 1) variable DNA contents of polar bodies, some of which do not contain the amount corresponding to the haploid germline genome size; 2) presence of pronuclei in newly laid embryo sacs; 3) gonomeric chromosomes in the second to fourth cleavage divisions and in the primordial germ cell and primordial endoderm cell during the fifth cleavage division; 4) timing of early embryonic cell stages, elimination of DNA, and divisions of the primordial germ cell and primordial endoderm cell at 22°C; and 5) persistence of a portion of the excised DNA "droplets" throughout embryogenesis. DNA elimination is a trait that spans multiple embryonic stages and a knowledge of the timing and variability of the associated cytological events with DNA elimination will promote the study of the molecular mechanisms involved in this trait. We propose the "genome yolk hypothesis" as a functional explanation for the persistence of the eliminated DNA that might serve as a resource during postdiminution cleavage divisions.
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Affiliation(s)
- Michelle K. Clower
- North Carolina Coastal Federation, 128 Grenville St., Manteo, NC 27954, USA
| | - Ashton S. Holub
- Department of Biology, MSC 7801, James Madison University, Harrisonburg, VA 22807, USA
| | - Rebecca T. Smith
- Eastern Shore Laboratory, Virginia Institute of Marine Science, Wachapreague, VA 23480, USA
| | - Grace A. Wyngaard
- Department of Biology, MSC 7801, James Madison University, Harrisonburg, VA 22807, USA
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243
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Orquera DP, de Souza FSJ. Evolution of the Rax family of developmental transcription factors in vertebrates. Mech Dev 2016; 144:163-170. [PMID: 27838261 DOI: 10.1016/j.mod.2016.11.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2016] [Revised: 11/01/2016] [Accepted: 11/07/2016] [Indexed: 02/09/2023]
Abstract
Rax proteins comprise a small family of paired-type, homeodomain-containing transcription factors with essential functions in eye and forebrain development. While invertebrates possess only one Rax gene, vertebrates can have several Rax paralogue genes, but the evolutionary history of the members of the family has not been studied in detail. Here, we present a thorough analysis of the evolutionary relationships between vertebrate Rax genes and proteins available in diverse genomic databases. Phylogenetic and synteny analyses indicate that Rax genes went through a duplication in an ancestor of all jawed vertebrates (Gnathostomata), giving rise to the ancestral vertebrate Rax1 and Rax2 genes. This duplication event is likely related to the proposed polyploidisations that occurred during early vertebrate evolution. Subsequent genome-wide duplications in the lineage of ray-finned fish (Actinopterygii) originated new Rax2 paralogues in the genomes of teleosts. In the lobe-finned fish lineage (Sarcopterygii), the N-terminal octapeptide domain of Rax2 was lost in a common ancestor of tetrapods, giving rise to a shorter version of Rax2 in this lineage. Within placental mammals, the Rax2 gene was lost altogether in an ancestor of rodents and lagomorphs (Glires). Finally, we discuss the scientific literature in the light of Rax gene evolution and propose new avenues of research on the function of this important family of transcriptional regulators.
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Affiliation(s)
- Daniela P Orquera
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular, Consejo Nacional de Investigaciones Científicas y Técnicas, 1428 Buenos Aires, Argentina
| | - Flávio S J de Souza
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular, Consejo Nacional de Investigaciones Científicas y Técnicas, 1428 Buenos Aires, Argentina; Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, 1428 Buenos Aires, Argentina.
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244
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Suzuki A, Komata H, Iwashita S, Seto S, Ikeya H, Tabata M, Kitano T. Evolution of the RH gene family in vertebrates revealed by brown hagfish (Eptatretus atami) genome sequences. Mol Phylogenet Evol 2016; 107:1-9. [PMID: 27746317 DOI: 10.1016/j.ympev.2016.10.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Revised: 10/04/2016] [Accepted: 10/08/2016] [Indexed: 01/02/2023]
Abstract
In vertebrates, there are four major genes in the RH (Rhesus) gene family, RH, RHAG, RHBG, and RHCG. These genes are thought to have been formed by the two rounds of whole-genome duplication (2R-WGD) in the common ancestor of all vertebrates. In our previous work, where we analyzed details of the gene duplications process of this gene family, three nucleotide sequences belonging to this family were identified in Far Eastern brook lamprey (Lethenteron reissneri), and the phylogenetic positions of the genes were determined. Lampreys, along with hagfishes, are cyclostomata (jawless fishes), which is a sister group of gnathostomata (jawed vertebrates). Although those results suggested that one gene was orthologous to the gnathostome RHCG genes, we did not identify clear orthologues for other genes. In this study, therefore, we identified three novel cDNA sequences that belong to the RH gene family using de novo transcriptome analysis of another cyclostome: the brown hagfish (Eptatretus atami). We also determined the nucleotide sequences for the RHBG and RHCG genes in a red stingray (Dasyatis akajei), which belongs to the cartilaginous fishes. The phylogenetic tree showed that two brown hagfish genes, which were probably duplicated in the cyclostome lineage, formed a cluster with the gnathostome RHAG genes, whereas another brown hagfish gene formed a cluster with the gnathostome RHCG genes. We estimated that the RH genes had a higher evolutionary rate than the RHAG, RHBG, and RHCG genes. Interestingly, in the RHBG genes, only the bird lineage showed a higher rate of nonsynonymous substitutions. It is likely that this higher rate was caused by a state of relaxed functional constraints rather than positive selection nor by pseudogenization.
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Affiliation(s)
- Akinori Suzuki
- Department of Biomolecular Functional Engineering, College of Engineering, Ibaraki University, 4-12-1 Nakanarusawa-cho, Hitachi 316-8511, Japan
| | - Hidero Komata
- Department of Biomolecular Functional Engineering, College of Engineering, Ibaraki University, 4-12-1 Nakanarusawa-cho, Hitachi 316-8511, Japan
| | - Shogo Iwashita
- Department of Biomolecular Functional Engineering, College of Engineering, Ibaraki University, 4-12-1 Nakanarusawa-cho, Hitachi 316-8511, Japan
| | - Shotaro Seto
- Department of Biomolecular Functional Engineering, College of Engineering, Ibaraki University, 4-12-1 Nakanarusawa-cho, Hitachi 316-8511, Japan
| | - Hironobu Ikeya
- Department of Biomolecular Functional Engineering, College of Engineering, Ibaraki University, 4-12-1 Nakanarusawa-cho, Hitachi 316-8511, Japan
| | - Mitsutoshi Tabata
- Department of Biomolecular Functional Engineering, College of Engineering, Ibaraki University, 4-12-1 Nakanarusawa-cho, Hitachi 316-8511, Japan
| | - Takashi Kitano
- Department of Biomolecular Functional Engineering, College of Engineering, Ibaraki University, 4-12-1 Nakanarusawa-cho, Hitachi 316-8511, Japan.
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Tostivint H, Dettaï A, Quan FB, Ravi V, Tay BH, Rodicio MC, Mazan S, Venkatesh B, Kenigfest NB. Identification of three somatostatin genes in lampreys. Gen Comp Endocrinol 2016; 237:89-97. [PMID: 27524287 DOI: 10.1016/j.ygcen.2016.08.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Revised: 07/29/2016] [Accepted: 08/11/2016] [Indexed: 12/17/2022]
Abstract
Somatostatins (SSs) are a structurally diverse family of neuropeptides that play important roles in the regulation of growth, development and metabolism in vertebrates. It has been recently proposed that the common ancestor of gnathostomes possessed three SS genes, namely SS1, SS2 and SS5. SS1 and SS2 are still present in most extant gnathostome species investigated so far while SS5 primarily occurs in chondrichthyes, actinopterygians and actinistia but not in tetrapods. Very little is known about the repertoire of SSs in cyclostomes, which are extant jawless vertebrates. In the present study, we report the cloning of the cDNAs encoding three distinct lamprey SS variants that we call SSa, SSb and SSc. SSa and SSb correspond to the two SS variants previously characterized in lamprey, while SSc appears to be a totally novel one. SSa exhibits the same sequence as gnathostome SS1. SSb differs from SSa by only one substitution (Thr12→Ser). SSc exhibits a totally unique structure (ANCRMFYWKTMAAC) that shares only 50% identity with SSa and SSb. SSa, SSb and SSc precursors do not exhibit any appreciable sequence similarity outside the C-terminal region containing the SS sequence. Phylogenetic analyses failed to clearly assign orthology relationships between lamprey and gnathostome SS genes. Synteny analysis suggests that the SSc gene arose before the split of the three gnathostome genes SS1, SS2 and SS5.
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Affiliation(s)
- Hervé Tostivint
- Evolution des Régulations Endocriniennes, UMR 7221 CNRS, Muséum National d'Histoire Naturelle, Sorbonne Université, Paris, France.
| | - Agnès Dettaï
- Institut de systématique et Evolution, UMR 7205 CNRS, UMPC, EPHE, Muséum National d'Histoire Naturelle, Sorbonne Université, Paris, France
| | - Feng B Quan
- Evolution des Régulations Endocriniennes, UMR 7221 CNRS, Muséum National d'Histoire Naturelle, Sorbonne Université, Paris, France
| | - Vydianathan Ravi
- Institute of Molecular and Cell Biology, A(∗)STAR, Biopolis, Singapore
| | - Boon-Hui Tay
- Institute of Molecular and Cell Biology, A(∗)STAR, Biopolis, Singapore
| | - Maria Celina Rodicio
- Department of Cell Biology and Ecology, CIBUS, Faculty of Biology, University of Santiago de Compostela, Spain
| | - Sylvie Mazan
- Biologie Intégrative des Organismes Marins, UMR 7232 CNRS, Observatoire Océanologique, Université Pierre et Marie Curie, Sorbonne Université, Banyuls-sur-Mer, France
| | - Byrappa Venkatesh
- Institute of Molecular and Cell Biology, A(∗)STAR, Biopolis, Singapore
| | - Natalia B Kenigfest
- Evolution des Régulations Endocriniennes, UMR 7221 CNRS, Muséum National d'Histoire Naturelle, Sorbonne Université, Paris, France; Laboratory of Molecular Mechanisms of Neuronal Interactions, Sechenov Insitute of Evolutionary Physiology and Biochemistry, Russian Academy of Sciences, St. Petersburg, Russia
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246
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A pre-metazoan origin of the CRK gene family and co-opted signaling network. Sci Rep 2016; 6:34349. [PMID: 27686861 PMCID: PMC5043372 DOI: 10.1038/srep34349] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Accepted: 08/11/2016] [Indexed: 12/11/2022] Open
Abstract
CRK and CRKL adapter proteins play essential roles in development and cancer through their SRC homology 2 and 3 (SH2 and SH3) domains. To gain insight into the origin of their shared functions, we have investigated their evolutionary history. We propose a term, crk/crkl ancestral (crka), for orthologs in invertebrates before the divergence of CRK and CRKL in the vertebrate ancestor. We have isolated two orthologs expressed in the choanoflagellate Monosiga brevicollis, a unicellular relative to the metazoans. Consistent with its highly-conserved three-dimensional structure, the SH2 domain of M. brevicollis crka1 can bind to the mammalian CRK/CRKL SH2 binding consensus phospho-YxxP, and to the SRC substrate/focal adhesion protein BCAR1 (p130CAS) in the presence of activated SRC. These results demonstrate an ancient origin of the CRK/CRKL SH2-target recognition specificity. Although BCAR1 orthologs exist only in metazoans as identified by an N-terminal SH3 domain, YxxP motifs, and a C-terminal FAT-like domain, some pre-metazoan transmembrane proteins include several YxxP repeats in their cytosolic region, suggesting that they are remotely related to the BCAR1 substrate domain. Since the tyrosine kinase SRC also has a pre-metazoan origin, co-option of BCAR1-related sequences may have rewired the crka-dependent network to mediate adhesion signals in the metazoan ancestor.
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247
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Abstract
Polyploidy-the increase in the number of whole chromosome sets-is an important evolutionary force in eukaryotes. Polyploidy is well recognized throughout the evolutionary history of plants and animals, where several ancient events have been hypothesized to be drivers of major evolutionary radiations. However, fungi provide a striking contrast: while numerous recent polyploids have been documented, ancient fungal polyploidy is virtually unknown. We present a survey of known fungal polyploids that confirms the absence of ancient fungal polyploidy events. Three hypotheses may explain this finding. First, ancient fungal polyploids are indeed rare, with unique aspects of fungal biology providing similar benefits without genome duplication. Second, fungal polyploids are not successful in the long term, leading to few extant species derived from ancient polyploidy events. Third, ancient fungal polyploids are difficult to detect, causing the real contribution of polyploidy to fungal evolution to be underappreciated. We consider each of these hypotheses in turn and propose that failure to detect ancient events is the most likely reason for the lack of observed ancient fungal polyploids. We examine whether existing data can provide evidence for previously unrecognized ancient fungal polyploidy events but discover that current resources are too limited. We contend that establishing whether unrecognized ancient fungal polyploidy events exist is important to ascertain whether polyploidy has played a key role in the evolution of the extensive complexity and diversity observed in fungi today and, thus, whether polyploidy is a driver of evolutionary diversifications across eukaryotes. Therefore, we conclude by suggesting ways to test the hypothesis that there are unrecognized polyploidy events in the deep evolutionary history of the fungi.
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248
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Katsu Y, Cziko PA, Chandsawangbhuwana C, Thornton JW, Sato R, Oka K, Takei Y, Baker ME, Iguchi T. A second estrogen receptor from Japanese lamprey (Lethenteron japonicum) does not have activities for estrogen binding and transcription. Gen Comp Endocrinol 2016; 236:105-114. [PMID: 27432813 DOI: 10.1016/j.ygcen.2016.07.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Revised: 06/28/2016] [Accepted: 07/14/2016] [Indexed: 11/30/2022]
Abstract
Estrogens regulate many physiological responses in vertebrates by binding to the estrogen receptor (ER), a ligand-activated transcription factor. To understand the evolution of vertebrate ERs and to investigate how estrogen acts in a jawless vertebrate, we used degenerate primer sets and PCR to isolate DNA fragments encoding two distinct ER subtypes, Esr1a and Esr1b from the Japanese lamprey, Lethenteron japonicum. Phylogenetic analysis indicates that these two ERs are the result of lineage-specific gene duplication within the jawless fishes, different from the previous duplication event of Esr1 (ERα) and Esr2 (ERβ) within the jawed vertebrates. Reporter gene assays show that lamprey Esr1a displays both constitutive and estrogen-dependent activation of gene transcription. Domain swapping experiments indicate that constitutive activity resides in the A/B domain of lamprey Esr1a. Unexpectedly, lamprey Esr1b does not bind estradiol and is not stimulated by other estrogens, androgens or corticosteroids. A 3D model of lamprey Esr1b suggests that although estradiol fits into the steroid binding site, some stabilizing contacts between the ligand and side chains that are found in human Esr1 and Esr2 are missing in lamprey Esr1b.
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Affiliation(s)
- Yoshinao Katsu
- Department of Biological Sciences, Hokkaido University, Sapporo, Japan; Graduate School of Life Science, Hokkaido University, Sapporo, Japan; Okazaki Institute for Integrative Bioscience, National Institutes of Natural Sciences, Okazaki, Japan
| | - Paul A Cziko
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, USA
| | | | - Joseph W Thornton
- Departments of Ecology and Evolution and Human Genetics, University of Chicago, Chicago, IL, USA
| | - Rui Sato
- Graduate School of Life Science, Hokkaido University, Sapporo, Japan
| | - Koari Oka
- Graduate School of Life Science, Hokkaido University, Sapporo, Japan
| | - Yoshio Takei
- Atmosphere and Ocean Research Institute, The University of Tokyo, Chiba, Japan
| | - Michael E Baker
- Department of Medicine, University of California, San Diego, CA, USA
| | - Taisen Iguchi
- Okazaki Institute for Integrative Bioscience, National Institutes of Natural Sciences, Okazaki, Japan; National Institute for Basic Biology, Okazaki, Japan.
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Karaz S, Courgeon M, Lepetit H, Bruno E, Pannone R, Tarallo A, Thouzé F, Kerner P, Vervoort M, Causeret F, Pierani A, D'Onofrio G. Neuronal fate specification by the Dbx1 transcription factor is linked to the evolutionary acquisition of a novel functional domain. EvoDevo 2016; 7:18. [PMID: 27525057 PMCID: PMC4983035 DOI: 10.1186/s13227-016-0055-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Accepted: 07/27/2016] [Indexed: 12/18/2022] Open
Abstract
Background Dbx1 is a homeodomain transcription factor involved in neuronal fate specification belonging to a widely conserved family among bilaterians. In mammals, Dbx1 was proposed to act as a transcriptional repressor by interacting with the Groucho corepressors to allow the specification of neurons involved in essential biological functions such as locomotion or breathing. Results Sequence alignments of Dbx1 proteins from different species allowed us to identify two conserved domains related to the Groucho-dependent Engrailed repressor domain (RD), as well as a newly described domain composed of clusterized acidic residues at the C-terminus (Cter) which is present in tetrapods but also several invertebrates. Using a heterologous luciferase assay, we showed that the two putative repressor domains behave as such in a Groucho-dependent manner, whereas the Cter does not bear any intrinsic transcriptional activity. Consistently with in vitro data, we found that both RDs are involved in cell fate specification using in vivo electroporation experiments in the chick spinal cord. Surprisingly, we show that the Cter domain is required for Dbx1 function in vivo, acting as a modulator of its repressive activity and/or imparting specificity. Conclusion Our results strongly suggest that the presence of a Cter domain among tetrapods is essential for Dbx1 to regulate neuronal diversity and, in turn, nervous system complexity. Electronic supplementary material The online version of this article (doi:10.1186/s13227-016-0055-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sonia Karaz
- Institut Jacques Monod, CNRS UMR 7592, Université Paris Diderot, Sorbonne Paris Cité, 75205 Paris Cedex, France
| | - Maximilien Courgeon
- Institut Jacques Monod, CNRS UMR 7592, Université Paris Diderot, Sorbonne Paris Cité, 75205 Paris Cedex, France
| | - Hélène Lepetit
- Institut Jacques Monod, CNRS UMR 7592, Université Paris Diderot, Sorbonne Paris Cité, 75205 Paris Cedex, France
| | - Eugenia Bruno
- Dept. BEOM, Stazione Zoologica A. Dohrn, Villa Comunale, 80121 Naples, Italy
| | - Raimondo Pannone
- Dept. BEOM, Stazione Zoologica A. Dohrn, Villa Comunale, 80121 Naples, Italy
| | - Andrea Tarallo
- Dept. BEOM, Stazione Zoologica A. Dohrn, Villa Comunale, 80121 Naples, Italy
| | - France Thouzé
- Institut Jacques Monod, CNRS UMR 7592, Université Paris Diderot, Sorbonne Paris Cité, 75205 Paris Cedex, France
| | - Pierre Kerner
- Institut Jacques Monod, CNRS UMR 7592, Université Paris Diderot, Sorbonne Paris Cité, 75205 Paris Cedex, France
| | - Michel Vervoort
- Institut Jacques Monod, CNRS UMR 7592, Université Paris Diderot, Sorbonne Paris Cité, 75205 Paris Cedex, France
| | - Frédéric Causeret
- Institut Jacques Monod, CNRS UMR 7592, Université Paris Diderot, Sorbonne Paris Cité, 75205 Paris Cedex, France
| | - Alessandra Pierani
- Institut Jacques Monod, CNRS UMR 7592, Université Paris Diderot, Sorbonne Paris Cité, 75205 Paris Cedex, France
| | - Giuseppe D'Onofrio
- Dept. BEOM, Stazione Zoologica A. Dohrn, Villa Comunale, 80121 Naples, Italy
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Noutahi E, Semeria M, Lafond M, Seguin J, Boussau B, Guéguen L, El-Mabrouk N, Tannier E. Efficient Gene Tree Correction Guided by Genome Evolution. PLoS One 2016; 11:e0159559. [PMID: 27513924 PMCID: PMC4981423 DOI: 10.1371/journal.pone.0159559] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Accepted: 07/04/2016] [Indexed: 12/31/2022] Open
Abstract
MOTIVATIONS Gene trees inferred solely from multiple alignments of homologous sequences often contain weakly supported and uncertain branches. Information for their full resolution may lie in the dependency between gene families and their genomic context. Integrative methods, using species tree information in addition to sequence information, often rely on a computationally intensive tree space search which forecloses an application to large genomic databases. RESULTS We propose a new method, called ProfileNJ, that takes a gene tree with statistical supports on its branches, and corrects its weakly supported parts by using a combination of information from a species tree and a distance matrix. Its low running time enabled us to use it on the whole Ensembl Compara database, for which we propose an alternative, arguably more plausible set of gene trees. This allowed us to perform a genome-wide analysis of duplication and loss patterns on the history of 63 eukaryote species, and predict ancestral gene content and order for all ancestors along the phylogeny. AVAILABILITY A web interface called RefineTree, including ProfileNJ as well as a other gene tree correction methods, which we also test on the Ensembl gene families, is available at: http://www-ens.iro.umontreal.ca/~adbit/polytomysolver.html. The code of ProfileNJ as well as the set of gene trees corrected by ProfileNJ from Ensembl Compara version 73 families are also made available.
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Affiliation(s)
- Emmanuel Noutahi
- Département d’Informatique (DIRO), Université de Montréal, H3C3J7 Montréal, Canada
| | - Magali Semeria
- LBBE, UMR CNRS 5558, Université de Lyon 1, F-69622 Villeurbanne, France
| | - Manuel Lafond
- Département d’Informatique (DIRO), Université de Montréal, H3C3J7 Montréal, Canada
| | - Jonathan Seguin
- Département d’Informatique (DIRO), Université de Montréal, H3C3J7 Montréal, Canada
| | - Bastien Boussau
- LBBE, UMR CNRS 5558, Université de Lyon 1, F-69622 Villeurbanne, France
| | - Laurent Guéguen
- LBBE, UMR CNRS 5558, Université de Lyon 1, F-69622 Villeurbanne, France
| | - Nadia El-Mabrouk
- Département d’Informatique (DIRO), Université de Montréal, H3C3J7 Montréal, Canada
| | - Eric Tannier
- LBBE, UMR CNRS 5558, Université de Lyon 1, F-69622 Villeurbanne, France
- INRIA Grenoble Rhône-Alpes, F-38334 Montbonnot, France
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