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Yu D, Ren Y, Uesaka M, Beavan AJS, Muffato M, Shen J, Li Y, Sato I, Wan W, Clark JW, Keating JN, Carlisle EM, Dearden RP, Giles S, Randle E, Sansom RS, Feuda R, Fleming JF, Sugahara F, Cummins C, Patricio M, Akanni W, D'Aniello S, Bertolucci C, Irie N, Alev C, Sheng G, de Mendoza A, Maeso I, Irimia M, Fromm B, Peterson KJ, Das S, Hirano M, Rast JP, Cooper MD, Paps J, Pisani D, Kuratani S, Martin FJ, Wang W, Donoghue PCJ, Zhang YE, Pascual-Anaya J. Hagfish genome elucidates vertebrate whole-genome duplication events and their evolutionary consequences. Nat Ecol Evol 2024; 8:519-535. [PMID: 38216617 DOI: 10.1038/s41559-023-02299-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 12/04/2023] [Indexed: 01/14/2024]
Abstract
Polyploidy or whole-genome duplication (WGD) is a major event that drastically reshapes genome architecture and is often assumed to be causally associated with organismal innovations and radiations. The 2R hypothesis suggests that two WGD events (1R and 2R) occurred during early vertebrate evolution. However, the timing of the 2R event relative to the divergence of gnathostomes (jawed vertebrates) and cyclostomes (jawless hagfishes and lampreys) is unresolved and whether these WGD events underlie vertebrate phenotypic diversification remains elusive. Here we present the genome of the inshore hagfish, Eptatretus burgeri. Through comparative analysis with lamprey and gnathostome genomes, we reconstruct the early events in cyclostome genome evolution, leveraging insights into the ancestral vertebrate genome. Genome-wide synteny and phylogenetic analyses support a scenario in which 1R occurred in the vertebrate stem-lineage during the early Cambrian, and 2R occurred in the gnathostome stem-lineage, maximally in the late Cambrian-earliest Ordovician, after its divergence from cyclostomes. We find that the genome of stem-cyclostomes experienced an additional independent genome triplication. Functional genomic and morphospace analyses demonstrate that WGD events generally contribute to developmental evolution with similar changes in the regulatory genome of both vertebrate groups. However, appreciable morphological diversification occurred only in the gnathostome but not in the cyclostome lineage, calling into question the general expectation that WGDs lead to leaps of bodyplan complexity.
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Affiliation(s)
- Daqi Yu
- Key Laboratory of Zoological Systematics and Evolution and State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yandong Ren
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China
| | - Masahiro Uesaka
- Laboratory for Evolutionary Morphology, RIKEN Center for Biosystems Dynamics Research (BDR), Kobe, Japan
- Department of Ecological Developmental Adaptability Life Sciences, Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - Alan J S Beavan
- Bristol Palaeobiology Group, School of Biological Sciences, University of Bristol, Bristol, UK
- School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Matthieu Muffato
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
- Tree of Life, Wellcome Sanger Institute, Hinxton, UK
| | - Jieyu Shen
- Key Laboratory of Zoological Systematics and Evolution and State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yongxin Li
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China
| | - Iori Sato
- Laboratory for Evolutionary Morphology, RIKEN Center for Biosystems Dynamics Research (BDR), Kobe, Japan
- iPS Cell Advanced Characterization and Development Team, RIKEN BioResource Research Center, Tsukuba, Japan
| | - Wenting Wan
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China
| | - James W Clark
- Bristol Palaeobiology Group, School of Biological Sciences, University of Bristol, Bristol, UK
- Milner Centre for Evolution, University of Bath, Claverton Down, Bath, UK
| | - Joseph N Keating
- Bristol Palaeobiology Group, School of Earth Sciences, University of Bristol, Bristol, UK
| | - Emily M Carlisle
- Bristol Palaeobiology Group, School of Earth Sciences, University of Bristol, Bristol, UK
| | - Richard P Dearden
- School of Geography, Earth and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham, UK
- Naturalis Biodiversity Center, Leiden, the Netherlands
| | - Sam Giles
- School of Geography, Earth and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham, UK
| | - Emma Randle
- Department of Earth and Environmental Sciences, University of Manchester, Manchester, UK
| | - Robert S Sansom
- Department of Earth and Environmental Sciences, University of Manchester, Manchester, UK
| | - Roberto Feuda
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - James F Fleming
- Keio University Institute for Advanced Biosciences, Tsuruoka, Japan
- Natural History Museum, University of Oslo, Oslo, Norway
| | - Fumiaki Sugahara
- Division of Biology, Hyogo Medical University, Nishinomiya, Japan
- Evolutionary Morphology Laboratory, RIKEN Cluster for Pioneering Research (CPR), Kobe, Japan
| | - Carla Cummins
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Mateus Patricio
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Wasiu Akanni
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Salvatore D'Aniello
- Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn Napoli, Villa Comunale, Napoli, Italy
| | - Cristiano Bertolucci
- Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn Napoli, Villa Comunale, Napoli, Italy
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Naoki Irie
- Research Center for Integrative Evolutionary Science, The Graduate University for Advanced Studies, SOKENDAI, Hayama, Japan
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Cantas Alev
- Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Kyoto, Japan
| | - Guojun Sheng
- International Research Center for Medical Sciences (IRCMS), Kumamoto University, Kumamoto, Japan
| | - Alex de Mendoza
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | - Ignacio Maeso
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona (UB), Barcelona, Spain
- Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona (UB), Barcelona, Spain
| | - Manuel Irimia
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- ICREA, Barcelona, Spain
| | - Bastian Fromm
- The Arctic University Museum of Norway, UiT - The Arctic University of Norway, Tromsø, Norway
| | - Kevin J Peterson
- Department of Biological Sciences, Dartmouth College, Hanover, NH, USA
| | - Sabyasachi Das
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA, USA
- Emory Vaccine Center, Emory University, Atlanta, GA, USA
| | - Masayuki Hirano
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA, USA
- Emory Vaccine Center, Emory University, Atlanta, GA, USA
| | - Jonathan P Rast
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA, USA
- Emory Vaccine Center, Emory University, Atlanta, GA, USA
| | - Max D Cooper
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA, USA
- Emory Vaccine Center, Emory University, Atlanta, GA, USA
| | - Jordi Paps
- Bristol Palaeobiology Group, School of Earth Sciences, University of Bristol, Bristol, UK
| | - Davide Pisani
- Bristol Palaeobiology Group, School of Biological Sciences, University of Bristol, Bristol, UK
- Bristol Palaeobiology Group, School of Earth Sciences, University of Bristol, Bristol, UK
| | - Shigeru Kuratani
- Laboratory for Evolutionary Morphology, RIKEN Center for Biosystems Dynamics Research (BDR), Kobe, Japan
- Evolutionary Morphology Laboratory, RIKEN Cluster for Pioneering Research (CPR), Kobe, Japan
| | - Fergal J Martin
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK.
| | - Wen Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China.
- CAS Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China.
| | - Philip C J Donoghue
- Bristol Palaeobiology Group, School of Earth Sciences, University of Bristol, Bristol, UK.
| | - Yong E Zhang
- Key Laboratory of Zoological Systematics and Evolution and State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.
- University of Chinese Academy of Sciences, Beijing, China.
- CAS Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China.
| | - Juan Pascual-Anaya
- Evolutionary Morphology Laboratory, RIKEN Cluster for Pioneering Research (CPR), Kobe, Japan.
- Department of Animal Biology, Faculty of Science, University of Málaga (UMA), Málaga, Spain.
- Edificio de Bioinnovación, Universidad de Málaga, Málaga, Spain.
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Papadogiannis V, Hockman D, Mercurio S, Ramsay C, Hintze M, Patthey C, Streit A, Shimeld SM. Evolution of the expression and regulation of the nuclear hormone receptor ERR gene family in the chordate lineage. Dev Biol 2023; 504:12-24. [PMID: 37696353 DOI: 10.1016/j.ydbio.2023.09.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 09/01/2023] [Accepted: 09/09/2023] [Indexed: 09/13/2023]
Abstract
The Estrogen Related Receptor (ERR) nuclear hormone receptor genes have a wide diversity of roles in vertebrate development. In embryos, ERR genes are expressed in several tissues, including the central and peripheral nervous systems. Here we seek to establish the evolutionary history of chordate ERR genes, their expression and their regulation. We examine ERR expression in mollusc, amphioxus and sea squirt embryos, finding the single ERR orthologue is expressed in the nervous system in all three, with muscle expression also found in the two chordates. We show that most jawed vertebrates and lampreys have four ERR paralogues, and that vertebrate ERR genes were ancestrally linked to Estrogen Receptor genes. One of the lamprey paralogues shares conserved expression domains with jawed vertebrate ERRγ in the embryonic vestibuloacoustic ganglion, eye, brain and spinal cord. Hypothesising that conserved expression derives from conserved regulation, we identify a suite of pan-vertebrate conserved non-coding sequences in ERR introns. We use transgenesis in lamprey and chicken embryos to show that these sequences are regulatory and drive reporter gene expression in the nervous system. Our data suggest an ancient association between ERR and the nervous system, including expression in cells associated with photosensation and mechanosensation. This includes the origin in the vertebrate common ancestor of a suite of regulatory elements in the 3' introns that drove nervous system expression and have been conserved from this point onwards.
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Affiliation(s)
| | - Dorit Hockman
- Division of Cell Biology, Department of Human Biology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa; Neuroscience Institute, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Silvia Mercurio
- Department of Environmental Science and Policy, Università Degli Studi di Milano, Via Celoria 2, 20133, Milano, Italy
| | - Claire Ramsay
- Department of Biology, University of Oxford, 11a Mansfield Road, Oxford, OX1 3SZ, UK
| | - Mark Hintze
- Centre for Craniofacial & Regenerative Biology, Faculty of Dentistry, Oral and Craniofacial Sciences, King's College London, London, UK
| | - Cedric Patthey
- Department of Radiosciences, Umeå University, 901 85, Umeå, Sweden
| | - Andrea Streit
- Centre for Craniofacial & Regenerative Biology, Faculty of Dentistry, Oral and Craniofacial Sciences, King's College London, London, UK
| | - Sebastian M Shimeld
- Department of Biology, University of Oxford, 11a Mansfield Road, Oxford, OX1 3SZ, UK.
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3
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Bhalla D, van Noort V. Molecular Evolution of Aryl Hydrocarbon Receptor Signaling Pathway Genes. J Mol Evol 2023; 91:628-646. [PMID: 37392220 DOI: 10.1007/s00239-023-10124-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 06/13/2023] [Indexed: 07/03/2023]
Abstract
The Aryl hydrocarbon receptor is an ancient transcriptional factor originally discovered as a sensor of dioxin. In addition to its function as a receptor of environmental toxicants, it plays an important role in development. Although a significant amount of research has been carried out to understand the AHR signal transduction pathway and its involvement in species' susceptibility to environmental toxicants, none of them to date has comprehensively studied its evolutionary origins. Studying the evolutionary origins of molecules can inform ancestral relationships of genes. The vertebrate genome has been shaped by two rounds of whole-genome duplications (WGD) at the base of vertebrate evolution approximately 600 million years ago, followed by lineage-specific gene losses, which often complicate the assignment of orthology. It is crucial to understand the evolutionary origins of this transcription factor and its partners, to distinguish orthologs from ancient non-orthologous homologs. In this study, we have investigated the evolutionary origins of proteins involved in the AHR pathway. Our results provide evidence of gene loss and duplications, crucial for understanding the functional connectivity of humans and model species. Multiple studies have shown that 2R-ohnologs (genes and proteins that have survived from the 2R-WGD) are enriched in signaling components relevant to developmental disorders and cancer. Our findings provide a link between the AHR pathway's evolutionary trajectory and its potential mechanistic involvement in pathogenesis.
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Affiliation(s)
- Diksha Bhalla
- Centre of Microbial and Plant Genetics, Faculty of Bioscience Engineering, KU Leuven, Leuven, Belgium.
| | - Vera van Noort
- Centre of Microbial and Plant Genetics, Faculty of Bioscience Engineering, KU Leuven, Leuven, Belgium
- Institute of Biology Leiden, Leiden University, Leiden, The Netherlands
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4
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Marlétaz F, Timoshevskaya N, Timoshevskiy V, Simakov O, Parey E, Gavriouchkina D, Suzuki M, Kubokawa K, Brenner S, Smith J, Rokhsar DS. The hagfish genome and the evolution of vertebrates. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.17.537254. [PMID: 37131617 PMCID: PMC10153176 DOI: 10.1101/2023.04.17.537254] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
As the only surviving lineages of jawless fishes, hagfishes and lampreys provide a critical window into early vertebrate evolution. Here, we investigate the complex history, timing, and functional role of genome-wide duplications in vertebrates in the light of a chromosome-scale genome of the brown hagfish Eptatretus atami. Using robust chromosome-scale (paralogon-based) phylogenetic methods, we confirm the monophyly of cyclostomes, document an auto-tetraploidization (1RV) that predated the origin of crown group vertebrates ~517 Mya, and establish the timing of subsequent independent duplications in the gnathostome and cyclostome lineages. Some 1RV gene duplications can be linked to key vertebrate innovations, suggesting that this early genomewide event contributed to the emergence of pan-vertebrate features such as neural crest. The hagfish karyotype is derived by numerous fusions relative to the ancestral cyclostome arrangement preserved by lampreys. These genomic changes were accompanied by the loss of genes essential for organ systems (eyes, osteoclast) that are absent in hagfish, accounting in part for the simplification of the hagfish body plan; other gene family expansions account for hagfishes' capacity to produce slime. Finally, we characterise programmed DNA elimination in somatic cells of hagfish, identifying protein-coding and repetitive elements that are deleted during development. As in lampreys, the elimination of these genes provides a mechanism for resolving genetic conflict between soma and germline by repressing germline/pluripotency functions. Reconstruction of the early genomic history of vertebrates provides a framework for further exploration of vertebrate novelties.
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Affiliation(s)
- Ferdinand Marlétaz
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, London, UK
- Molecular Genetics Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | | | | | - Oleg Simakov
- Molecular Genetics Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
- Department of Molecular Evolution and Development, University of Vienna, Vienna, Austria
| | - Elise Parey
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Daria Gavriouchkina
- Molecular Genetics Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
- Present address: UK Dementia Research Institute, University College London, London, UK
| | - Masakazu Suzuki
- Department of Science, Graduate School of Integrated Science and Technology, Shizuoka University, Shizuoka, Japan
| | - Kaoru Kubokawa
- Ocean Research Institute, The University of Tokyo, Tokyo, Japan
| | - Sydney Brenner
- Comparative and Medical Genomics Laboratory, Institute of Molecular and Cell Biology, A*STAR, Biopolis, Singapore 138673, Singapore
- Deceased
| | - Jeramiah Smith
- Department of Biology, University of Kentucky, Lexington, KY, USA
| | - Daniel S Rokhsar
- Molecular Genetics Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
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5
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Kuraku S, Kaiya H, Tanaka T, Hyodo S. Evolution of Vertebrate Hormones and Their Receptors: Insights from Non-Osteichthyan Genomes. Annu Rev Anim Biosci 2023; 11:163-182. [PMID: 36400012 DOI: 10.1146/annurev-animal-050922-071351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Homeostatic control and reproductive functions of humans are regulated at the molecular levels largely by peptide hormones secreted from endocrine and/or neuroendocrine cells in the central nervous system and peripheral organs. Homologs of those hormones and their receptors function similarly in many vertebrate species distantly related to humans, but the evolutionary history of the endocrine system involving those factors has been obscured by the scarcity of genome DNA sequence information of some taxa that potentially contain their orthologs. Focusing on non-osteichthyan vertebrates, namely jawless and cartilaginous fishes, this article illustrates how investigating genome sequence information assists our understanding of the diversification of vertebrate gene repertoires in four broad themes: (a) the presence or absence of genes, (b) multiplication and maintenance of paralogs, (c) differential fates of duplicated paralogs, and (d) the evolutionary timing of gene origins.
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Affiliation(s)
- Shigehiro Kuraku
- Molecular Life History Laboratory, Department of Genomics and Evolutionary Biology, National Institute of Genetics, Mishima, Japan; .,Department of Genetics, Sokendai (Graduate University for Advanced Studies), Mishima, Japan.,Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research (BDR), Kobe, Japan
| | - Hiroyuki Kaiya
- Grandsoul Research Institute of Immunology, Inc., Uda, Japan
| | - Tomohiro Tanaka
- Department of Gastroenterology and Metabolism, Graduate School of Medical Sciences, Nagoya City University, Nagoya, Japan
| | - Susumu Hyodo
- Laboratory of Physiology, Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Japan
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Joyce W, Ripley DM, Gillis T, Black AC, Shiels HA, Hoffmann FG. A Revised Perspective on the Evolution of Troponin I and Troponin T Gene Families in Vertebrates. Genome Biol Evol 2022; 15:6904147. [PMID: 36518048 PMCID: PMC9825255 DOI: 10.1093/gbe/evac173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 11/29/2022] [Accepted: 12/05/2022] [Indexed: 12/23/2022] Open
Abstract
The troponin (Tn) complex, responsible for the Ca2+ activation of striated muscle, is composed of three interacting protein subunits: TnC, TnI, and TnT, encoded by TNNC, TNNI, and TNNT genes. TNNI and TNNT are sister gene families, and in mammals the three TNNI paralogs (TNNI1, TNNI2, TNNI3), which encode proteins with tissue-specific expression, are each in close genomic proximity with one of the three TNNT paralogs (TNNT2, TNNT3, TNNT1, respectively). It has been widely presumed that all vertebrates broadly possess genes of these same three classes, although earlier work has overlooked jawless fishes (cyclostomes) and cartilaginous fishes (chimeras, rays, and sharks), which are distantly related to other jawed vertebrates. With a new phylogenetic and synteny analysis of a diverse array of vertebrates including these taxonomic groups, we define five distinct TNNI classes (TNNI1-5), with TNNI4 and TNNI5 being only present in non-amniote vertebrates and typically found in tandem, and four classes of TNNT (TNNT1-4). These genes are located in four genomic loci that were generated by the 2R whole-genome duplications. TNNI3, encoding "cardiac TnI" in tetrapods, was independently lost in cartilaginous and ray-finned fishes. Instead, ray-finned fishes predominantly express TNNI1 in the heart. TNNI5 is highly expressed in shark hearts and contains a N-terminal extension similar to that of TNNI3 found in tetrapod hearts. Given that TNNI3 and TNNI5 are distantly related, this supports the hypothesis that the N-terminal extension may be an ancestral feature of vertebrate TNNI and not an innovation unique to TNNI3, as has been commonly believed.
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Affiliation(s)
| | - Daniel M Ripley
- Division of Cardiovascular Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester M13 9PL, United Kingdom
| | - Todd Gillis
- Department of Integrative Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Amanda Coward Black
- Department of Biochemistry, Molecular Biology, Entomology, and Plant Pathology, Mississippi State University, Starkville, Mississippi 39762, USA
| | - Holly A Shiels
- Division of Cardiovascular Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester M13 9PL, United Kingdom
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7
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Gaunt SJ. Seeking Sense in the Hox Gene Cluster. J Dev Biol 2022; 10:jdb10040048. [PMID: 36412642 PMCID: PMC9680502 DOI: 10.3390/jdb10040048] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 10/31/2022] [Accepted: 11/09/2022] [Indexed: 11/18/2022] Open
Abstract
The Hox gene cluster, responsible for patterning of the head-tail axis, is an ancestral feature of all bilaterally symmetrical animals (the Bilateria) that remains intact in a wide range of species. We can say that the Hox cluster evolved successfully only once since it is commonly the same in all groups, with labial-like genes at one end of the cluster expressed in the anterior embryo, and Abd-B-like genes at the other end of the cluster expressed posteriorly. This review attempts to make sense of the Hox gene cluster and to address the following questions. How did the Hox cluster form in the protostome-deuterostome last common ancestor, and why was this with a particular head-tail polarity? Why is gene clustering usually maintained? Why is there collinearity between the order of genes along the cluster and the positions of their expressions along the embryo? Why do the Hox gene expression domains overlap along the embryo? Why have vertebrates duplicated the Hox cluster? Why do Hox gene knockouts typically result in anterior homeotic transformations? How do animals adapt their Hox clusters to evolve new structural patterns along the head-tail axis?
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Affiliation(s)
- Stephen J Gaunt
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
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8
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Dores RM, McKinley G, Meyers A, Martin M, Shaughnessy CA. Structure/Function Studies on the Activation Motif of Two Non-Mammalian Mrap1 Orthologs, and Observations on the Phylogeny of Mrap1, Including a Novel Characterization of an Mrap1 from the Chondrostean Fish, Polyodon spathula. Biomolecules 2022; 12:1681. [PMID: 36421695 PMCID: PMC9688151 DOI: 10.3390/biom12111681] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 11/03/2022] [Accepted: 11/09/2022] [Indexed: 08/12/2023] Open
Abstract
In derived bony vertebrates, activation of the melanocortin-2 receptor (Mc2r) by its ACTH ligand requires chaperoning by the Mc2r accessory protein (Mrap1). The N-terminal domain of the non-mammalian tetrapod MRAP1 from chicken (c; Gallus gallus) has the putative activation motif, W18D19Y20I21, and the N-terminal domain in the neopterygian ray-finned fish Mrap1 from bowfin (bf; Amia calva) has the putative activation motif, Y18D19Y20I21. The current study used an alanine-substitution paradigm to test the hypothesis that only the Y20 position in the Mrap1 ortholog of these non-mammalian vertebrates is required for activation of the respective Mc2r ortholog. Instead, we found that for cMRAP1, single alanine-substitution resulted in a gradient of inhibition of activation (Y20 >> D19 = W18 > I21). For bfMrap1, single alanine-substitution also resulted in a gradient of inhibition of activation (Y20 >> D19 > I21 > Y18). This study also included an analysis of Mc2r activation in an older lineage of ray-finned fish, the paddlefish (p), Polyodon spathula (subclass Chondronstei). Currently no mrap1 gene has been found in the paddlefish genome. When pmc2r was expressed alone in our CHO cell/cAMP reporter gene assay, no activation was observed following stimulation with ACTH. However, when pmc2r was co-expressed with either cmrap1 or bfmrap1 robust dose response curves were generated. These results indicate that the formation of an Mc2r/Mrap1 heterodimer emerged early in the radiation of the bony vertebrates.
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Affiliation(s)
- Robert M. Dores
- Department of Biological Sciences, University of Denver, Denver, CO 80210, USA
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9
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Discovery of prolactin-like in lamprey: Role in osmoregulation and new insight into the evolution of the growth hormone/prolactin family. Proc Natl Acad Sci U S A 2022; 119:e2212196119. [PMID: 36161944 DOI: 10.1073/pnas.2212196119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We used a representative of one of the oldest extant vertebrate lineages (jawless fish or agnathans) to investigate the early evolution and function of the growth hormone (GH)/prolactin (PRL) family. We identified a second member of the GH/PRL family in an agnathan, the sea lamprey (Petromyzon marinus). Structural, phylogenetic, and synteny analyses supported the identification of this hormone as prolactin-like (PRL-L), which has led to added insight into the evolution of the GH/PRL family. At least two ancestral genes were present in early vertebrates, which gave rise to distinct GH and PRL-L genes in lamprey. A series of gene duplications, gene losses, and chromosomal rearrangements account for the diversity of GH/PRL-family members in jawed vertebrates. Lamprey PRL-L is produced in the proximal pars distalis of the pituitary and is preferentially bound by the lamprey PRL receptor, whereas lamprey GH is preferentially bound by the lamprey GH receptor. Pituitary PRL-L messenger RNA (mRNA) levels were low in larvae, then increased significantly in mid-metamorphic transformers (stage 3); thereafter, levels subsided in final-stage transformers and metamorphosed juveniles. The abundance of PRL-L mRNA and immunoreactive protein increased in the pituitary of juveniles under hypoosmotic conditions, and treatment with PRL-L blocked seawater-associated inhibition of freshwater ion transporters. These findings clarify the origin and divergence of GH/PRL family genes in early vertebrates and reveal a function of PRL-L in osmoregulation of sea lamprey, comparable to a role of PRLs that is conserved in jawed vertebrates.
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Annona G, Sato I, Pascual-Anaya J, Osca D, Braasch I, Voss R, Stundl J, Soukup V, Ferrara A, Fontenot Q, Kuratani S, Postlethwait JH, D'Aniello S. Evolution of the nitric oxide synthase family in vertebrates and novel insights in gill development. Proc Biol Sci 2022; 289:20220667. [PMID: 35946155 PMCID: PMC9363997 DOI: 10.1098/rspb.2022.0667] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 07/19/2022] [Indexed: 12/20/2022] Open
Abstract
Nitric oxide (NO) is an ancestral key signalling molecule essential for life and has enormous versatility in biological systems, including cardiovascular homeostasis, neurotransmission and immunity. Although our knowledge of NO synthases (Nos), the enzymes that synthesize NO in vivo, is substantial, the origin of a large and diversified repertoire of nos gene orthologues in fishes with respect to tetrapods remains a puzzle. The recent identification of nos3 in the ray-finned fish spotted gar, which was considered lost in this lineage, changed this perspective. This finding prompted us to explore nos gene evolution, surveying vertebrate species representing key evolutionary nodes. This study provides noteworthy findings: first, nos2 experienced several lineage-specific gene duplications and losses. Second, nos3 was found to be lost independently in two different teleost lineages, Elopomorpha and Clupeocephala. Third, the expression of at least one nos paralogue in the gills of developing shark, bichir, sturgeon, and gar, but not in lamprey, suggests that nos expression in this organ may have arisen in the last common ancestor of gnathostomes. These results provide a framework for continuing research on nos genes' roles, highlighting subfunctionalization and reciprocal loss of function that occurred in different lineages during vertebrate genome duplications.
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Affiliation(s)
- Giovanni Annona
- Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Napoli 80121, Italy
| | - Iori Sato
- Laboratory for Evolutionary Morphology, RIKEN Center for Biosystems Dynamics Research (BDR), Kobe 650-0047, Japan
| | - Juan Pascual-Anaya
- Evolutionary Morphology Laboratory, RIKEN Cluster for Pioneering Research (CPR), Chuo-ku, Kobe, Hyogo 650-0047, Japan
- Department of Animal Biology, Faculty of Sciences, University of Málaga, Spain
- Andalusian Centre for Nanomedicine and Biotechnology (BIONAND), Málaga, Spain
| | - David Osca
- Faculty of Marine Sciences, University Institute of Environmental Studies and Natural Resources (IUNAT), University of Las Palmas de Gran Canaria, Canary Islands, Spain
| | - Ingo Braasch
- Department of Integrative Biology and Program in Ecology, Evolution and Behavior (EEB), Michigan State University, East Lansing, MI 48824, USA
| | - Randal Voss
- Department of Neuroscience, Spinal Cord and Brain Injury Research Center, and Ambystoma Genetic Stock Center, University of Kentucky, Lexington, KY, USA
| | - Jan Stundl
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
- South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, Faculty of Fisheries and Protection of Waters, University of South Bohemia in Ceske Budejovice, Vodnany, Czech Republic
| | - Vladimir Soukup
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Allyse Ferrara
- Department of Biological Sciences, Nicholls State University, Thibodaux, LA 70301, USA
| | - Quenton Fontenot
- Department of Biological Sciences, Nicholls State University, Thibodaux, LA 70301, USA
| | - Shigeru Kuratani
- Laboratory for Evolutionary Morphology, RIKEN Center for Biosystems Dynamics Research (BDR), Kobe 650-0047, Japan
- Evolutionary Morphology Laboratory, RIKEN Cluster for Pioneering Research (CPR), Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | | | - Salvatore D'Aniello
- Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Napoli 80121, Italy
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11
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Papadogiannis V, Pennati A, Parker HJ, Rothbächer U, Patthey C, Bronner ME, Shimeld SM. Hmx gene conservation identifies the origin of vertebrate cranial ganglia. Nature 2022; 605:701-705. [PMID: 35585239 DOI: 10.1038/s41586-022-04742-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 04/07/2022] [Indexed: 12/30/2022]
Abstract
The evolutionary origin of vertebrates included innovations in sensory processing associated with the acquisition of a predatory lifestyle1. Vertebrates perceive external stimuli through sensory systems serviced by cranial sensory ganglia, whose neurons arise predominantly from cranial placodes; however, the understanding of the evolutionary origin of placodes and cranial sensory ganglia is hampered by the anatomical differences between living lineages and the difficulty in assigning homology between cell types and structures. Here we show that the homeobox transcription factor Hmx is a constitutive component of vertebrate sensory ganglion development and that in the tunicate Ciona intestinalis, Hmx is necessary and sufficient to drive the differentiation programme of bipolar tail neurons, cells previously thought to be homologues of neural crest2,3. Using Ciona and lamprey transgenesis, we demonstrate that a unique, tandemly duplicated enhancer pair regulated Hmx expression in the stem-vertebrate lineage. We also show notably robust vertebrate Hmx enhancer function in Ciona, demonstrating that deep conservation of the upstream regulatory network spans the evolutionary origin of vertebrates. These experiments demonstrate regulatory and functional conservation between Ciona and vertebrate Hmx, and point to bipolar tail neurons as homologues of cranial sensory ganglia.
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Affiliation(s)
- Vasileios Papadogiannis
- Department of Zoology, University of Oxford, Oxford, UK.,Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Gournes, Crete, Greece
| | - Alessandro Pennati
- Department of Zoology, University of Oxford, Oxford, UK.,Institute of Zoology and Center of Molecular Biosciences, University of Innsbruck, Innsbruck, Austria
| | - Hugo J Parker
- Stowers Institute for Medical Research, Kansas City, MO, USA
| | - Ute Rothbächer
- Institute of Zoology and Center of Molecular Biosciences, University of Innsbruck, Innsbruck, Austria
| | - Cedric Patthey
- Department of Radiation Sciences, Oncology, Umeå University, Umeå, Sweden
| | - Marianne E Bronner
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
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12
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Kourtidis A, Dighera B, Risner A, Hackemack R, Nikolaidis N. Origin and Evolution of the Multifaceted Adherens Junction Component Plekha7. Front Cell Dev Biol 2022; 10:856975. [PMID: 35399503 PMCID: PMC8983885 DOI: 10.3389/fcell.2022.856975] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 02/10/2022] [Indexed: 11/13/2022] Open
Abstract
Plekha7 is a key adherens junction component involved in numerous functions in mammalian cells. Plekha7 is the most studied member of the PLEKHA protein family, which includes eight members with diverse functions. However, the evolutionary history of Plekha7 remains unexplored. Here, we outline the phylogeny and identify the origins of this gene and its paralogs. We show that Plekha7, together with Plekha4, Plekha5, and Plekha6, belong to a subfamily that we name PLEKHA4/5/6/7. This subfamily is distinct from the other Plekha proteins, which form two additional separate subfamilies, namely PLEKHA1/2 and PLEKHA3/8. Sequence, phylogenetic, exon-intron organization, and syntenic analyses reveal that the PLEKHA4/5/6/7 subfamily is represented by a single gene in invertebrates, which remained single in the last common ancestor of all chordates and underwent gene duplications distinctly in jawless and jawed vertebrates. In the latter species, a first round of gene duplications gave rise to the Plekha4/7 and Plekha5/6 pairs and a second round to the four extant members of the subfamily. These observations are consistent with the 1R/2R hypothesis of vertebrate genome evolution. Plekha7 and Plekha5 also exist in two copies in ray-finned fishes, due to the Teleostei-specific whole genome duplication. Similarities between the vertebrate Plekha4/5/6/7 members and non-chordate sequences are restricted to their N-terminal PH domains, whereas similarities across the remaining protein molecule are only sporadically found among few invertebrate species and are limited to the coiled-coil and extreme C-terminal ends. The vertebrate Plekha4/5/6/7 proteins contain extensive intrinsically disordered domains, which are topologically and structurally conserved in all chordates, but not in non-chordate invertebrates. In summary, our study sheds light on the origins and evolution of Plekha7 and the PLEKHA4/5/6/7 subfamily and unveils new critical information suitable for future functional studies of this still understudied group of proteins.
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Affiliation(s)
- Antonis Kourtidis
- Department of Regenerative Medicine and Cell Biology, Medical University of South Carolina, Charleston, SC, United States
| | - Bryan Dighera
- Department of Biological Science, Center for Applied Biotechnology Studies, Center for Computational and Applied Mathematics, College of Natural Sciences and Mathematics, California State University, Fullerton, Fullerton, CA, United States
| | - Alyssa Risner
- Department of Regenerative Medicine and Cell Biology, Medical University of South Carolina, Charleston, SC, United States
| | - Rob Hackemack
- Department of Biological Science, Center for Applied Biotechnology Studies, Center for Computational and Applied Mathematics, College of Natural Sciences and Mathematics, California State University, Fullerton, Fullerton, CA, United States
| | - Nikolas Nikolaidis
- Department of Biological Science, Center for Applied Biotechnology Studies, Center for Computational and Applied Mathematics, College of Natural Sciences and Mathematics, California State University, Fullerton, Fullerton, CA, United States
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13
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14
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Parker HJ, De Kumar B, Pushel I, Bronner ME, Krumlauf R. Analysis of lamprey meis genes reveals that conserved inputs from Hox, Meis and Pbx proteins control their expression in the hindbrain and neural tube. Dev Biol 2021; 479:61-76. [PMID: 34310923 DOI: 10.1016/j.ydbio.2021.07.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 06/10/2021] [Accepted: 07/22/2021] [Indexed: 11/23/2022]
Abstract
Meis genes are known to play important roles in the hindbrain and neural crest cells of jawed vertebrates. To explore the roles of Meis genes in head development during evolution of vertebrates, we have identified four meis genes in the sea lamprey genome and characterized their patterns of expression and regulation, with a focus on the hindbrain and pharynx. Each of the lamprey meis genes displays temporally and spatially dynamic patterns of expression, some of which are coupled to rhombomeric domains in the developing hindbrain and select pharyngeal arches. Studies of Meis loci in mouse and zebrafish have identified enhancers that are bound by Hox and TALE (Meis and Pbx) proteins, implicating these factors in the direct regulation of Meis expression. We examined the lamprey meis loci and identified a series of cis-elements conserved between lamprey and jawed vertebrate meis genes. In transgenic reporter assays we demonstrated that these elements act as neural enhancers in lamprey embryos, directing reporter expression in appropriate domains when compared to expression of their associated endogenous meis gene. Sequence alignments reveal that these conserved elements are in similar relative positions of the meis loci and contain a series of consensus binding motifs for Hox and TALE proteins. This suggests that ancient Hox and TALE-responsive enhancers regulated expression of ancestral vertebrate meis genes in segmental domains in the hindbrain and have been retained in the meis loci during vertebrate evolution. The presence of conserved Meis, Pbx and Hox binding sites in these lamprey enhancers links Hox and TALE factors to regulation of lamprey meis genes in the developing hindbrain, indicating a deep ancestry for these regulatory interactions prior to the divergence of jawed and jawless vertebrates.
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Affiliation(s)
- Hugo J Parker
- Stowers Institute for Medical Research, Kansas City, MO, 64110, USA
| | - Bony De Kumar
- Stowers Institute for Medical Research, Kansas City, MO, 64110, USA
| | - Irina Pushel
- Stowers Institute for Medical Research, Kansas City, MO, 64110, USA
| | - Marianne E Bronner
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Robb Krumlauf
- Stowers Institute for Medical Research, Kansas City, MO, 64110, USA; Department of Anatomy and Cell Biology, Kansas University Medical Center, Kansas City, KS, 66160, USA.
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15
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Generation of knock-in lampreys by CRISPR-Cas9-mediated genome engineering. Sci Rep 2021; 11:19836. [PMID: 34615907 PMCID: PMC8494898 DOI: 10.1038/s41598-021-99338-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 09/22/2021] [Indexed: 11/08/2022] Open
Abstract
The lamprey represents the oldest group of living vertebrates and has been a key organism in various research fields such as evolutionary developmental biology and neuroscience. However, no knock-in technique for this animal has been established yet, preventing application of advanced genetic techniques. Here, we report efficient generation of F0 knock-in lampreys by CRISPR-Cas9-mediated genome editing. A donor plasmid containing a heat-shock promoter was co-injected with a short guide RNA (sgRNA) for genome digestion, a sgRNA for donor plasmid digestion, and Cas9 mRNA. Targeting different genetic loci, we succeeded in generating knock-in lampreys expressing photoconvertible protein Dendra2 as well as those expressing EGFP. With its simplicity, design flexibility, and high efficiency, we propose that the present method has great versatility for various experimental uses in lamprey research and that it can also be applied to other “non-model” organisms.
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16
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Hoffmann FG, Storz JF, Kuraku S, Vandewege MW, Opazo JC. Whole-Genome Duplications and the Diversification of the Globin-X Genes of Vertebrates. Genome Biol Evol 2021; 13:evab205. [PMID: 34480557 PMCID: PMC8525914 DOI: 10.1093/gbe/evab205] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/23/2021] [Indexed: 12/28/2022] Open
Abstract
Globin-X (GbX) is an enigmatic member of the vertebrate globin gene family with a wide phyletic distribution that spans protostomes and deuterostomes. Unlike canonical globins such as hemoglobins and myoglobins, functional data suggest that GbX does not have a primary respiratory function. Instead, evidence suggests that the monomeric, membrane-bound GbX may play a role in cellular signaling or protection against the oxidation of membrane lipids. Recently released genomes from key vertebrates provide an excellent opportunity to address questions about the early stages of the evolution of GbX in vertebrates. We integrate bioinformatics, synteny, and phylogenetic analyses to characterize the diversity of GbX genes in nonteleost ray-finned fishes, resolve relationships between the GbX genes of cartilaginous fish and bony vertebrates, and demonstrate that the GbX genes of cyclostomes and gnathostomes derive from independent duplications. Our study highlights the role that whole-genome duplications (WGDs) have played in expanding the repertoire of genes in vertebrate genomes. Our results indicate that GbX paralogs have a remarkably high rate of retention following WGDs relative to other globin genes and provide an evolutionary framework for interpreting results of experiments that examine functional properties of GbX and patterns of tissue-specific expression. By identifying GbX paralogs that are products of different WGDs, our results can guide the design of experimental work to explore whether gene duplicates that originate via WGDs have evolved novel functional properties or expression profiles relative to singleton or tandemly duplicated copies of GbX.
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Affiliation(s)
- Federico G Hoffmann
- Department of Biochemistry, Molecular Biology, Entomology, and Plant Pathology, Mississippi State University, Starkville, MS, USA
- Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Starkville, MS, USA
| | - Jay F Storz
- School of Biological Sciences, University of Nebraska, Lincoln, NE, USA
| | - Shigehiro Kuraku
- Molecular Life History Laboratory, Department of Genomics and Evolutionary Biology, National Institute of Genetics, Mishima, Japan
- Department of Genetics, Sokendai (Graduate University for Advanced Studies), Mishima, Japan
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan
| | | | - Juan C Opazo
- Integrative Biology Group, Universidad Austral de Chile, Valdivia, Chile
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
- Millennium Nucleus of Ion Channel-Associated Diseases (MiNICAD), Valdivia, Chile
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17
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Srikulnath K, Ahmad SF, Singchat W, Panthum T. Why Do Some Vertebrates Have Microchromosomes? Cells 2021; 10:2182. [PMID: 34571831 PMCID: PMC8466491 DOI: 10.3390/cells10092182] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 08/17/2021] [Accepted: 08/17/2021] [Indexed: 12/27/2022] Open
Abstract
With more than 70,000 living species, vertebrates have a huge impact on the field of biology and research, including karyotype evolution. One prominent aspect of many vertebrate karyotypes is the enigmatic occurrence of tiny and often cytogenetically indistinguishable microchromosomes, which possess distinctive features compared to macrochromosomes. Why certain vertebrate species carry these microchromosomes in some lineages while others do not, and how they evolve remain open questions. New studies have shown that microchromosomes exhibit certain unique characteristics of genome structure and organization, such as high gene densities, low heterochromatin levels, and high rates of recombination. Our review focuses on recent concepts to expand current knowledge on the dynamic nature of karyotype evolution in vertebrates, raising important questions regarding the evolutionary origins and ramifications of microchromosomes. We introduce the basic karyotypic features to clarify the size, shape, and morphology of macro- and microchromosomes and report their distribution across different lineages. Finally, we characterize the mechanisms of different evolutionary forces underlying the origin and evolution of microchromosomes.
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Affiliation(s)
- Kornsorn Srikulnath
- Animal Genomics and Bioresource Research Center (AGB Research Center), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (S.F.A.); (W.S.); (T.P.)
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
- The International Undergraduate Program in Bioscience and Technology, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
- Amphibian Research Center, Hiroshima University, 1-3-1, Kagamiyama, Higashihiroshima 739-8526, Japan
| | - Syed Farhan Ahmad
- Animal Genomics and Bioresource Research Center (AGB Research Center), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (S.F.A.); (W.S.); (T.P.)
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
- The International Undergraduate Program in Bioscience and Technology, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Worapong Singchat
- Animal Genomics and Bioresource Research Center (AGB Research Center), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (S.F.A.); (W.S.); (T.P.)
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Thitipong Panthum
- Animal Genomics and Bioresource Research Center (AGB Research Center), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (S.F.A.); (W.S.); (T.P.)
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
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18
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Garcia-Concejo A, Larhammar D. Protein kinase C family evolution in jawed vertebrates. Dev Biol 2021; 479:77-90. [PMID: 34329618 DOI: 10.1016/j.ydbio.2021.07.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Revised: 07/02/2021] [Accepted: 07/22/2021] [Indexed: 11/18/2022]
Abstract
Protein kinase C (PKC) was one of the first kinases identified in human cells. It is now known to constitute a family of kinases that respond to diacylglycerol, phosphatidylserine and for some family members, Ca2+. They have a plethora of different functions, such as cell cycle regulation, immune response and memory formation. In mammals, 12 PKC family members have been described, usually divided into 4 different subfamilies. We present here a comprehensive evolutionary analysis of the PKC genes in jawed vertebrates with special focus on the impact of the two tetraploidizations (1R and 2R) before the radiation of jawed vertebrates and the teleost tetraploidization (3R), as illuminated by synteny and paralogon analysis including many neighboring gene families. We conclude that the vertebrate predecessor had five PKC genes, as tunicates and lancelets still do, and that the PKC family should therefore ideally be organized into five subfamilies. The 1R and 2R events led to a total of 12 genes distributed among these five subfamilies. All 12 genes are still present in some of the major lineages of jawed vertebrates, including mammals, whereas birds and cartilaginous fishes have lost one member. The 3R event added another nine genes in teleosts, bringing the total to 21 genes. The zebrafish, a common experimental model animal, has retained 19. We have found no independent gene duplications. Thus, the genome doublings completely account for the complexity of this gene family in jawed vertebrates and have thereby had a huge impact on their evolution.
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Affiliation(s)
- Adrian Garcia-Concejo
- Department of Neuroscience, Unit of Pharmacology, Science for Life Laboratory, Uppsala University, Box 593, SE-751 24, Uppsala, Sweden.
| | - Dan Larhammar
- Department of Neuroscience, Unit of Pharmacology, Science for Life Laboratory, Uppsala University, Box 593, SE-751 24, Uppsala, Sweden
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19
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Reconstruction of proto-vertebrate, proto-cyclostome and proto-gnathostome genomes provides new insights into early vertebrate evolution. Nat Commun 2021; 12:4489. [PMID: 34301952 PMCID: PMC8302630 DOI: 10.1038/s41467-021-24573-z] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 06/25/2021] [Indexed: 02/07/2023] Open
Abstract
Ancient polyploidization events have had a lasting impact on vertebrate genome structure, organization and function. Some key questions regarding the number of ancient polyploidization events and their timing in relation to the cyclostome-gnathostome divergence have remained contentious. Here we generate de novo long-read-based chromosome-scale genome assemblies for the Japanese lamprey and elephant shark. Using these and other representative genomes and developing algorithms for the probabilistic macrosynteny model, we reconstruct high-resolution proto-vertebrate, proto-cyclostome and proto-gnathostome genomes. Our reconstructions resolve key questions regarding the early evolutionary history of vertebrates. First, cyclostomes diverged from the lineage leading to gnathostomes after a shared tetraploidization (1R) but before a gnathostome-specific tetraploidization (2R). Second, the cyclostome lineage experienced an additional hexaploidization. Third, 2R in the gnathostome lineage was an allotetraploidization event, and biased gene loss from one of the subgenomes shaped the gnathostome genome by giving rise to remarkably conserved microchromosomes. Thus, our reconstructions reveal the major evolutionary events and offer new insights into the origin and evolution of vertebrate genomes.
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20
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Aase-Remedios ME, Ferrier DEK. Improved Understanding of the Role of Gene and Genome Duplications in Chordate Evolution With New Genome and Transcriptome Sequences. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.703163] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Comparative approaches to understanding chordate genomes have uncovered a significant role for gene duplications, including whole genome duplications (WGDs), giving rise to and expanding gene families. In developmental biology, gene families created and expanded by both tandem and WGDs are paramount. These genes, often involved in transcription and signalling, are candidates for underpinning major evolutionary transitions because they are particularly prone to retention and subfunctionalisation, neofunctionalisation, or specialisation following duplication. Under the subfunctionalisation model, duplication lays the foundation for the diversification of paralogues, especially in the context of gene regulation. Tandemly duplicated paralogues reside in the same regulatory environment, which may constrain them and result in a gene cluster with closely linked but subtly different expression patterns and functions. Ohnologues (WGD paralogues) often diversify by partitioning their expression domains between retained paralogues, amidst the many changes in the genome during rediploidisation, including chromosomal rearrangements and extensive gene losses. The patterns of these retentions and losses are still not fully understood, nor is the full extent of the impact of gene duplication on chordate evolution. The growing number of sequencing projects, genomic resources, transcriptomics, and improvements to genome assemblies for diverse chordates from non-model and under-sampled lineages like the coelacanth, as well as key lineages, such as amphioxus and lamprey, has allowed more informative comparisons within developmental gene families as well as revealing the extent of conserved synteny across whole genomes. This influx of data provides the tools necessary for phylogenetically informed comparative genomics, which will bring us closer to understanding the evolution of chordate body plan diversity and the changes underpinning the origin and diversification of vertebrates.
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21
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Bayramov AV, Ermakova GV, Kuchryavyy AV, Zaraisky AG. Genome Duplications as the Basis of Vertebrates’ Evolutionary Success. Russ J Dev Biol 2021. [DOI: 10.1134/s1062360421030024] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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22
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Tamaki T, Kagawa N, Fukushima N. The Japanese lamprey (Lethenteron camtschaticum) expresses functional lysophosphatidic acid receptors. Biochem Biophys Res Commun 2021; 568:1-7. [PMID: 34166971 DOI: 10.1016/j.bbrc.2021.06.035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 06/08/2021] [Indexed: 11/25/2022]
Abstract
Lysophosphatidic acid (LPA) signaling plays diverse roles in the development of various vertebrates such as mammals and fish. The lamprey is a fish that retains ancestral features of vertebrates, but information regarding lamprey LPA receptor genes is limited. Here, using information from the lamprey genome database, we cloned two LPA receptor genes, Lpar1 and Lpar5, from the Japanese lamprey (Lethenteron camtschaticum). Lamprey Lpar1 had a high amino acid identity to mouse and medaka fish Lpar1, whereas Lpar5 amino acid sequences were more diverse between species. Our functional analyses using a heterologous expression system demonstrated that Lpar1 and Lpar5 responded to LPA treatment with G12/13-associated cellular responses, which are indicative of cytoskeletal actions. The existence of functional LPA receptors in the Japanese lamprey suggests that LPA receptor-dependent signals contribute to lamprey growth and development.
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Affiliation(s)
- Takeru Tamaki
- Division of Molecular Neurobiology, Department of Life Science, Kindai University, Higashiosaka, Japan
| | - Nao Kagawa
- Division of Animal Genetics, Department of Life Science, Kindai University, Higashiosaka, Japan
| | - Nobuyuki Fukushima
- Division of Molecular Neurobiology, Department of Life Science, Kindai University, Higashiosaka, Japan.
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Geng M, Hua Y, Liu Y, Quan J, Hu X, Su P, Li Y, Liu X, Li Q, Zhu T. Evolutionary history and functional characterization of Lj-TICAM-a and Lj-TICAM-b formed via lineage-specific tandem duplication in lamprey (Lampetra japonica). Genomics 2021; 113:2756-2768. [PMID: 34147633 DOI: 10.1016/j.ygeno.2021.06.022] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 05/06/2021] [Accepted: 06/06/2021] [Indexed: 02/06/2023]
Abstract
Toll/interleukin-1 receptor domain-containing adaptor molecule (TICAM) genes respond to infections. We identified TICAM-a and TICAM-b in Lampetra japonica and investigated their evolutionary history and potential function via comparative genomics and molecular evolution analyses. They are arranged in tandem and evolved from a multi-exon to a single-exon structure. Lj-TICAM-a and Lj-TICAM-b might be the ancestral gene of the vertebrate TICAM genes. Lj-TICAM-b arose via a lamprey-specific tandem duplication event. Both genes are expressed in many tissues during an immune response, and exhibit different responses to peptidoglycan, indicating their functional divergence. Simultaneous overexpression of both proteins activated nuclear factor κB expression and co-immunoprecipitation assays indicated that they might form a complex for signal transduction. However, unlike in mammals, the TICAM-dependent signaling pathway in lamprey might rely on TRAF3 rather than on TRAF6. These results suggest that both Lj-TICAM-a and Lj-TICAM-b play a role in host defenses.
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Affiliation(s)
- Ming Geng
- College of Life Sciences, Liaoning Normal University, Dalian 116081, China; Lamprey Research Center, Liaoning Normal University, Dalian 116081, China; Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian 116081, China
| | - Yishan Hua
- College of Life Sciences, Liaoning Normal University, Dalian 116081, China; Lamprey Research Center, Liaoning Normal University, Dalian 116081, China; Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian 116081, China
| | - Yu Liu
- College of Life Sciences, Liaoning Normal University, Dalian 116081, China; Lamprey Research Center, Liaoning Normal University, Dalian 116081, China; Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian 116081, China
| | - Jian Quan
- College of Life Sciences, Liaoning Normal University, Dalian 116081, China; Lamprey Research Center, Liaoning Normal University, Dalian 116081, China; Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian 116081, China
| | - Xueting Hu
- College of Life Sciences, Liaoning Normal University, Dalian 116081, China
| | - Peng Su
- College of Life Sciences, Liaoning Normal University, Dalian 116081, China; Lamprey Research Center, Liaoning Normal University, Dalian 116081, China; Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian 116081, China
| | - Yingying Li
- College of Life Sciences, Liaoning Normal University, Dalian 116081, China; Lamprey Research Center, Liaoning Normal University, Dalian 116081, China; Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian 116081, China
| | - Xin Liu
- College of Life Sciences, Liaoning Normal University, Dalian 116081, China; Lamprey Research Center, Liaoning Normal University, Dalian 116081, China; Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian 116081, China
| | - Qingwei Li
- College of Life Sciences, Liaoning Normal University, Dalian 116081, China; Lamprey Research Center, Liaoning Normal University, Dalian 116081, China; Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian 116081, China.
| | - Ting Zhu
- College of Life Sciences, Liaoning Normal University, Dalian 116081, China; Lamprey Research Center, Liaoning Normal University, Dalian 116081, China; Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian 116081, China.
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24
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Functional Domains and Evolutionary History of the PMEL and GPNMB Family Proteins. Molecules 2021; 26:molecules26123529. [PMID: 34207849 PMCID: PMC8273697 DOI: 10.3390/molecules26123529] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 05/31/2021] [Accepted: 06/02/2021] [Indexed: 11/17/2022] Open
Abstract
The ancient paralogs premelanosome protein (PMEL) and glycoprotein nonmetastatic melanoma protein B (GPNMB) have independently emerged as intriguing disease loci in recent years. Both proteins possess common functional domains and variants that cause a shared spectrum of overlapping phenotypes and disease associations: melanin-based pigmentation, cancer, neurodegenerative disease and glaucoma. Surprisingly, these proteins have yet to be shown to physically or genetically interact within the same cellular pathway. This juxtaposition inspired us to compare and contrast this family across a breadth of species to better understand the divergent evolutionary trajectories of two related, but distinct, genes. In this study, we investigated the evolutionary history of PMEL and GPNMB in clade-representative species and identified TMEM130 as the most ancient paralog of the family. By curating the functional domains in each paralog, we identified many commonalities dating back to the emergence of the gene family in basal metazoans. PMEL and GPNMB have gained functional domains since their divergence from TMEM130, including the core amyloid fragment (CAF) that is critical for the amyloid potential of PMEL. Additionally, the PMEL gene has acquired the enigmatic repeat domain (RPT), composed of a variable number of imperfect tandem repeats; this domain acts in an accessory role to control amyloid formation. Our analyses revealed the vast variability in sequence, length and repeat number in homologous RPT domains between craniates, even within the same taxonomic class. We hope that these analyses inspire further investigation into a gene family that is remarkable from the evolutionary, pathological and cell biology perspectives.
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25
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Shark and ray genomics for disentangling their morphological diversity and vertebrate evolution. Dev Biol 2021; 477:262-272. [PMID: 34102168 DOI: 10.1016/j.ydbio.2021.06.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 05/17/2021] [Accepted: 06/01/2021] [Indexed: 11/24/2022]
Abstract
Developmental studies of sharks and rays (elasmobranchs) have provided much insight into the process of morphological evolution of vertebrates. Although those studies are supposedly fueled by large-scale molecular sequencing information, whole-genome sequences of sharks and rays were made available only recently. One compelling difficulty of elasmobranch developmental biology is the low accessibility to embryonic study materials and their slow development. Another limiting factor is the relatively large size of their genomes. Moreover, their large body sizes restrict sustainable captive breeding, while their high body fluid osmolarity prevents reproducible cell culturing for in vitro experimentation, which has also limited our knowledge of their chromosomal organization for validation of genome sequencing products. This article focuses on egg-laying elasmobranch species used in developmental biology and provides an overview of the characteristics of the shark and ray genomes revealed to date. Developmental studies performed on a gene-by-gene basis are also reviewed from a whole-genome perspective. Among the popular regulatory genes studied in developmental biology, I scrutinize shark homologs of Wnt genes that highlight vanishing repertoires in many other vertebrate lineages, as well as Hox genes that underwent an unexpected modification unique to the elasmobranch lineage. These topics are discussed together with insights into the reconstruction of developmental programs in the common ancestor of vertebrates and its subsequent evolutionary trajectories that mark the features that are unique to, and those characterizing the diversity among, cartilaginous fishes.
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26
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Hoencamp C, Dudchenko O, Elbatsh AMO, Brahmachari S, Raaijmakers JA, van Schaik T, Sedeño Cacciatore Á, Contessoto VG, van Heesbeen RGHP, van den Broek B, Mhaskar AN, Teunissen H, St Hilaire BG, Weisz D, Omer AD, Pham M, Colaric Z, Yang Z, Rao SSP, Mitra N, Lui C, Yao W, Khan R, Moroz LL, Kohn A, St Leger J, Mena A, Holcroft K, Gambetta MC, Lim F, Farley E, Stein N, Haddad A, Chauss D, Mutlu AS, Wang MC, Young ND, Hildebrandt E, Cheng HH, Knight CJ, Burnham TLU, Hovel KA, Beel AJ, Mattei PJ, Kornberg RD, Warren WC, Cary G, Gómez-Skarmeta JL, Hinman V, Lindblad-Toh K, Di Palma F, Maeshima K, Multani AS, Pathak S, Nel-Themaat L, Behringer RR, Kaur P, Medema RH, van Steensel B, de Wit E, Onuchic JN, Di Pierro M, Lieberman Aiden E, Rowland BD. 3D genomics across the tree of life reveals condensin II as a determinant of architecture type. Science 2021; 372:984-989. [PMID: 34045355 PMCID: PMC8172041 DOI: 10.1126/science.abe2218] [Citation(s) in RCA: 109] [Impact Index Per Article: 36.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 04/16/2021] [Indexed: 01/01/2023]
Abstract
We investigated genome folding across the eukaryotic tree of life. We find two types of three-dimensional (3D) genome architectures at the chromosome scale. Each type appears and disappears repeatedly during eukaryotic evolution. The type of genome architecture that an organism exhibits correlates with the absence of condensin II subunits. Moreover, condensin II depletion converts the architecture of the human genome to a state resembling that seen in organisms such as fungi or mosquitoes. In this state, centromeres cluster together at nucleoli, and heterochromatin domains merge. We propose a physical model in which lengthwise compaction of chromosomes by condensin II during mitosis determines chromosome-scale genome architecture, with effects that are retained during the subsequent interphase. This mechanism likely has been conserved since the last common ancestor of all eukaryotes.
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Affiliation(s)
- Claire Hoencamp
- Division of Gene Regulation, Netherlands Cancer Institute, 1066 CX Amsterdam, Netherlands
| | - Olga Dudchenko
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005, USA
| | - Ahmed M O Elbatsh
- Division of Gene Regulation, Netherlands Cancer Institute, 1066 CX Amsterdam, Netherlands
| | | | - Jonne A Raaijmakers
- Division of Cell Biology, Oncode Institute, Netherlands Cancer Institute, 1066 CX Amsterdam, Netherlands
| | - Tom van Schaik
- Division of Gene Regulation, Oncode Institute, Netherlands Cancer Institute, 1066 CX Amsterdam, Netherlands
| | | | - Vinícius G Contessoto
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005, USA
- Department of Physics, Institute of Biosciences, Letters and Exact Sciences, São Paulo State University (UNESP), São José do Rio Preto - SP, 15054-000, Brazil
| | - Roy G H P van Heesbeen
- Division of Cell Biology, Oncode Institute, Netherlands Cancer Institute, 1066 CX Amsterdam, Netherlands
| | - Bram van den Broek
- BioImaging Facility, Netherlands Cancer Institute, 1066 CX Amsterdam, Netherlands
| | - Aditya N Mhaskar
- Division of Gene Regulation, Netherlands Cancer Institute, 1066 CX Amsterdam, Netherlands
| | - Hans Teunissen
- Division of Gene Regulation, Oncode Institute, Netherlands Cancer Institute, 1066 CX Amsterdam, Netherlands
| | - Brian Glenn St Hilaire
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - David Weisz
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Arina D Omer
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA
| | - Melanie Pham
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA
| | - Zane Colaric
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA
| | - Zhenzhen Yang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech, Pudong 201210, China
| | - Suhas S P Rao
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Namita Mitra
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Christopher Lui
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA
| | - Weijie Yao
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ruqayya Khan
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Leonid L Moroz
- Whitney Laboratory and Department of Neuroscience, University of Florida, Gainesville, FL 32611, USA
| | - Andrea Kohn
- Whitney Laboratory and Department of Neuroscience, University of Florida, Gainesville, FL 32611, USA
| | - Judy St Leger
- Department of Biosciences, Cornell University College of Veterinary Medicine, Ithaca, NY 14853, USA
| | | | | | | | - Fabian Lim
- Department of Medicine and Molecular Biology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Emma Farley
- Department of Medicine and Molecular Biology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK Gatersleben), 06466 Seeland, Germany
- Center of Integrated Breeding Research (CiBreed), Department of Crop Sciences, Georg-August-University Göttingen, 37075 Göttingen, Germany
- UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA 6009, Australia
| | - Alexander Haddad
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA
| | - Daniel Chauss
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ayse Sena Mutlu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Meng C Wang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX 77030, USA
- Howard Hughes Medical Institute, Baylor College of Medicine, Houston, TX 77030, USA
| | - Neil D Young
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, VIC 3010, Australia
| | - Evin Hildebrandt
- Avian Diseases and Oncology Laboratory, US Department of Agriculture, Agricultural Research Service, East Lansing, MI 48823, USA
| | - Hans H Cheng
- Avian Diseases and Oncology Laboratory, US Department of Agriculture, Agricultural Research Service, East Lansing, MI 48823, USA
| | | | - Theresa L U Burnham
- Department of Wildlife, Fish, and Conservation Biology, University of California, Davis, Davis, CA 95616, USA
- Coastal and Marine Institute and Department of Biology, San Diego State University, San Diego, CA 92106, USA
| | - Kevin A Hovel
- Coastal and Marine Institute and Department of Biology, San Diego State University, San Diego, CA 92106, USA
| | - Andrew J Beel
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Pierre-Jean Mattei
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Roger D Kornberg
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Wesley C Warren
- Department of Animal Sciences, University of Missouri, Columbia, MO 65211, USA
| | - Gregory Cary
- The Jackson Laboratory, Bar Harbor, ME 04609, USA
| | - José Luis Gómez-Skarmeta
- Centro Andaluz de Biología del Desarrollo CSIC, Universidad Pablo de Olavide, 41013 Sevilla, Spain
| | - Veronica Hinman
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Kerstin Lindblad-Toh
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, 751 23 Uppsala, Sweden
| | - Federica Di Palma
- Department of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK
| | - Kazuhiro Maeshima
- Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
- Department of Genetics, Sokendai (Graduate University for Advanced Studies), Mishima, Shizuoka 411-8540, Japan
| | - Asha S Multani
- Department of Genetics, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Sen Pathak
- Department of Genetics, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Liesl Nel-Themaat
- Department of Genetics, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Richard R Behringer
- Department of Genetics, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Parwinder Kaur
- UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA 6009, Australia
| | - René H Medema
- Division of Cell Biology, Oncode Institute, Netherlands Cancer Institute, 1066 CX Amsterdam, Netherlands
| | - Bas van Steensel
- Division of Gene Regulation, Oncode Institute, Netherlands Cancer Institute, 1066 CX Amsterdam, Netherlands
| | - Elzo de Wit
- Division of Gene Regulation, Oncode Institute, Netherlands Cancer Institute, 1066 CX Amsterdam, Netherlands
| | - José N Onuchic
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005, USA
- Departments of Physics and Astronomy, Chemistry, and Biosciences, Rice University, Houston, TX 77005, USA
| | - Michele Di Pierro
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005, USA
- Department of Physics, Northeastern University, Boston, MA 02115, USA
| | - Erez Lieberman Aiden
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA.
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005, USA
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech, Pudong 201210, China
- UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA 6009, Australia
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Benjamin D Rowland
- Division of Gene Regulation, Netherlands Cancer Institute, 1066 CX Amsterdam, Netherlands.
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Yamamoto H, Kon T, Omori Y, Furukawa T. Functional and Evolutionary Diversification of Otx2 and Crx in Vertebrate Retinal Photoreceptor and Bipolar Cell Development. Cell Rep 2021; 30:658-671.e5. [PMID: 31968244 DOI: 10.1016/j.celrep.2019.12.072] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 11/06/2019] [Accepted: 12/18/2019] [Indexed: 11/26/2022] Open
Abstract
Otx family homeoproteins Otx2 and Crx are expressed in photoreceptor precursor cells and bind to the common DNA-binding consensus sequence, but these two proteins have distinct functions in retinal development. To examine the functional substitutability of Otx2 and Crx, we generate knockin mouse lines in which Crx is replaced by Otx2 and vice versa. We find that Otx2 and Crx cannot be substituted in photoreceptor development. Subsequently, we investigate the function of Otx2 in photoreceptor and bipolar cell development. High Otx2 levels induce photoreceptor cell fate but not bipolar cell fate, whereas reduced Otx2 expression impairs bipolar cell maturation and survival. Furthermore, we identify Otx2 and Crx in the lamprey genome by using synteny analysis, suggesting that the last common ancestor of vertebrates possesses both Otx2 and Crx. We find that the retinal Otx2 expression pattern is different between lampreys and mice, suggesting that neofunctionalization of Otx2 occurred in the jawed vertebrate lineage.
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Affiliation(s)
- Haruka Yamamoto
- Laboratory for Molecular and Developmental Biology, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Tetsuo Kon
- Laboratory for Molecular and Developmental Biology, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Yoshihiro Omori
- Laboratory for Molecular and Developmental Biology, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Takahisa Furukawa
- Laboratory for Molecular and Developmental Biology, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan.
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28
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Sobrido-Cameán D, Yáñez-Guerra LA, Deber A, Freire-Delgado M, Cacheiro-Vázquez R, Rodicio MC, Tostivint H, Anadón R, Barreiro-Iglesias A. Differential expression of somatostatin genes in the central nervous system of the sea lamprey. Brain Struct Funct 2021; 226:1031-1052. [PMID: 33532926 DOI: 10.1007/s00429-021-02224-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 01/19/2021] [Indexed: 01/29/2023]
Abstract
The identification of three somatostatin (SST) genes (SSTa, SSTb, and SSTc) in lampreys (Tostivint et al. Gen Comp Endocrinol 237:89-97 https://doi.org/10.1016/j.ygcen.2016.08.006 , 2016) prompted us to study their expression in the brain and spinal cord of the sea lamprey by in situ hybridization. These three genes were only expressed in equivalent neuronal populations in the hypothalamus. In other regions, SST transcripts showed clear differential expression. In the telencephalon, SSTc-positive cells were observed in the medial pallium, ventral part of the lateral pallium, striatum, subhippocampal lobe, and preoptic region. In the diencephalon, SSTa-positive cells were observed in the thalamus and SSTc-positive cells in the prethalamus, posterior tubercle, pretectal area, and nucleus of the medial longitudinal fascicle. In the midbrain, SSTc-positive cells were observed in the torus semicircularis, lateral reticular area, and perioculomotor tegmentum. Different SSTa- and SSTc-positive populations were observed in the isthmus. SSTc neurons were also observed in the rostral octavolateralis area and caudal rhombencephalon. In the spinal cord, SSTa was expressed in cerebrospinal-fluid-contacting (CSF-c) neurons and SSTc in non-CSF-c interneurons. Comparison with previous immunohistochemical studies using anti-SST-14 antibodies strongly suggests that SST-14-like neurons correspond with the SSTa populations. Thus, the SSTc populations were not reported previously in immunohistochemical studies. Cluster-based analyses and alignments of mature peptides suggested that SSTa is an ortholog of SST1 and that SSTb is closely related to SST2 and SST6. These results provide important new insights into the evolution of the somatostatinergic system in vertebrates.
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Affiliation(s)
- D Sobrido-Cameán
- Department of Functional Biology, Faculty of Biology, CIBUS, Universidade de Santiago de Compostela, 15782, Santiago de Compostela, A Coruña, Spain.,Department of Zoology, University of Cambridge, Cambridge, UK
| | | | - A Deber
- Department of Functional Biology, Faculty of Biology, CIBUS, Universidade de Santiago de Compostela, 15782, Santiago de Compostela, A Coruña, Spain
| | - M Freire-Delgado
- Department of Functional Biology, Faculty of Biology, CIBUS, Universidade de Santiago de Compostela, 15782, Santiago de Compostela, A Coruña, Spain
| | - R Cacheiro-Vázquez
- Department of Functional Biology, Faculty of Biology, CIBUS, Universidade de Santiago de Compostela, 15782, Santiago de Compostela, A Coruña, Spain
| | - M C Rodicio
- Department of Functional Biology, Faculty of Biology, CIBUS, Universidade de Santiago de Compostela, 15782, Santiago de Compostela, A Coruña, Spain
| | - H Tostivint
- Molecular Physiology and Adaptation, UMR7221, CNRS and Muséum National D'Histoire Naturelle, Paris, France
| | - R Anadón
- Department of Functional Biology, Faculty of Biology, CIBUS, Universidade de Santiago de Compostela, 15782, Santiago de Compostela, A Coruña, Spain
| | - A Barreiro-Iglesias
- Department of Functional Biology, Faculty of Biology, CIBUS, Universidade de Santiago de Compostela, 15782, Santiago de Compostela, A Coruña, Spain.
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29
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Mikalsen SO, í Kongsstovu S, Tausen M. Connexins during 500 Million Years-From Cyclostomes to Mammals. Int J Mol Sci 2021; 22:1584. [PMID: 33557313 PMCID: PMC7914757 DOI: 10.3390/ijms22041584] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 01/25/2021] [Accepted: 01/26/2021] [Indexed: 12/27/2022] Open
Abstract
It was previously shown that the connexin gene family had relatively similar subfamily structures in several vertebrate groups. Still, many details were left unclear. There are essentially no data between tunicates, which have connexins that cannot be divided into the classic subfamilies, and teleosts, where the subfamilies are easily recognized. There are also relatively few data for the groups that diverged between the teleosts and mammals. As many of the previously analyzed genomes have been improved, and many more genomes are available, we reanalyzed the connexin gene family and included species from all major vertebrate groups. The major results can be summarized as follows: (i) The same connexin subfamily structures are found in all Gnathostomata (jawed vertebrates), with some variations due to genome duplications, gene duplications and gene losses. (ii) In contrast to previous findings, birds do not have a lower number of connexins than other tetrapods. (iii) The cyclostomes (lampreys and hagfishes) possess genes in the alpha, beta, gamma and delta subfamilies, but only some of the genes show a phylogenetic affinity to specific genes in jawed vertebrates. Thus, two major evolutionary transformations have occurred in this gene family, from tunicates to cyclostomes and from cyclostomes to jawed vertebrates.
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Affiliation(s)
- Svein-Ole Mikalsen
- Faculty of Science and Technology, University of Faroe Islands, FO-100 Tórshavn, Faroe Islands; (S.í.K.); (M.T.)
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30
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Dornburg A, Wang Z, Wang J, Mo ES, López-Giráldez F, Townsend JP. Comparative Genomics within and across Bilaterians Illuminates the Evolutionary History of ALK and LTK Proto-Oncogene Origination and Diversification. Genome Biol Evol 2020; 13:5983394. [PMID: 33196781 PMCID: PMC7851593 DOI: 10.1093/gbe/evaa228] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/23/2020] [Indexed: 12/14/2022] Open
Abstract
Comparative genomic analyses have enormous potential for identifying key genes central to human health phenotypes, including those that promote cancers. In particular, the successful development of novel therapeutics using model species requires phylogenetic analyses to determine molecular homology. Accordingly, we investigate the evolutionary histories of anaplastic lymphoma kinase (ALK)—which can underlie tumorigenesis in neuroblastoma, nonsmall cell lung cancer, and anaplastic large-cell lymphoma—its close relative leukocyte tyrosine kinase (LTK) and their candidate ligands. Homology of ligands identified in model organisms to those functioning in humans remains unclear. Therefore, we searched for homologs of the human genes across metazoan genomes, finding that the candidate ligands Jeb and Hen-1 were restricted to nonvertebrate species. In contrast, the ligand augmentor (AUG) was only identified in vertebrates. We found two ALK-like and four AUG-like protein-coding genes in lamprey. Of these six genes, only one ALK-like and two AUG-like genes exhibited early embryonic expression that parallels model mammal systems. Two copies of AUG are present in nearly all jawed vertebrates. Our phylogenetic analysis strongly supports the presence of previously unrecognized functional convergences of ALK and LTK between actinopterygians and sarcopterygians—despite contemporaneous, highly conserved synteny of ALK and LTK. These findings provide critical guidance regarding the propriety of fish and mammal models with regard to model organism-based investigation of these medically important genes. In sum, our results provide the phylogenetic context necessary for effective investigations of the functional roles and biology of these critically important receptors.
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Affiliation(s)
- Alex Dornburg
- Department of Bioinformatics and Genomics, University of North Carolina Charlotte
| | - Zheng Wang
- Department of Ecology and Evolutionary Biology, Yale University, New Haven.,Department of Biostatistics, Yale School of Public Health, New Haven, Connecticut
| | - Junrui Wang
- Department of Ecology and Evolutionary Biology, Yale University, New Haven.,Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Elizabeth S Mo
- Yale Combined Program in the Biological and Biomedical Sciences, Yale School of Medicine, Yale University, New Haven
| | | | - Jeffrey P Townsend
- Department of Ecology and Evolutionary Biology, Yale University, New Haven.,Department of Biostatistics, Yale School of Public Health, New Haven, Connecticut.,Program in Microbiology, Yale University, New Haven
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31
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Zhu T, Li Y, Pang Y, Han Y, Li J, Wang Z, Liu X, Li H, Hua Y, Jiang H, Teng H, Quan J, Liu Y, Geng M, Li M, Hui F, Liu J, Qiu Q, Li Q, Ren Y. Chromosome-level genome assembly of Lethenteron reissneri provides insights into lamprey evolution. Mol Ecol Resour 2020; 21:448-463. [PMID: 33053263 DOI: 10.1111/1755-0998.13279] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Revised: 09/29/2020] [Accepted: 10/01/2020] [Indexed: 11/29/2022]
Abstract
The reissner lamprey Lethenteron reissneri, belonging to the class Cyclostomata, serves as a bridge between invertebrates and jawed vertebrates, and is considered the sister group of jawed vertebrates. However, despite this evolutionary significance, the genetic mechanisms underlying the adaptive evolution of the lamprey lineage remain unclear. Here, we assembled a 1.06 Gb chromosome-level draft genome of L. reissneri, with 72 chromosomes (ranging in length from 4.5 Mb to 25.9 Mb) and a scaffold N50 length of 13.23 Mb. Genome quality comparisons revealed that the reissner lamprey genome has higher completeness and contiguity than the previously published sea lamprey and Japanese lamprey genomes. Moreover, reissner lamprey, sea lamprey, and Japanese lamprey species share similar transposable element profiles and Hox gene cluster compositions, suggesting that a burst of transposable element activity and whole genome duplication occurred before their divergence. Additionally, the Lip gene copy numbers, which have been studied for their functions in the host defence system, were found to be expanded uniquely in lamprey lineages, suggesting key roles for these genes in lamprey evolution and adaptation. We also identified two neural-related genes, Nrn1 and Unc13a, with copy number expansions in jawed vertebrates, which may be functionally relevant to the origin of lamprey brains. Hence, this study not only provides the first chromosome-level reference genome for Cyclostomata, but also highlights features of the unique biology and adaptive evolution of the lamprey lineage.
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Affiliation(s)
- Ting Zhu
- College of Life Science, Liaoning Normal University, Dalian, China.,Lamprey Research Center, Liaoning Normal University, Dalian, China
| | - Yongxin Li
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China
| | - Yue Pang
- College of Life Science, Liaoning Normal University, Dalian, China.,Lamprey Research Center, Liaoning Normal University, Dalian, China
| | - Yinglun Han
- College of Life Science, Liaoning Normal University, Dalian, China.,Lamprey Research Center, Liaoning Normal University, Dalian, China
| | - Jun Li
- College of Life Science, Liaoning Normal University, Dalian, China.,Lamprey Research Center, Liaoning Normal University, Dalian, China
| | - Zhongkai Wang
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China
| | - Xin Liu
- College of Life Science, Liaoning Normal University, Dalian, China.,Lamprey Research Center, Liaoning Normal University, Dalian, China
| | - Haorong Li
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China
| | - Yishan Hua
- College of Life Science, Liaoning Normal University, Dalian, China.,Lamprey Research Center, Liaoning Normal University, Dalian, China
| | - Hui Jiang
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China
| | - Hongming Teng
- College of Life Science, Liaoning Normal University, Dalian, China.,Lamprey Research Center, Liaoning Normal University, Dalian, China
| | - Jian Quan
- College of Life Science, Liaoning Normal University, Dalian, China.,Lamprey Research Center, Liaoning Normal University, Dalian, China
| | - Yu Liu
- College of Life Science, Liaoning Normal University, Dalian, China.,Lamprey Research Center, Liaoning Normal University, Dalian, China
| | - Ming Geng
- College of Life Science, Liaoning Normal University, Dalian, China.,Lamprey Research Center, Liaoning Normal University, Dalian, China
| | - Meiao Li
- College of Life Science, Liaoning Normal University, Dalian, China.,Lamprey Research Center, Liaoning Normal University, Dalian, China
| | - Fan Hui
- College of Life Science, Liaoning Normal University, Dalian, China.,Lamprey Research Center, Liaoning Normal University, Dalian, China
| | - Jinzhao Liu
- College of Life Science, Liaoning Normal University, Dalian, China.,Lamprey Research Center, Liaoning Normal University, Dalian, China
| | - Qiang Qiu
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China
| | - Qingwei Li
- College of Life Science, Liaoning Normal University, Dalian, China.,Lamprey Research Center, Liaoning Normal University, Dalian, China
| | - Yandong Ren
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China
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32
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Li J, Liu H, Ma Q, Song X, Pang Y, Su P, Sun F, Gou M, Lu J, Shan Y, Guan H, Liu X, Li Q, Han Y. VLRs expression were significantly affected by complement C3 knockdown morphants in Lampetra morii. FISH & SHELLFISH IMMUNOLOGY 2020; 106:307-317. [PMID: 32681885 DOI: 10.1016/j.fsi.2020.07.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 07/01/2020] [Accepted: 07/08/2020] [Indexed: 06/11/2023]
Abstract
The complement component 3 of the lamprey, a jawless vertebrate, functions as an opsonin during the phagocytosis of rabbit red cells. Furthermore, lamprey C3 may be activated and cleaved into C3b, which is attached to the surface of target cells in the cytolytic process. However, the mechanism mediating the biological function of C3 in the lamprey is unknown. To our knowledge, this study is the first to show that variable lymphocyte receptors (VLRs) expression were significantly affected by complement C3 knockdown morphants in Lampetra morii. We identified the C3 gene in the lamprey genome based on its orthologs, conserved synteny, functional domains, phylogenetic tree, and conserved motifs. Additionally, we determined the optimal infection concentration of Aeromonas hydrophila to perform immune stimulation experiments in the lamprey larvae. The quantitative real-time polymerase chain reaction and immunofluorescence analyses revealed that the expression of Lampetra morii C3 (lmC3) was significantly upregulated in the larvae infected with 107 CFU/mL of A. hydrophila. The lmC3 morphants (lmC3 MO) of lamprey larvae were generated by morpholino-mediated knockdown. The lmC3 MO larvae were highly susceptible to A. hydrophila infection, which indicated that lmC3 is critical in lamprey immune response. The expression of a selected panel of orthologous genes was comparatively analyzed in the infected wild type, infected lmC3 MO, infected control MO, uninfected wild type and uninfected lmC3 MO one-month-old ammocoete larvae. The knockdown of lmC3 strongly affected the expression of VLRA+/VLRB+/VLRC+-associated genes, which was also confirmed by immunohistochemical analysis. Thus, VLR expression were significantly affected by complement C3 knockdown morphants in Lampetra morii.
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Affiliation(s)
- Jun Li
- College of Life Science, Liaoning Normal University, Dalian, 116029, China; Lamprey Research Center, Liaoning Normal University, Dalian, 116029, China; Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian, 116034, China
| | - Huaixiu Liu
- College of Life Science, Liaoning Normal University, Dalian, 116029, China; Lamprey Research Center, Liaoning Normal University, Dalian, 116029, China; Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian, 116034, China
| | - Qinghua Ma
- College of Life Science, Liaoning Normal University, Dalian, 116029, China; Lamprey Research Center, Liaoning Normal University, Dalian, 116029, China; Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian, 116034, China
| | - Xiaoping Song
- College of Life Science, Liaoning Normal University, Dalian, 116029, China; Lamprey Research Center, Liaoning Normal University, Dalian, 116029, China; Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian, 116034, China; Affiliated Zhongshan Hospital of Dalian University, Dalian, 116001, China
| | - Yue Pang
- College of Life Science, Liaoning Normal University, Dalian, 116029, China; Lamprey Research Center, Liaoning Normal University, Dalian, 116029, China; Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian, 116034, China
| | - Peng Su
- College of Life Science, Liaoning Normal University, Dalian, 116029, China; Lamprey Research Center, Liaoning Normal University, Dalian, 116029, China; Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian, 116034, China
| | - Feng Sun
- College of Life Science, Liaoning Normal University, Dalian, 116029, China; Lamprey Research Center, Liaoning Normal University, Dalian, 116029, China; Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian, 116034, China
| | - Meng Gou
- College of Life Science, Liaoning Normal University, Dalian, 116029, China; Lamprey Research Center, Liaoning Normal University, Dalian, 116029, China; Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian, 116034, China
| | - Jingjing Lu
- College of Life Science, Liaoning Normal University, Dalian, 116029, China; Lamprey Research Center, Liaoning Normal University, Dalian, 116029, China; Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian, 116034, China
| | - Yue Shan
- College of Life Science, Liaoning Normal University, Dalian, 116029, China; Lamprey Research Center, Liaoning Normal University, Dalian, 116029, China; Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian, 116034, China
| | - Haoran Guan
- College of Life Science, Liaoning Normal University, Dalian, 116029, China; Lamprey Research Center, Liaoning Normal University, Dalian, 116029, China; Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian, 116034, China
| | - Xin Liu
- College of Life Science, Liaoning Normal University, Dalian, 116029, China; Lamprey Research Center, Liaoning Normal University, Dalian, 116029, China; Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian, 116034, China
| | - Qingwei Li
- College of Life Science, Liaoning Normal University, Dalian, 116029, China; Lamprey Research Center, Liaoning Normal University, Dalian, 116029, China; Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian, 116034, China.
| | - Yinglun Han
- College of Life Science, Liaoning Normal University, Dalian, 116029, China; Lamprey Research Center, Liaoning Normal University, Dalian, 116029, China; Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian, 116034, China.
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Li J, Ma Q, Liu H, Song X, Pang Y, Su P, Sun F, Gou M, Lu J, Shan Y, Liu X, Li Q, Han Y. Complement component C1q plays a critical role in VLRA/VLRC-mediated immune response. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2020; 111:103750. [PMID: 32447013 DOI: 10.1016/j.dci.2020.103750] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 05/18/2020] [Accepted: 05/18/2020] [Indexed: 05/07/2023]
Abstract
In jawless vertebrates, the lamprey complement component C1q (LC1q) acts as a lectin and activates lamprey complement component C3 (LC3) in association with mannose-binding lectin (MBL)-associated serine protease (MASP) via the lectin pathway. Furthermore, LC1q may interact with variable lymphocyte receptor B (VLRB) in a complex with antigens and mediate the activation of LC3, leading to cytolysis. In the present study, we found, for the first time, that LC1q plays a critical role in VLRA/VLRC-mediated immune response. Escherichia coli, Shigella flexneri, Aeromonas hydrophila, Pseudomonas plecoglossicida, Aeromonas allosaccharophila, P. luteola, Brevundimonas diminuta, and Bacillus cereus were isolated from infected Lampetra morii in our laboratory and identified using the 16s rRNA method. A. hydrophila was confirmed as a rapidly spreading lethal pathogen in the larvae of L. morii and was used in subsequent immune stimulation experiments. The results of real-time quantitative polymerase chain reaction (Q-PCR) and immunofluorescence analyses indicated that the RNA and protein expression levels of LC1q were upregulated following exposure to 107 cfu/mL of A. hydrophila, compared to the levels of the naïve group. We obtained LC1q morphants (LC1q MO) of lamprey larvae by morpholino-mediated knockdowns. We found that LC1q played key roles in the embryonic development of lamprey. The median lethal time (LT50) of LC1q MO larvae was 2 d after being exposed to the pathogens, whereas the LT50 of control MO was 5 d. The drastic decrease in LT50 values after LC1q knockdown implies that LC1q plays a critical role in lamprey immune response. Gene expression profiles of LC1q-deficient A. hydrophila, control MO A. hydrophila, wild type A. hydrophila, and naive 1-month-old ammocoetes larvae were compared by examining the expression levels of a selected panel of orthologous genes. It is worth mentioning that LC1q MO affected the VLRA+/VLRC + population genes but did not affect the VLRB + populations. Immunohistochemical data indicated that LC1q deficiency also affected VLRA and VLRC but not VLRB. Thus, LC1q plays a critical role in VLRA/VLRC-mediated immune response in lamprey.
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Affiliation(s)
- Jun Li
- College of Life Science, Liaoning Normal University, Dalian, 116029, China; Lamprey Research Center, Liaoning Normal University, Dalian, 116029, China; Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian, 116034, China; Liaoning Key Laboratory of Aquatic Animal Infectious Diseases Control and Prevention, Liaoning Institute of Freshwater Fisheries Sciences, Liaoyang, 111000, China
| | - Qinghua Ma
- College of Life Science, Liaoning Normal University, Dalian, 116029, China; Lamprey Research Center, Liaoning Normal University, Dalian, 116029, China; Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian, 116034, China
| | - Huaixiu Liu
- College of Life Science, Liaoning Normal University, Dalian, 116029, China; Lamprey Research Center, Liaoning Normal University, Dalian, 116029, China; Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian, 116034, China
| | - Xiaoping Song
- College of Life Science, Liaoning Normal University, Dalian, 116029, China; Lamprey Research Center, Liaoning Normal University, Dalian, 116029, China; Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian, 116034, China; Affiliated Zhongshan Hospital of Dalian University, Dalian 116001, China
| | - Yue Pang
- College of Life Science, Liaoning Normal University, Dalian, 116029, China; Lamprey Research Center, Liaoning Normal University, Dalian, 116029, China; Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian, 116034, China
| | - Peng Su
- College of Life Science, Liaoning Normal University, Dalian, 116029, China; Lamprey Research Center, Liaoning Normal University, Dalian, 116029, China; Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian, 116034, China
| | - Feng Sun
- College of Life Science, Liaoning Normal University, Dalian, 116029, China; Lamprey Research Center, Liaoning Normal University, Dalian, 116029, China; Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian, 116034, China
| | - Meng Gou
- College of Life Science, Liaoning Normal University, Dalian, 116029, China; Lamprey Research Center, Liaoning Normal University, Dalian, 116029, China; Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian, 116034, China
| | - Jingjing Lu
- College of Life Science, Liaoning Normal University, Dalian, 116029, China; Lamprey Research Center, Liaoning Normal University, Dalian, 116029, China; Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian, 116034, China
| | - Yue Shan
- College of Life Science, Liaoning Normal University, Dalian, 116029, China; Lamprey Research Center, Liaoning Normal University, Dalian, 116029, China; Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian, 116034, China
| | - Xin Liu
- College of Life Science, Liaoning Normal University, Dalian, 116029, China; Lamprey Research Center, Liaoning Normal University, Dalian, 116029, China; Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian, 116034, China
| | - Qingwei Li
- College of Life Science, Liaoning Normal University, Dalian, 116029, China; Lamprey Research Center, Liaoning Normal University, Dalian, 116029, China; Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian, 116034, China
| | - Yinglun Han
- College of Life Science, Liaoning Normal University, Dalian, 116029, China; Lamprey Research Center, Liaoning Normal University, Dalian, 116029, China; Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian, 116034, China.
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Han Y, Li J, Pang Y, Xu L, Ma Q, Liu H, Song X, Su P, Sun F, Gou M, Lu J, Shan Y, Liu X, Li Q. Lamprey VLRB participates in pathogen detection, VLRB/L-BLNK/L-NF-κB (B-like cells) signal transduction, and development. FISH & SHELLFISH IMMUNOLOGY 2020; 105:446-456. [PMID: 32512043 DOI: 10.1016/j.fsi.2020.05.030] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 05/03/2020] [Accepted: 05/11/2020] [Indexed: 06/11/2023]
Abstract
In jawed vertebrates, B cell receptors (BCR) are primary pathogen detectors that activate downstream signaling pathways to express adaptive immune effectors. In jawless vertebrates, the variable lymphocyte receptors (VLR) B positive lymphocytes can express and secrete specific VLRB molecules in an analogous manner to that of immunoglobulins by B cells in jawed vertebrates. Our study is the first to demonstrate the possibility of incubation of fertilized eggs and artificial breeding of Lampetra morii larvae throughout their life cycle under laboratory condition. We also found that VLRB, lamprey B-cell linker (L-BLNK), and lamprey nuclear factor-kappa B (L-NF-κB) play key roles in early larval development. Aeromonas hydrophila was found to be a lethal pathogen of L. morii larvae causing rapid infection at a concentration of 107 cfu/mL qRT-PCR results revealed that gene expression levels of VLRB, L-BLNK, and L-NF-κB were up-regulated significantly. Ten-day infection trials showed that VLRB, L-BLNK, and L-NF-κB are crucial for lamprey immune response. Furthermore, the expression levels of L-BLNK and L-NF-κB were down-regulated drastically both at mRNA and protein levels after bacterial infection than in the naive group of VLRB morphants. A similar expression pattern of VLRB and L-BLNK was found in L-NF-κB morphants post bacterial infection. The results were strikingly different in the other two morphants. The VLRB and L-NF-κB expression levels were found to be down-regulated at mRNA and protein levels by less than 30% and 45%, respectively, in L-BLNK morphants compared to those in the naive group. These results indicate that L-BLNK and L-NF-κB might participate in VLRB-mediated immune response. Additionally, in VLRB morphants, the mRNA expression levels of some genes, especially the ones expressed in VLRB+ lymphocytes but not in VLRA+ lymphocytes, were found to be affected. Therefore, these findings of B-like lymphocytes in lamprey offer key evidence with regard to the evolution of adaptive immunity.
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Affiliation(s)
- Yinglun Han
- College of Life Science, Liaoning Normal University, Dalian, 116029, China; Lamprey Research Center, Liaoning Normal University, Dalian, 116029, China; Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian, 116034, China
| | - Jun Li
- College of Life Science, Liaoning Normal University, Dalian, 116029, China; Lamprey Research Center, Liaoning Normal University, Dalian, 116029, China; Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian, 116034, China; Liaoning Key Laboratory of Aquatic Animal Infectious Diseases Control and Prevention, Liaoning Institute of Freshwater Fisheries Sciences, Liaoyang, 111000, China
| | - Yue Pang
- College of Life Science, Liaoning Normal University, Dalian, 116029, China; Lamprey Research Center, Liaoning Normal University, Dalian, 116029, China; Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian, 116034, China
| | - Lei Xu
- College of Life Science, Liaoning Normal University, Dalian, 116029, China; Lamprey Research Center, Liaoning Normal University, Dalian, 116029, China; Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian, 116034, China; Beijing Cheng Mao Xing Ye Technology CO., LTD, Beijing, 100029, China
| | - Qinghua Ma
- College of Life Science, Liaoning Normal University, Dalian, 116029, China; Lamprey Research Center, Liaoning Normal University, Dalian, 116029, China; Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian, 116034, China
| | - Huaixiu Liu
- College of Life Science, Liaoning Normal University, Dalian, 116029, China; Lamprey Research Center, Liaoning Normal University, Dalian, 116029, China; Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian, 116034, China
| | - Xiaoping Song
- College of Life Science, Liaoning Normal University, Dalian, 116029, China; Lamprey Research Center, Liaoning Normal University, Dalian, 116029, China; Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian, 116034, China
| | - Peng Su
- College of Life Science, Liaoning Normal University, Dalian, 116029, China; Lamprey Research Center, Liaoning Normal University, Dalian, 116029, China; Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian, 116034, China
| | - Feng Sun
- College of Life Science, Liaoning Normal University, Dalian, 116029, China; Lamprey Research Center, Liaoning Normal University, Dalian, 116029, China; Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian, 116034, China
| | - Meng Gou
- College of Life Science, Liaoning Normal University, Dalian, 116029, China; Lamprey Research Center, Liaoning Normal University, Dalian, 116029, China; Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian, 116034, China
| | - Jingjing Lu
- College of Life Science, Liaoning Normal University, Dalian, 116029, China; Lamprey Research Center, Liaoning Normal University, Dalian, 116029, China; Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian, 116034, China
| | - Yue Shan
- College of Life Science, Liaoning Normal University, Dalian, 116029, China; Lamprey Research Center, Liaoning Normal University, Dalian, 116029, China; Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian, 116034, China
| | - Xin Liu
- College of Life Science, Liaoning Normal University, Dalian, 116029, China; Lamprey Research Center, Liaoning Normal University, Dalian, 116029, China; Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian, 116034, China.
| | - Qingwei Li
- College of Life Science, Liaoning Normal University, Dalian, 116029, China; Lamprey Research Center, Liaoning Normal University, Dalian, 116029, China; Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian, 116034, China.
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35
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Discovery of four Noggin genes in lampreys suggests two rounds of ancient genome duplication. Commun Biol 2020; 3:501. [PMID: 32913324 PMCID: PMC7483449 DOI: 10.1038/s42003-020-01234-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 07/20/2020] [Indexed: 01/10/2023] Open
Abstract
The secreted protein Noggin1 was the first discovered natural embryonic inducer produced by cells of the Spemann organizer. Thereafter, it was shown that vertebrates have a whole family of Noggin genes with different expression patterns and functional properties. For example, Noggin1 and Noggin2 inhibit the activity of BMP, Nodal/Activin and Wnt-beta-catenin signalling, while Noggin4 cannot suppress BMP but specifically modulates Wnt signalling. In this work, we described and investigated phylogeny and expression patterns of four Noggin genes in lampreys, which represent the most basally divergent group of extant vertebrates, the cyclostomes, belonging to the superclass Agnatha. Assuming that lampreys have Noggin homologues in all representatives of another superclass of vertebrates, the Gnathostomata, we propose a model for Noggin family evolution in vertebrates. This model is in agreement with the hypotheses suggesting two rounds of genome duplication in the ancestor of vertebrates before the divergence of Agnatha and Gnathostomata. Ermakova et al. report four Noggin genes in lampreys and using phylogenetics, gene synteny analysis, and in situ hybridization, suggest that the Noggin gene underwent two rounds of duplication and evolved specific functions before the divergence of vertebrate and lamprey lineages. These findings offer insight into early vertebrate genome and developmental evolution.
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36
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Kusakabe R, Higuchi S, Tanaka M, Kadota M, Nishimura O, Kuratani S. Novel developmental bases for the evolution of hypobranchial muscles in vertebrates. BMC Biol 2020; 18:120. [PMID: 32907560 PMCID: PMC7488077 DOI: 10.1186/s12915-020-00851-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 08/18/2020] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Vertebrates are characterized by possession of hypobranchial muscles (HBMs). Cyclostomes, or modern jawless vertebrates, possess a rudimentary and superficial HBM lateral to the pharynx, whereas the HBM in jawed vertebrates is internalized and anteroposteriorly specified. Precursor cells of the HBM, marked by expression of Lbx1, originate from somites and undergo extensive migration before becoming innervated by the hypoglossal nerve. How the complex form of HBM arose in evolution is relevant to the establishment of the vertebrate body plan, but despite having long been assumed to be similar to that of limb muscles, modification of developmental mechanisms of HBM remains enigmatic. RESULTS Here we characterize the expression of Lbx genes in lamprey and hagfish (cyclostomes) and catshark (gnathostome; jawed vertebrates). We show that the expression patterns of the single cyclostome Lbx homologue, Lbx-A, do not resemble the somitic expression of mammalian Lbx1. Disruption of Lbx-A revealed that LjLbx-A is required for the formation of both HBM and body wall muscles, likely due to the insufficient extension of precursor cells rather than to hindered muscle differentiation. Both homologues of Lbx in the catshark were expressed in the somitic muscle primordia, unlike in amniotes. During catshark embryogenesis, Lbx2 is expressed in the caudal HBM as well as in the abdominal rectus muscle, similar to lamprey Lbx-A, whereas Lbx1 marks the rostral HBM and pectoral fin muscle. CONCLUSIONS We conclude that the vertebrate HBM primarily emerged as a specialized somatic muscle to cover the pharynx, and the anterior internalized HBM of the gnathostomes is likely a novelty added rostral to the cyclostome-like HBM, for which duplication and functionalization of Lbx genes would have been a prerequisite.
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Affiliation(s)
- Rie Kusakabe
- Laboratory for Evolutionary Morphology, RIKEN Center for Biosystems Dynamics Research (BDR), 2-2-3 Minatojima-minami, Chuo-ku, Kobe, Hyogo, 650-0047, Japan.
| | - Shinnosuke Higuchi
- Laboratory for Evolutionary Morphology, RIKEN Center for Biosystems Dynamics Research (BDR), 2-2-3 Minatojima-minami, Chuo-ku, Kobe, Hyogo, 650-0047, Japan
- Department of Biology, Graduate School of Science, Kobe University, Kobe, 657-8501, Japan
- Department of Molecular Biology and Biochemistry, Graduate School of Biomedical & Health Sciences, Hiroshima University, Hiroshima, 734-8553, Japan
| | - Masako Tanaka
- Laboratory for Evolutionary Morphology, RIKEN Center for Biosystems Dynamics Research (BDR), 2-2-3 Minatojima-minami, Chuo-ku, Kobe, Hyogo, 650-0047, Japan
| | - Mitsutaka Kadota
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research (BDR), Kobe, 650-0047, Japan
| | - Osamu Nishimura
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research (BDR), Kobe, 650-0047, Japan
| | - Shigeru Kuratani
- Laboratory for Evolutionary Morphology, RIKEN Center for Biosystems Dynamics Research (BDR), 2-2-3 Minatojima-minami, Chuo-ku, Kobe, Hyogo, 650-0047, Japan
- Evolutionary Morphology Laboratory, RIKEN Cluster for Pioneering Research (CPR), Kobe, 650-0047, Japan
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Zhang Z, Zhang Q, Dexheimer TS, Ren J, Neubig RR, Li W. Two highly related odorant receptors specifically detect α-bile acid pheromones in sea lamprey ( Petromyzon marinus). J Biol Chem 2020; 295:12153-12166. [PMID: 32636305 PMCID: PMC7443511 DOI: 10.1074/jbc.ra119.011532] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 07/01/2020] [Indexed: 10/23/2022] Open
Abstract
Pheromones play critical roles in habitat identification and reproductive behavior synchronization in the sea lamprey (Petromyzon marinus). The bile acid 3-keto petromyzonol sulfate (3kPZS) is a major component of the sex pheromone mixture from male sea lamprey that induces specific olfactory and behavioral responses in conspecific individuals. Olfactory receptors interact directly with pheromones, which is the first step in their detection, but identifying the cognate receptors of specific pheromones is often challenging. Here, we deorphanized two highly related odorant receptors (ORs), OR320a and OR320b, of P. marinus that respond to 3kPZS. In a heterologous expression system coupled to a cAMP-responsive CRE-luciferase, OR320a and OR320b specifically responded to C24 5α-bile acids, and both receptors were activated by the same set of 3kPZS analogs. OR320a displayed larger responses to all 3kPZS analogs than did OR320b. This difference appeared to be largely determined by a single amino acid residue, Cys-792.56, the C-terminal sixth residue relative to the most conserved residue in the second transmembrane domain (2.56) of OR320a. This region of TM2 residues 2.56-2.60 apparently is critical for the detection of steroid compounds by odorant receptors in lamprey, zebrafish, and humans. Finally, we identified OR320 orthologs in Japanese lamprey (Lethenteron camtschaticum), suggesting that the OR320 family may be widely present in lamprey species and that OR320 may be under purifying selection. Our results provide a system to examine the origin of olfactory steroid detection in vertebrates and to define a highly conserved molecular mechanism for steroid-ligand detection by G protein-coupled receptors.
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Affiliation(s)
- Zhe Zhang
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, China; International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, China; Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai Ocean University, Shanghai, China
| | - Qinghua Zhang
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, China; International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, China; Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai Ocean University, Shanghai, China
| | - Thomas S Dexheimer
- Department of Pharmacology and Toxicology, Michigan State University, East Lansing, Michigan, USA
| | - Jianfeng Ren
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, China; International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, China; Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai Ocean University, Shanghai, China
| | - Richard R Neubig
- Department of Pharmacology and Toxicology, Michigan State University, East Lansing, Michigan, USA.
| | - Weiming Li
- Department of Fisheries and Wildlife, Michigan State University, East Lansing, Michigan, USA.
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Cardoso JCR, Bergqvist CA, Larhammar D. Corticotropin-Releasing Hormone (CRH) Gene Family Duplications in Lampreys Correlate With Two Early Vertebrate Genome Doublings. Front Neurosci 2020; 14:672. [PMID: 32848532 PMCID: PMC7406891 DOI: 10.3389/fnins.2020.00672] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 06/02/2020] [Indexed: 01/18/2023] Open
Abstract
The ancestor of gnathostomes (jawed vertebrates) is generally considered to have undergone two rounds of whole genome duplication (WGD). The timing of these WGD events relative to the divergence of the closest relatives of the gnathostomes, the cyclostomes, has remained contentious. Lampreys and hagfishes are extant cyclostomes whose gene families can shed light on the relationship between the WGDs and the cyclostome-gnathostome divergence. Previously, we have characterized in detail the evolution of the gnathostome corticotropin-releasing hormone (CRH) family and found that its five members arose from two ancestral genes that existed before the WGDs. The two WGDs resulted, after secondary losses, in one triplet consisting of CRH1, CRH2, and UCN1, and one pair consisting of UCN2 and UCN3. All five genes exist in representatives for cartilaginous fishes, ray-finned fishes, and lobe-finned fishes. Differential losses have occurred in some lineages. We present here analyses of CRH-family members in lamprey and hagfish by comparing sequences and gene synteny with gnathostomes. We found five CRH-family genes in each of two lamprey species (Petromyzon marinus and Lethenteron camtschaticum) and two genes in a hagfish (Eptatretus burgeri). Synteny analyses show that all five lamprey CRH-family genes have similar chromosomal neighbors as the gnathostome genes. The most parsimonious explanation is that the lamprey CRH-family genes are orthologs of the five gnathostome genes and thus arose in the same chromosome duplications. This suggests that lampreys and gnathostomes share the same two WGD events and that these took place before the lamprey-gnathostome divergence.
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Affiliation(s)
- João C R Cardoso
- Comparative Endocrinology and Integrative Biology, Centre of Marine Sciences, Universidade do Algarve, Faro, Portugal
| | - Christina A Bergqvist
- Department of Neuroscience, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Dan Larhammar
- Department of Neuroscience, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
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Ocampo Daza D, Haitina T. Reconstruction of the Carbohydrate 6-O Sulfotransferase Gene Family Evolution in Vertebrates Reveals Novel Member, CHST16, Lost in Amniotes. Genome Biol Evol 2020; 12:993-1012. [PMID: 32652010 PMCID: PMC7353957 DOI: 10.1093/gbe/evz274] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/10/2019] [Indexed: 12/24/2022] Open
Abstract
Glycosaminoglycans are sulfated polysaccharide molecules, essential for many biological processes. The 6-O sulfation of glycosaminoglycans is carried out by carbohydrate 6-O sulfotransferases (C6OSTs), previously named Gal/GalNAc/GlcNAc 6-O sulfotransferases. Here, for the first time, we present a detailed phylogenetic reconstruction, analysis of gene synteny conservation and propose an evolutionary scenario for the C6OST family in major vertebrate groups, including mammals, birds, nonavian reptiles, amphibians, lobe-finned fishes, ray-finned fishes, cartilaginous fishes, and jawless vertebrates. The C6OST gene expansion likely started early in the chordate lineage, giving rise to four ancestral genes after the divergence of tunicates and before the emergence of extant vertebrates. The two rounds of whole-genome duplication in early vertebrate evolution (1R/2R) only contributed two additional C6OST subtype genes, increasing the vertebrate repertoire from four genes to six, divided into two branches. The first branch includes CHST1 and CHST3 as well as a previously unrecognized subtype, CHST16 that was lost in amniotes. The second branch includes CHST2, CHST7, and CHST5. Subsequently, local duplications of CHST5 gave rise to CHST4 in the ancestor of tetrapods, and to CHST6 in the ancestor of primates. The teleost-specific gene duplicates were identified for CHST1, CHST2, and CHST3 and are result of whole-genome duplication (3R) in the teleost lineage. We could also detect multiple, more recent lineage-specific duplicates. Thus, the vertebrate repertoire of C6OST genes has been shaped by gene duplications and gene losses at several stages of vertebrate evolution, with implications for the evolution of skeleton, nervous system, and cell-cell interactions.
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Affiliation(s)
- Daniel Ocampo Daza
- Department of Organismal Biology, Uppsala University, Sweden
- School of Natural Sciences, University of California Merced
| | - Tatjana Haitina
- Department of Organismal Biology, Uppsala University, Sweden
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40
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Bayramov AV, Ermakova GV, Zaraisky AG. Genetic Mechanisms of the Early Development of the Telencephalon, a Unique Segment of the Vertebrate Central Nervous System, as Reflecting Its Emergence and Evolution. Russ J Dev Biol 2020. [DOI: 10.1134/s1062360420030054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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41
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The non-visual opsins expressed in deep brain neurons projecting to the retina in lampreys. Sci Rep 2020; 10:9669. [PMID: 32541666 PMCID: PMC7295746 DOI: 10.1038/s41598-020-66679-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 05/26/2020] [Indexed: 11/23/2022] Open
Abstract
In lower vertebrates, brain photoreceptor cells express vertebrate-specific non-visual opsins. We previously revealed that a pineal-related organ-specific opsin, parapinopsin, is UV-sensitive and allows pineal wavelength discrimination in lampreys and teleost. The Australian pouched lamprey was recently reported as having two parapinopsin-related genes. We demonstrate that a parapinopsin-like opsin from the Japanese river lamprey exhibits different molecular properties and distribution than parapinopsin. This opsin activates Gi-type G protein in a mammalian cell culture assay in a light-dependent manner. Heterologous action spectroscopy revealed that the opsin forms a violet to blue-sensitive pigment. Interestingly, the opsin is co-localised with green-sensitive P-opsin in the cells of the M5 nucleus of Schober (M5NS) in the mesencephalon of the river and brook lamprey. Some opsins-containing cells of the river lamprey have cilia and others an axon projecting to the retina. The opsins of the brook lamprey are co-localised in the cilia of centrifugal neurons projecting to the retina, suggesting that cells expressing the parapinopsin-like opsin and P-opsin are sensitive to violet to green light. Moreover, we found neural connections between M5NS cells expressing the opsins and the retina. These findings suggest that the retinal activity might be modulated by brain photoreception.
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42
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Simakov O, Marlétaz F, Yue JX, O'Connell B, Jenkins J, Brandt A, Calef R, Tung CH, Huang TK, Schmutz J, Satoh N, Yu JK, Putnam NH, Green RE, Rokhsar DS. Deeply conserved synteny resolves early events in vertebrate evolution. Nat Ecol Evol 2020; 4:820-830. [PMID: 32313176 PMCID: PMC7269912 DOI: 10.1038/s41559-020-1156-z] [Citation(s) in RCA: 169] [Impact Index Per Article: 42.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Accepted: 02/19/2020] [Indexed: 01/24/2023]
Abstract
Although it is widely believed that early vertebrate evolution was shaped by ancient whole-genome duplications, the number, timing and mechanism of these events remain elusive. Here, we infer the history of vertebrates through genomic comparisons with a new chromosome-scale sequence of the invertebrate chordate amphioxus. We show how the karyotypes of amphioxus and diverse vertebrates are derived from 17 ancestral chordate linkage groups (and 19 ancestral bilaterian groups) by fusion, rearrangement and duplication. We resolve two distinct ancient duplications based on patterns of chromosomal conserved synteny. All extant vertebrates share the first duplication, which occurred in the mid/late Cambrian by autotetraploidization (that is, direct genome doubling). In contrast, the second duplication is found only in jawed vertebrates and occurred in the mid-late Ordovician by allotetraploidization (that is, genome duplication following interspecific hybridization) from two now-extinct progenitors. This complex genomic history parallels the diversification of vertebrate lineages in the fossil record.
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Affiliation(s)
- Oleg Simakov
- Molecular Genetics Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan.
- Department of Neuroscience and Developmental Biology, University of Vienna, Vienna, Austria.
| | - Ferdinand Marlétaz
- Molecular Genetics Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Jia-Xing Yue
- Université Côte d'Azur, CNRS, INSERM, IRCAN, Nice, France
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Brendan O'Connell
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Jerry Jenkins
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Alexander Brandt
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | | | - Che-Huang Tung
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
| | - Tzu-Kai Huang
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
| | - Jeremy Schmutz
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Nori Satoh
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Jr-Kai Yu
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
| | | | - Richard E Green
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Daniel S Rokhsar
- Molecular Genetics Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan.
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
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43
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Zhang Z, Gao X, Zhang Q, Li W. Constitutive activity of a spermine receptor is maintained by a single site in the C-terminal. Biochem Biophys Res Commun 2020; 526:389-395. [PMID: 32222281 DOI: 10.1016/j.bbrc.2020.03.053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 03/08/2020] [Indexed: 11/28/2022]
Abstract
Olfactory receptors are G-protein coupled receptors (GPCRs) that enable olfactory epithelia to detect odorants. These GPCRs may also show constitutive activity, which play important roles in the development and responses of odorant receptor neurons. However, little is known about the molecular characteristics that support the constitutive activities in olfactory receptors. Here, we characterize a pair of olfactory receptor orthologs that show similar ligand-dependent activity but different levels of constitutive activity, and elucidate the molecular characteristics that maintain the constitutive activity. Previously, PmTAAR348, a sea lamprey (Petromyzon marinus) olfactory receptor that is activated by the male sex pheromone spermine has been reported. In this study, we identified LmTAAR348 of Northeast Chinese lamprey (Lethenteron morii) as an ortholog of PmTAAR348. When expressed in HEK293T cell lines, both receptors showed similar levels of activation when exposed to spermine. However, the constitutive activity of LmTAAR348 was 100-fold higher than that of PmTAAR348. Using site-directed mutagenesis, we screened all 13 amino acid residues (aa) that differed between the two orthologs and found that a switch in position 340 reversed the constitutive activity levels between LmTAAR348 and PmTAAR348. Mutating the remaining 12 aa did not affect the ligand-dependent or constitutive activation. Moreover, both the ligand-dependent and constitutive activation of TAAR348 are Golf (G protein ⍺ subunit olfactory type) independent. We conclude that a single aa in the C-terminal maintains the constitutive activity in a spermine receptor.
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Affiliation(s)
- Zhe Zhang
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, 201306, China; International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, 201306, China; Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai Ocean University, Shanghai, 201306, China
| | - Xiang Gao
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, 201306, China; International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, 201306, China; Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai Ocean University, Shanghai, 201306, China
| | - Qinghua Zhang
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, 201306, China; International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, 201306, China; Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai Ocean University, Shanghai, 201306, China
| | - Weming Li
- Department of Fisheries and Wildlife, Michigan State University, East Lansing, MI, 48824, USA.
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44
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Kon T, Furukawa T. Origin and evolution of the Rax homeobox gene by comprehensive evolutionary analysis. FEBS Open Bio 2020; 10:657-673. [PMID: 32144893 PMCID: PMC7137802 DOI: 10.1002/2211-5463.12832] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2019] [Revised: 02/26/2020] [Accepted: 03/04/2020] [Indexed: 12/20/2022] Open
Abstract
Rax is one of the key transcription factors crucial for vertebrate eye development. In this study, we conducted comprehensive evolutionary analysis of Rax. We found that Bilateria and Cnidaria possess Rax, but Placozoa, Porifera, and Ctenophora do not, implying that the origin of the Rax gene dates back to the common ancestor of Cnidaria and Bilateria. The results of molecular phylogenetic and synteny analyses on Rax loci between jawed and jawless vertebrates indicate that segmental duplication of the Rax locus occurred in an early common ancestor of jawed vertebrates, resulting in two Rax paralogs in jawed vertebrates, Rax and Rax2. By analyzing 86 mammalian genomes from all four major groups of mammals, we found that at least five independent Rax2 gene loss events occurred in mammals. This study may provide novel insights into the evolution of the eye.
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Affiliation(s)
- Tetsuo Kon
- Laboratory for Molecular and Developmental Biology, Institute for Protein Research, Osaka University, Suita, Japan
| | - Takahisa Furukawa
- Laboratory for Molecular and Developmental Biology, Institute for Protein Research, Osaka University, Suita, Japan
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45
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Gong N, Ferreira-Martins D, McCormick SD, Sheridan MA. Divergent genes encoding the putative receptors for growth hormone and prolactin in sea lamprey display distinct patterns of expression. Sci Rep 2020; 10:1674. [PMID: 32015405 PMCID: PMC6997183 DOI: 10.1038/s41598-020-58344-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 01/14/2020] [Indexed: 01/08/2023] Open
Abstract
Growth hormone receptor (GHR) and prolactin receptor (PRLR) in jawed vertebrates were thought to arise after the divergence of gnathostomes from a basal vertebrate. In this study we have identified two genes encoding putative GHR and PRLR in sea lamprey (Petromyzon marinus) and Arctic lamprey (Lethenteron camtschaticum), extant members of one of the oldest vertebrate groups, agnathans. Phylogenetic analysis revealed that lamprey GHR and PRLR cluster at the base of gnathostome GHR and PRLR clades, respectively. This indicates that distinct GHR and PRLR arose prior to the emergence of the lamprey branch of agnathans. In the sea lamprey, GHR and PRLR displayed a differential but overlapping pattern of expression; GHR had high expression in liver and heart tissues, whereas PRLR was expressed highly in the brain and moderately in osmoregulatory tissues. Branchial PRLR mRNA levels were significantly elevated by stage 5 of metamorphosis and remained elevated through stage 7, whereas levels of GHR mRNA were only elevated in the final stage (7). Branchial expression of GHR increased following seawater (SW) exposure of juveniles, but expression of PRLR was not significantly altered. The results indicate that GHR and PRLR may both participate in metamorphosis and that GHR may mediate SW acclimation.
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Affiliation(s)
- Ningping Gong
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, 79409, USA.
| | - Diogo Ferreira-Martins
- Department of Biology, University of Massachusetts, Amherst, MA, USA.,U.S. Geological Survey, Leetown Science Center, S.O. Conte Anadromous Fish Research Laboratory, Turners Falls, MA, 01376, USA
| | - Stephen D McCormick
- Department of Biology, University of Massachusetts, Amherst, MA, USA.,U.S. Geological Survey, Leetown Science Center, S.O. Conte Anadromous Fish Research Laboratory, Turners Falls, MA, 01376, USA
| | - Mark A Sheridan
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, 79409, USA.
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46
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Mayasich SA, Clarke BL. Vasotocin and the origins of the vasopressin/oxytocin receptor gene family. VITAMINS AND HORMONES 2020; 113:1-27. [DOI: 10.1016/bs.vh.2019.08.018] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/13/2023]
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47
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Lampreys, the jawless vertebrates, contain three Pax6 genes with distinct expression in eye, brain and pancreas. Sci Rep 2019; 9:19559. [PMID: 31863055 PMCID: PMC6925180 DOI: 10.1038/s41598-019-56085-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2019] [Accepted: 12/02/2019] [Indexed: 12/22/2022] Open
Abstract
The transcription factor Pax6 is crucial for the development of the central nervous system, eye, olfactory system and pancreas, and is implicated in human disease. While a single Pax6 gene exists in human and chicken, Pax6 occurs as a gene family in other vertebrates, with two members in elephant shark, Xenopus tropicalis and Anolis lizard and three members in teleost fish such as stickleback and medaka. However, the complement of Pax6 genes in jawless vertebrates (cyclostomes), the sister group of jawed vertebrates (gnathostomes), is unknown. Using a combination of BAC sequencing and genome analysis, we discovered three Pax6 genes in lampreys. Unlike the paired-less Pax6 present in some gnathostomes, all three lamprey Pax6 have a highly conserved full-length paired domain. All three Pax6 genes are expressed in the eye and brain, with variable expression in other tissues. Notably, lamprey Pax6α transcripts are found in the pancreas, a vertebrate-specific organ, indicating the involvement of Pax6 in development of the pancreas in the vertebrate ancestor. Multi-species sequence comparisons revealed only a single conserved non-coding element, in the lamprey Pax6β locus, with similarity to the PAX6 neuroretina enhancer. Using a transgenic zebrafish enhancer assay we demonstrate functional conservation of this element over 500 million years of vertebrate evolution.
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48
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Shaughnessy CA, McCormick SD. Functional characterization and osmoregulatory role of the Na +-K +-2Cl - cotransporter in the gill of sea lamprey ( Petromyzon marinus), a basal vertebrate. Am J Physiol Regul Integr Comp Physiol 2019; 318:R17-R29. [PMID: 31617750 DOI: 10.1152/ajpregu.00125.2019] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The present study provides molecular and functional characterization of Na+-K+-2Cl- cotransporter (NKCC1/Slc12a2) in the gills of sea lamprey (Petromyzon marinus), the most basal extant vertebrate with an osmoregulatory strategy. We report the full-length peptide sequence for the lamprey Na-K-Cl cotransporter 1 (NKCC1), which we show groups strongly with and occupies a basal position among other vertebrate NKCC1 sequences. In postmetamorphic juvenile lamprey, nkcc1 mRNA was present in many tissues but was fivefold higher in the gill than any other examined tissue, and NKCC1 protein was only detected in the gill. Gill mRNA and protein abundances of NKCC1 and Na+-K+-ATPase (NKA/Atp1a1) were significantly upregulated (20- to 200-fold) during late metamorphosis in fresh water, coinciding with the development of salinity tolerance, and were upregulated an additional twofold after acclimation to seawater (SW). Immunohistochemistry revealed that NKCC1 in the gill is found in filamental ionocytes coexpressing NKA, which develop during metamorphosis in preparation for SW entry. Lamprey treated with bumetanide, a widely used pharmacological inhibitor of NKCC1, exhibited higher plasma Cl- and osmolality as well as reduced muscle water content after 24 h in SW; there were no effects of bumetanide in freshwater-acclimated lamprey. This work provides the first functional characterization of NKCC1 as a mechanism for branchial salt secretion in lampreys, providing evidence that this mode of Cl- secretion has been present among vertebrates for ~550 million years.
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Affiliation(s)
- Ciaran A Shaughnessy
- Graduate Program in Organismic and Evolutionary Biology, University of Massachusetts, Amherst, Massachusetts
| | - Stephen D McCormick
- United States.Geological Survey, Leetown Science Center, Conte Anadromous Fish Research Laboratory, Turners Falls, Massachusetts.,Department of Biology, University of Massachusetts, Amherst, Massachusetts
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49
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Characterization and Evolution of Germ1, an Element that Undergoes Diminution in Lampreys (Cyclostomata: Petromyzontidae). J Mol Evol 2019; 87:298-308. [PMID: 31486871 DOI: 10.1007/s00239-019-09909-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 08/23/2019] [Indexed: 12/23/2022]
Abstract
The sea lamprey (Petromyzon marinus) undergoes substantial genomic alterations during embryogenesis in which specific sequences are deleted from the genome of somatic cells yet retained in cells of the germ line. One element that undergoes diminution in P. marinus is Germ1, which consists of a somatically rare (SR) region and a fragment of 28S rDNA. Although the SR-region has been used as a marker for genomic alterations in lampreys, the evolutionary significance of its diminution is unknown. We examined the Germ1 element in five additional species of lamprey to better understand its evolutionary significance. Each representative species contained sequences similar enough to the Germ1 element of P. marinus to be detected via PCR and Southern hybridizations, although the SR-regions of Lampetra aepyptera and Lethenteron appendix are quite divergent from the homologous sequences of Petromyzon and three species of Ichthyomyzon. Lamprey Germ1 sequences have a number of features characteristic of the R2 retrotransposon, a mobile element that specifically targets 28S rDNA. Phylogenetic analyses of the SR-regions revealed patterns generally consistent with relationships among the species included in our study, although the 28S-fragments of each species/genus were most closely related to its own functional rDNA, suggesting that the two components of Germ1 were assembled independently in each lineage. Southern hybridizations showed evidence of genomic alterations involving Germ1 in each species. Our results suggest that Germ1 is a R2 retroelement that occurs in the genome of P. marinus and other petromyzontid lampreys, and that its diminution is incidental to the reduction in rDNA copies during embryogenesis.
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Leung B, Shimeld SM. Evolution of vertebrate spinal cord patterning. Dev Dyn 2019; 248:1028-1043. [PMID: 31291046 DOI: 10.1002/dvdy.77] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 06/14/2019] [Accepted: 06/15/2019] [Indexed: 12/17/2022] Open
Abstract
The vertebrate spinal cord is organized across three developmental axes, anterior-posterior (AP), dorsal-ventral (DV), and medial-lateral (ML). Patterning of these axes is regulated by canonical intercellular signaling pathways: the AP axis by Wnt, fibroblast growth factor, and retinoic acid (RA), the DV axis by Hedgehog, Tgfβ, and Wnt, and the ML axis where proliferation is controlled by Notch. Developmental time plays an important role in which signal does what and when. Patterning across the three axes is not independent, but linked by interactions between signaling pathway components and their transcriptional targets. Combined this builds a sophisticated organ with many different types of cell in specific AP, DV, and ML positions. Two living lineages share phylum Chordata with vertebrates, amphioxus, and tunicates, while the jawless fish such as lampreys, survive as the most basally divergent vertebrate lineage. Genes and mechanisms shared between lampreys and other vertebrates tell us what predated vertebrates, while those also shared with other chordates tell us what evolved early in chordate evolution. Between these lie vertebrate innovations: genetic and developmental changes linked to evolution of new morphology. These include gene duplications, differences in how signals are received, and new regulatory connections between signaling pathways and their target genes.
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Affiliation(s)
- Brigid Leung
- Department of Zoology, University of Oxford, Oxford, UK
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