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Abu Nahia K, Sulej A, Migdał M, Ochocka N, Ho R, Kamińska B, Zagorski M, Winata CL. scRNA-seq reveals the diversity of the developing cardiac cell lineage and molecular players in heart rhythm regulation. iScience 2024; 27:110083. [PMID: 38872974 PMCID: PMC11170199 DOI: 10.1016/j.isci.2024.110083] [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: 10/06/2023] [Revised: 01/26/2024] [Accepted: 05/20/2024] [Indexed: 06/15/2024] Open
Abstract
We utilized scRNA-seq to delineate the diversity of cell types in the zebrafish heart. Transcriptome profiling of over 50,000 cells at 48 and 72 hpf defined at least 18 discrete cell lineages of the developing heart. Utilizing well-established gene signatures, we identified a population of cells likely to be the primary pacemaker and characterized the transcriptome profile defining this critical cell type. Two previously uncharacterized genes, atp1b3b and colec10, were found to be enriched in the sinoatrial cardiomyocytes. CRISPR/Cas9-mediated knockout of these two genes significantly reduced heart rate, implicating their role in cardiac development and conduction. Additionally, we describe other cardiac cell lineages, including the endothelial and neural cells, providing their expression profiles as a resource. Our results established a detailed atlas of the developing heart, providing valuable insights into cellular and molecular mechanisms, and pinpointed potential new players in heart rhythm regulation.
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Affiliation(s)
- Karim Abu Nahia
- International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Agata Sulej
- International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Maciej Migdał
- International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Natalia Ochocka
- Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology, Warsaw, Poland
| | - Richard Ho
- Institute of Theoretical Physics and Mark Kac Center for Complex Systems Research, Jagiellonian University, Cracow, Poland
- The Njord Centre, Department of Physics, University of Oslo, Oslo, Norway
| | - Bożena Kamińska
- Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology, Warsaw, Poland
| | - Marcin Zagorski
- Institute of Theoretical Physics and Mark Kac Center for Complex Systems Research, Jagiellonian University, Cracow, Poland
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2
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Healey HM, Penn HB, Small CM, Bassham S, Goyal V, Woods MA, Cresko WA. Single Cell RNA Sequencing Provides Clues for the Developmental Genetic Basis of Syngnathidae's Evolutionary Adaptations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.08.588518. [PMID: 38645265 PMCID: PMC11030337 DOI: 10.1101/2024.04.08.588518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
Seahorses, pipefishes, and seadragons are fishes from the family Syngnathidae that have evolved extraordinary traits including male pregnancy, elongated snouts, loss of teeth, and dermal bony armor. The developmental genetic and cellular changes that led to the evolution of these traits are largely unknown. Recent syngnathid genomes revealed suggestive gene content differences and provide the opportunity for detailed genetic analyses. We created a single cell RNA sequencing atlas of Gulf pipefish embryos to understand the developmental basis of four traits: derived head shape, toothlessness, dermal armor, and male pregnancy. We completed marker gene analyses, built genetic networks, and examined spatial expression of select genes. We identified osteochondrogenic mesenchymal cells in the elongating face that express regulatory genes bmp4, sfrp1a, and prdm16. We found no evidence for tooth primordia cells, and we observed re-deployment of osteoblast genetic networks in developing dermal armor. Finally, we found that epidermal cells expressed nutrient processing and environmental sensing genes, potentially relevant for the brooding environment. The examined pipefish evolutionary innovations are composed of recognizable cell types, suggesting derived features originate from changes within existing gene networks. Future work addressing syngnathid gene networks across multiple stages and species is essential for understanding how their novelties evolved.
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Affiliation(s)
- Hope M Healey
- Institute of Ecology and Evolution, University of Oregon
| | - Hayden B Penn
- Institute of Ecology and Evolution, University of Oregon
| | - Clayton M Small
- Institute of Ecology and Evolution, University of Oregon
- School of Computer and Data Science, University of Oregon
| | - Susan Bassham
- Institute of Ecology and Evolution, University of Oregon
| | - Vithika Goyal
- Institute of Ecology and Evolution, University of Oregon
| | - Micah A Woods
- Institute of Ecology and Evolution, University of Oregon
| | - William A Cresko
- Institute of Ecology and Evolution, University of Oregon
- Knight Campus for Accelerating Scientific Impact, University of Oregon
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3
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Proffitt MR, Liu X, Ortlund EA, Smith GT. Evolution of androgen receptors contributes to species variation in androgenic regulation of communication signals in electric fishes. Mol Cell Endocrinol 2023; 578:112068. [PMID: 37714403 PMCID: PMC10695101 DOI: 10.1016/j.mce.2023.112068] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 08/31/2023] [Accepted: 09/11/2023] [Indexed: 09/17/2023]
Abstract
Hormones and receptors coevolve to generate species diversity in hormone action. We compared the structure and function of androgen receptors (ARs) across fishes, with a focus on ARs in ghost knifefishes (Apteronotidae). Apteronotids, like many other teleosts, have two ARs (ARα and ARβ). ARβ is largely conserved, whereas ARα sequences vary considerably across species. The ARα ligand binding domain (LBD) has evolved under positive selection, and differences in the LBD across apteronotid species are associated with diversity in androgenic regulation of behavior. The Apteronotus leptorhynchus ARα LBD differs substantially from that of the Apteronotus albifrons ARα or the ancestral AR. Structural modeling and transactivation assays demonstrated that A. leptorhynchus ARα cannot bind androgens. We propose a model whereby relative expression of ARα versus ARβ in the brain, coupled with loss of androgen binding by ARα in A. leptorhynchus might explain reversals in androgenic regulation and sex differences in electrocommunication behavior.
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Affiliation(s)
- Melissa Renee Proffitt
- Department of Biology and Center for the Integrative Study of Animal Behavior, Indiana University, Bloomington, IN, USA
| | - Xu Liu
- Department of Biochemistry, Emory University, Atlanta, GA, USA
| | - Eric A Ortlund
- Department of Biochemistry, Emory University, Atlanta, GA, USA
| | - G Troy Smith
- Department of Biology and Center for the Integrative Study of Animal Behavior, Indiana University, Bloomington, IN, USA.
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4
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Gafranek JT, D'Aniello E, Ravisankar P, Thakkar K, Vagnozzi RJ, Lim HW, Salomonis N, Waxman JS. Sinus venosus adaptation models prolonged cardiovascular disease and reveals insights into evolutionary transitions of the vertebrate heart. Nat Commun 2023; 14:5509. [PMID: 37679366 PMCID: PMC10485058 DOI: 10.1038/s41467-023-41184-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 08/24/2023] [Indexed: 09/09/2023] Open
Abstract
How two-chambered hearts in basal vertebrates have evolved from single-chamber hearts found in ancestral chordates remains unclear. Here, we show that the teleost sinus venosus (SV) is a chamber-like vessel comprised of an outer layer of smooth muscle cells. We find that in adult zebrafish nr2f1a mutants, which lack atria, the SV comes to physically resemble the thicker bulbus arteriosus (BA) at the arterial pole of the heart through an adaptive, hypertensive response involving smooth muscle proliferation due to aberrant hemodynamic flow. Single cell transcriptomics show that smooth muscle and endothelial cell populations within the adapting SV also take on arterial signatures. Bulk transcriptomics of the blood sinuses flanking the tunicate heart reinforce a model of greater equivalency in ancestral chordate BA and SV precursors. Our data simultaneously reveal that secondary complications from congenital heart defects can develop in adult zebrafish similar to those in humans and that the foundation of equivalency between flanking auxiliary vessels may remain latent within basal vertebrate hearts.
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Affiliation(s)
- Jacob T Gafranek
- Molecular and Developmental Biology Graduate Program, University of Cincinnati College of Medicine, Cincinnati, OH, 45267, USA
- Division of Molecular Cardiovascular Biology and Heart Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Enrico D'Aniello
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, 80121, Napoli, Italy
| | - Padmapriyadarshini Ravisankar
- Division of Molecular Cardiovascular Biology and Heart Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Kairavee Thakkar
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
- Department of Pharmacology and Systems Physiology, University of Cincinnati, College of Medicine, Cincinnati, OH, 45267, USA
| | - Ronald J Vagnozzi
- Division of Cardiology, Gates Center for Regenerative Medicine, Consortium for Fibrosis Research and Translation (CFReT), University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Hee-Woong Lim
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
- Department of Pediatrics, University of Cincinnati, College of Medicine, Cincinnati, OH, 45267, USA
| | - Nathan Salomonis
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
- Department of Pediatrics, University of Cincinnati, College of Medicine, Cincinnati, OH, 45267, USA
| | - Joshua S Waxman
- Division of Molecular Cardiovascular Biology and Heart Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA.
- Department of Pediatrics, University of Cincinnati, College of Medicine, Cincinnati, OH, 45267, USA.
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA.
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5
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Hoareau M, El Kholti N, Debret R, Lambert E. Characterization of the Zebrafish Elastin a ( elnasa12235) Mutant: A New Model of Elastinopathy Leading to Heart Valve Defects. Cells 2023; 12:1436. [PMID: 37408270 DOI: 10.3390/cells12101436] [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: 03/17/2023] [Revised: 05/18/2023] [Accepted: 05/19/2023] [Indexed: 07/07/2023] Open
Abstract
Elastic fibers are extracellular macromolecules that provide resilience and elastic recoil to elastic tissues and organs in vertebrates. They are composed of an elastin core surrounded by a mantle of fibrillin-rich microfibrils and are essentially produced during a relatively short period around birth in mammals. Thus, elastic fibers have to resist many physical, chemical, and enzymatic constraints occurring throughout their lives, and their high stability can be attributed to the elastin protein. Various pathologies, called elastinopathies, are linked to an elastin deficiency, such as non-syndromic supravalvular aortic stenosis (SVAS), Williams-Beuren syndrome (WBS), and autosomal dominant cutis laxa (ADCL). To understand these diseases, as well as the aging process related to elastic fiber degradation, and to test potential therapeutic molecules in order to compensate for elastin impairments, different animal models have been proposed. Considering the many advantages of using zebrafish, we here characterize a zebrafish mutant for the elastin a paralog (elnasa12235) with a specific focus on the cardiovascular system and highlight premature heart valve defects at the adult stage.
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Affiliation(s)
- Marie Hoareau
- Laboratoire de Biologie Tissulaire et Ingénierie Thérapeutique (LBTI), UMR CNRS 5305, Institut de Biologie et Chimie des Protéines, Université de Lyon 1, 7 Passage du Vercors, CEDEX 07, F-69367 Lyon, France
| | - Naïma El Kholti
- Laboratoire de Biologie Tissulaire et Ingénierie Thérapeutique (LBTI), UMR CNRS 5305, Institut de Biologie et Chimie des Protéines, Université de Lyon 1, 7 Passage du Vercors, CEDEX 07, F-69367 Lyon, France
| | - Romain Debret
- Laboratoire de Biologie Tissulaire et Ingénierie Thérapeutique (LBTI), UMR CNRS 5305, Institut de Biologie et Chimie des Protéines, Université de Lyon 1, 7 Passage du Vercors, CEDEX 07, F-69367 Lyon, France
| | - Elise Lambert
- Laboratoire de Biologie Tissulaire et Ingénierie Thérapeutique (LBTI), UMR CNRS 5305, Institut de Biologie et Chimie des Protéines, Université de Lyon 1, 7 Passage du Vercors, CEDEX 07, F-69367 Lyon, France
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6
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Dimos B, Phelps M. A homology guide for Pacific salmon genus Oncorhynchus resolves patterns of ohnolog retention, resolution and local adaptation following the salmonid-specific whole-genome duplication event. Ecol Evol 2023; 13:e9994. [PMID: 37091557 PMCID: PMC10119027 DOI: 10.1002/ece3.9994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 03/17/2023] [Accepted: 03/21/2023] [Indexed: 04/25/2023] Open
Abstract
Salmonid fishes have emerged as a tractable model to study whole-genome duplications (WGDs) as this group has undergone four rounds of WGDs. While most of the salmonid genome has returned to a diploid state, a significant proportion of genes are maintained as duplicates and are referred to as ohnologs. The fact that much of the modern salmonid gene repertoire is comprised of ohnologs, while other genes have returned to their singleton state creates complications for genetic studies by obscuring homology relationships. The difficulty this creates is particularly prominent in Pacific salmonids belonging to genus Oncorhynchus who are the focus of intense genetics-based conservation and management efforts owing to the important ecological and cultural roles these fish play. To address this gap, we generated a homology guide for six species of Oncorhynchus with available genomes and used this guide to describe patterns of ohnolog retention and resolution. Overall, we find that ohnologs comprise approximately half of each species modern gene repertoires, which are functionally enriched for genes involved in DNA binding, while the less numerous singleton genes are heavily enriched in dosage-sensitive processes such as mitochondrial metabolism. Additionally, by reanalyzing published expression data from locally adapted strains of O. mykiss, we show that numerous ohnologs exhibit adaptive expression profiles; however, ohnologs are not more likely to display adaptive signatures than either paralogs or singletons. Finally, we demonstrate the utility of our homology guide by investigating the evolutionary relationship among genes highlighted as playing a role in salmonid life-history traits or gene editing targets.
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Affiliation(s)
- Bradford Dimos
- Department of Animal SciencesWashington State UniversityPullmanWashingtonUSA
| | - Michael Phelps
- Department of Animal SciencesWashington State UniversityPullmanWashingtonUSA
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7
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Wighard SS, Athanasouli M, Witte H, Rödelsperger C, Sommer RJ. A New Hope: A Hermaphroditic Nematode Enables Analysis of a Recent Whole Genome Duplication Event. Genome Biol Evol 2022; 14:6868937. [PMID: 36461901 PMCID: PMC9763058 DOI: 10.1093/gbe/evac169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 11/03/2022] [Accepted: 11/22/2022] [Indexed: 12/05/2022] Open
Abstract
Whole genome duplication (WGD) is often considered a major driver of evolution that leads to phenotypic novelties. However, the importance of WGD for evolution is still controversial because most documented WGD events occurred anciently and few experimental systems amenable to genetic analysis are available. Here, we report a recent WGD event in the hermaphroditic nematode Allodiplogaster sudhausi and present a comparison with a gonochoristic (male/female) sister species that did not undergo WGD. Self-fertilizing reproduction of A. sudhausi makes it amenable to functional analysis and an ideal system to study WGD events. We document WGD in A. sudhausi through karyotype analysis and whole genome sequencing, the latter of which allowed us to 1) identify functional bias in retention of protein domains and metabolic pathways, 2) show most duplicate genes are under evolutionary constraint, 3) show a link between sequence and expression divergence, and 4) characterize differentially expressed duplicates. We additionally show WGD is associated with increased body size and an abundance of repeat elements (36% of the genome), including a recent expansion of the DNA-hAT/Ac transposon family. Finally, we demonstrate the use of CRISPR/Cas9 to generate mutant knockouts, whereby two WGD-derived duplicate genes display functional redundancy in that they both need to be knocked out to generate a phenotype. Together, we present a novel experimental system that is convenient for examining and characterizing WGD-derived genes both computationally and functionally.
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Affiliation(s)
- Sara S Wighard
- Department for Integrative Evolutionary Biology, Max Planck Institute for Biology Tübingen, Max Planck Ring 9, 72076 Tübingen, Germany
| | - Marina Athanasouli
- Department for Integrative Evolutionary Biology, Max Planck Institute for Biology Tübingen, Max Planck Ring 9, 72076 Tübingen, Germany
| | - Hanh Witte
- Department for Integrative Evolutionary Biology, Max Planck Institute for Biology Tübingen, Max Planck Ring 9, 72076 Tübingen, Germany
| | - Christian Rödelsperger
- Department for Integrative Evolutionary Biology, Max Planck Institute for Biology Tübingen, Max Planck Ring 9, 72076 Tübingen, Germany
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8
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Usui Y, Kimoto M, Hanashima A, Hashimoto K, Mohri S. Cardiac hemodynamics and ventricular stiffness of sea-run cherry salmon (Oncorhynchus masou masou) differ critically from those of landlocked masu salmon. PLoS One 2022; 17:e0267264. [PMID: 36331913 PMCID: PMC9635730 DOI: 10.1371/journal.pone.0267264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 10/25/2022] [Indexed: 11/06/2022] Open
Abstract
Ventricular diastolic mechanical properties are important determinants of cardiac function and are optimized by changes in cardiac structure and physical properties. Oncorhynchus masou masou is an anadromous migratory fish of the Salmonidae family, and several ecological studies on it have been conducted; however, the cardiac functions of the fish are not well known. Therefore, we investigated ventricular diastolic function in landlocked (masu salmon) and sea-run (cherry salmon) types at 29–30 months post fertilization. Pulsed-wave Doppler echocardiography showed that the atrioventricular inflow waveforms of cherry salmon were biphasic with early diastolic filling and atrial contraction, whereas those of masu salmon were monophasic with atrial contraction. In addition, end-diastolic pressure–volume relationship analysis revealed that the dilatability per unit myocardial mass of the ventricle in cherry salmon was significantly suppressed compared to that in masu salmon, suggesting that the ventricle of the cherry salmon was relatively stiffer (relative ventricular stiffness index; p = 0.0263). Contrastingly, the extensibility of cardiomyocytes, characterized by the expression pattern of Connectin isoforms in their ventricles, was similar in both types. Histological analysis showed that the percentage of the collagen accumulation area in the compact layer of cherry salmon increased compared with that of the masu salmon, which may contribute to ventricle stiffness. Although the heart mass of cherry salmon was about 11-fold greater than that of masu salmon, there was no difference in the morphology of the isolated cardiomyocytes, suggesting that the heart of the cherry salmon grows by cardiomyocyte proliferation, but not cell hypertrophy. The cardiac physiological function of the teleosts varies with differences in their developmental processes and life history. Our multidimensional analysis of the O. masou heart may provide a clue to the process by which the heart acquires a biphasic blood-filling pattern, i.e., a ventricular diastolic suction.
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Affiliation(s)
- Yuu Usui
- First Department of Physiology, Kawasaki Medical School, Kurashiki, Japan
- * E-mail:
| | - Misaki Kimoto
- First Department of Physiology, Kawasaki Medical School, Kurashiki, Japan
| | - Akira Hanashima
- First Department of Physiology, Kawasaki Medical School, Kurashiki, Japan
| | - Ken Hashimoto
- First Department of Physiology, Kawasaki Medical School, Kurashiki, Japan
| | - Satoshi Mohri
- First Department of Physiology, Kawasaki Medical School, Kurashiki, Japan
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9
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Parey E, Louis A, Montfort J, Guiguen Y, Roest Crollius H, Berthelot C. An atlas of fish genome evolution reveals delayed rediploidization following the teleost whole-genome duplication. Genome Res 2022; 32:gr.276953.122. [PMID: 35961774 PMCID: PMC9528989 DOI: 10.1101/gr.276953.122] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 08/09/2022] [Indexed: 11/25/2022]
Abstract
Teleost fishes are ancient tetraploids descended from an ancestral whole-genome duplication that may have contributed to the impressive diversification of this clade. Whole-genome duplications can occur via self-doubling (autopolyploidy) or via hybridization between different species (allopolyploidy). The mode of tetraploidization conditions evolutionary processes by which duplicated genomes return to diploid meiotic pairing, and subsequent genetic divergence of duplicated genes (cytological and genetic rediploidization). How teleosts became tetraploid remains unresolved, leaving a fundamental gap in the interpretation of their functional evolution. As a result of the whole-genome duplication, identifying orthologous and paralogous genomic regions across teleosts is challenging, hindering genome-wide investigations into their polyploid history. Here, we combine tailored gene phylogeny methodology together with a state-of-the-art ancestral karyotype reconstruction to establish the first high-resolution comparative atlas of paleopolyploid regions across 74 teleost genomes. We then leverage this atlas to investigate how rediploidization occurred in teleosts at the genome-wide level. We uncover that some duplicated regions maintained tetraploidy for more than 60 million years, with three chromosome pairs diverging genetically only after the separation of major teleost families. This evidence suggests that the teleost ancestor was an autopolyploid. Further, we find evidence for biased gene retention along several duplicated chromosomes, contradicting current paradigms that asymmetrical evolution is specific to allopolyploids. Altogether, our results offer novel insights into genome evolutionary dynamics following ancient polyploidizations in vertebrates.
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Affiliation(s)
- Elise Parey
- Institut de Biologie de l'Ecole normale supérieure (IBENS), Département de Biologie, Ecole normale supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France
- INRAE, LPGP, 35000, Rennes, France
| | - Alexandra Louis
- Institut de Biologie de l'Ecole normale supérieure (IBENS), Département de Biologie, Ecole normale supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France
| | | | | | - Hugues Roest Crollius
- Institut de Biologie de l'Ecole normale supérieure (IBENS), Département de Biologie, Ecole normale supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France
| | - Camille Berthelot
- Institut de Biologie de l'Ecole normale supérieure (IBENS), Département de Biologie, Ecole normale supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France
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10
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Pottier M, Le Thi VA, Primard-Brisset C, Marion J, Wolf Bianchi M, Victor C, Déjardin A, Pilate G, Thomine S. Duplication of NRAMP3 gene in poplars generated two homologous transporters with distinct functions. Mol Biol Evol 2022; 39:msac129. [PMID: 35700212 PMCID: PMC9234761 DOI: 10.1093/molbev/msac129] [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: 12/15/2021] [Revised: 05/28/2022] [Accepted: 06/02/2022] [Indexed: 12/02/2022] Open
Abstract
Transition metals are essential for a wealth of metabolic reactions, but their concentrations need to be tightly controlled across cells and cell compartments, as metal excess or imbalance has deleterious effects. Metal homeostasis is achieved by a combination of metal transport across membranes and metal binding to a variety of molecules. Gene duplication is a key process in evolution, as emergence of advantageous mutations on one of the copies can confer a new function. Here, we report that the poplar genome contains two paralogues encoding NRAMP3 metal transporters localized in tandem. All Populus species analyzed had two copies of NRAMP3, whereas only one could be identified in Salix species indicating that duplication occurred when the two genera separated. Both copies are under purifying selection and encode functional transporters, as shown by expression in the yeast heterologous expression system. However, genetic complementation revealed that only one of the paralogues has retained the original function in release of metals stored in the vacuole previously characterized in A. thaliana. Confocal imaging showed that the other copy has acquired a distinct localization to the Trans Golgi Network (TGN). Expression in poplar suggested that the copy of NRAMP3 localized on the TGN has a novel function in the control of cell-to-cell transport of manganese. This work provides a clear case of neo-functionalization through change in the subcellular localization of a metal transporter as well as evidence for the involvement of the secretory pathway in cell-to-cell transport of manganese.
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Affiliation(s)
- Mathieu Pottier
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Van Anh Le Thi
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Catherine Primard-Brisset
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Jessica Marion
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Michele Wolf Bianchi
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Cindy Victor
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | | | | | - Sébastien Thomine
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
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11
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Zebrafish as a Model to Study Vascular Elastic Fibers and Associated Pathologies. Int J Mol Sci 2022; 23:ijms23042102. [PMID: 35216218 PMCID: PMC8875079 DOI: 10.3390/ijms23042102] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 02/09/2022] [Accepted: 02/12/2022] [Indexed: 02/06/2023] Open
Abstract
Many extensible tissues such as skin, lungs, and blood vessels require elasticity to function properly. The recoil of elastic energy stored during a stretching phase is provided by elastic fibers, which are mostly composed of elastin and fibrillin-rich microfibrils. In arteries, the lack of elastic fibers leads to a weakening of the vessel wall with an increased risk to develop cardiovascular defects such as stenosis, aneurysms, and dissections. The development of new therapeutic molecules involves preliminary tests in animal models that recapitulate the disease and whose response to drugs should be as close as possible to that of humans. Due to its superior in vivo imaging possibilities and the broad tool kit for forward and reverse genetics, the zebrafish has become an important model organism to study human pathologies. Moreover, it is particularly adapted to large scale studies, making it an attractive model in particular for the first steps of investigations. In this review, we discuss the relevance of the zebrafish model for the study of elastic fiber-related vascular pathologies. We evidence zebrafish as a compelling alternative to conventional mouse models.
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12
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Facchinello N, Astone M, Audano M, Oberkersch RE, Spizzotin M, Calura E, Marques M, Crisan M, Mitro N, Santoro MM. Oxidative pentose phosphate pathway controls vascular mural cell coverage by regulating extracellular matrix composition. Nat Metab 2022; 4:123-140. [PMID: 35102339 PMCID: PMC7612297 DOI: 10.1038/s42255-021-00514-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 12/06/2021] [Indexed: 12/11/2022]
Abstract
Vascular mural cells (vMCs) play an essential role in the development and maturation of the vasculature by promoting vessel stabilization through their interactions with endothelial cells. Whether endothelial metabolism influences mural cell recruitment and differentiation is unknown. Here, we show that the oxidative pentose phosphate pathway (oxPPP) in endothelial cells is required for establishing vMC coverage of the dorsal aorta during early vertebrate development in zebrafish and mice. We demonstrate that laminar shear stress and blood flow maintain oxPPP activity, which in turn, promotes elastin expression in blood vessels through production of ribose-5-phosphate. Elastin is both necessary and sufficient to drive vMC recruitment and maintenance when the oxPPP is active. In summary, our work demonstrates that endothelial cell metabolism regulates blood vessel maturation by controlling vascular matrix composition and vMC recruitment.
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Affiliation(s)
- Nicola Facchinello
- Laboratory of Angiogenesis and Cancer Metabolism, DiBio, University of Padua, Padua, Italy
| | - Matteo Astone
- Laboratory of Angiogenesis and Cancer Metabolism, DiBio, University of Padua, Padua, Italy
| | - Matteo Audano
- Department of Pharmacological and Biomolecular Sciences (DiSFeB), University of Milan, Milan, Italy
| | - Roxana E Oberkersch
- Laboratory of Angiogenesis and Cancer Metabolism, DiBio, University of Padua, Padua, Italy
| | - Marianna Spizzotin
- Laboratory of Angiogenesis and Cancer Metabolism, DiBio, University of Padua, Padua, Italy
| | - Enrica Calura
- Department of Biology, University of Padua, Padua, Italy
| | - Madalena Marques
- Centre for Cardiovascular Science and Centre for Regenerative Medicine/Institute for Regeneration and Repair, University of Edinburgh, Edinburgh, UK
| | - Mihaela Crisan
- Centre for Cardiovascular Science and Centre for Regenerative Medicine/Institute for Regeneration and Repair, University of Edinburgh, Edinburgh, UK
| | - Nico Mitro
- Department of Pharmacological and Biomolecular Sciences (DiSFeB), University of Milan, Milan, Italy
| | - Massimo M Santoro
- Laboratory of Angiogenesis and Cancer Metabolism, DiBio, University of Padua, Padua, Italy.
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13
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Keen AN, Mackrill JJ, Gardner P, Shiels HA. Compliance of the fish outflow tract is altered by thermal acclimation through connective tissue remodelling. J R Soc Interface 2021; 18:20210492. [PMID: 34784777 PMCID: PMC8596013 DOI: 10.1098/rsif.2021.0492] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
To protect the gill capillaries from high systolic pulse pressure, the fish heart contains a compliant non-contractile chamber called the bulbus arteriosus which is part of the outflow tract (OFT) which extends from the ventricle to the ventral aorta. Thermal acclimation alters the form and function of the fish atria and ventricle to ensure appropriate cardiac output at different temperatures, but its impact on the OFT is unknown. Here we used ex vivo pressure-volume curves to demonstrate remodelling of passive stiffness in the rainbow trout (Oncorhynchus mykiss) bulbus arteriosus following more than eight weeks of thermal acclimation to 5, 10 and 18°C. We then combined novel, non-biased Fourier transform infrared spectroscopy with classic histological staining to show that changes in compliance were achieved by changes in tissue collagen-to-elastin ratio. In situ gelatin zymography and SDS-PAGE zymography revealed that collagen remodelling was underpinned, at least in part, by changes in activity and abundance of collagen degrading matrix metalloproteinases. Collectively, we provide the first indication of bulbus arteriosus thermal remodelling in a fish and suggest this remodelling ensures optimal blood flow and blood pressure in the OFT during temperature change.
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Affiliation(s)
- Adam N Keen
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK.,Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - John J Mackrill
- Department of Physiology, University College Cork, Cork, County Cork, Ireland
| | - Peter Gardner
- School of Chemical Engineering and Analytical Science, Manchester Institute of Biotechnology, University of Manchester, UK
| | - Holly A Shiels
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
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14
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Abu Nahia K, Migdał M, Quinn TA, Poon KL, Łapiński M, Sulej A, Liu J, Mondal SS, Pawlak M, Bugajski Ł, Piwocka K, Brand T, Kohl P, Korzh V, Winata C. Genomic and physiological analyses of the zebrafish atrioventricular canal reveal molecular building blocks of the secondary pacemaker region. Cell Mol Life Sci 2021; 78:6669-6687. [PMID: 34557935 PMCID: PMC8558220 DOI: 10.1007/s00018-021-03939-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 08/06/2021] [Accepted: 09/10/2021] [Indexed: 01/06/2023]
Abstract
The atrioventricular canal (AVC) is the site where key structures responsible for functional division between heart regions are established, most importantly, the atrioventricular (AV) conduction system and cardiac valves. To elucidate the mechanism underlying AVC development and function, we utilized transgenic zebrafish line sqet31Et expressing EGFP in the AVC to isolate this cell population and profile its transcriptome at 48 and 72 hpf. The zebrafish AVC transcriptome exhibits hallmarks of mammalian AV node, including the expression of genes implicated in its development and those encoding connexins forming low conductance gap junctions. Transcriptome analysis uncovered protein-coding and noncoding transcripts enriched in AVC, which have not been previously associated with this structure, as well as dynamic expression of epithelial-to-mesenchymal transition markers and components of TGF-β, Notch, and Wnt signaling pathways likely reflecting ongoing AVC and valve development. Using transgenic line Tg(myl7:mermaid) encoding voltage-sensitive fluorescent protein, we show that abolishing the pacemaker-containing sinoatrial ring (SAR) through Isl1 loss of function resulted in spontaneous activation in the AVC region, suggesting that it possesses inherent automaticity although insufficient to replace the SAR. The SAR and AVC transcriptomes express partially overlapping species of ion channels and gap junction proteins, reflecting their distinct roles. Besides identifying conserved aspects between zebrafish and mammalian conduction systems, our results established molecular hallmarks of the developing AVC which underlies its role in structural and electrophysiological separation between heart chambers. This data constitutes a valuable resource for studying AVC development and function, and identification of novel candidate genes implicated in these processes.
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Affiliation(s)
- Karim Abu Nahia
- International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland
| | - Maciej Migdał
- International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland
| | - T Alexander Quinn
- Department of Physiology and Biophysics, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Kar-Lai Poon
- Institute of Molecular and Cell Biology, 61 Biopolis Dr, Singapore , Singapore.,Developmental Dynamics, National Heart and Lung Institute, Imperial College London, London, UK
| | - Maciej Łapiński
- International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland
| | - Agata Sulej
- International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland
| | - Jiandong Liu
- McAllister Heart Institute, University of North Carolina, Chapel Hill, USA
| | - Shamba S Mondal
- International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland
| | - Michał Pawlak
- International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland
| | | | | | - Thomas Brand
- Developmental Dynamics, National Heart and Lung Institute, Imperial College London, London, UK
| | - Peter Kohl
- Institute for Experimental Cardiovascular Medicine, University Heart Centre, Faculty of Medicine, and Faculty of Engineering, University of Freiburg, Freiburg im Breisgau, Germany
| | - Vladimir Korzh
- International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland.
| | - Cecilia Winata
- International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland.
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15
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Wang Y, Guo B. The divergence of alternative splicing between ohnologs in teleost fishes. BMC Ecol Evol 2021; 21:98. [PMID: 34034651 PMCID: PMC8146666 DOI: 10.1186/s12862-021-01833-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 05/19/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Gene duplication and alternative splicing (AS) are two distinct mechanisms generating new materials for genetic innovations. The evolutionary link between gene duplication and AS is still controversial, due to utilizing duplicates from inconsistent ages of duplication events in earlier studies. With the aid of RNA-seq data, we explored evolutionary scenario of AS divergence between duplicates with ohnologs that resulted from the teleost genome duplication event in zebrafish, medaka, and stickleback. RESULTS Ohnologs in zebrafish have fewer AS forms compared to their singleton orthologs, supporting the function-sharing model of AS divergence between duplicates. Ohnologs in stickleback have more AS forms compared to their singleton orthologs, which supports the accelerated model of AS divergence between duplicates. The evolution of AS in ohnologs in medaka supports a combined scenario of the function-sharing and the accelerated model of AS divergence between duplicates. We also found a small number of ohnolog pairs in each of the three teleosts showed significantly asymmetric AS divergence. For example, the well-known ovary-factor gene cyp19a1a has no AS form but its ohnolog cyp19a1b has multiple AS forms in medaka, suggesting that functional divergence between duplicates might have result from AS divergence. CONCLUSIONS We found that a combined scenario of function-sharing and accelerated models for AS evolution in ohnologs in teleosts and rule out the independent model that assumes a lack of correlation between gene duplication and AS. Our study thus provided insights into the link between gene duplication and AS in general and ohnolog divergence in teleosts from AS perspective in particular.
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Affiliation(s)
- Yuwei Wang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Baocheng Guo
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China. .,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650201, China.
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16
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Mousavi SE, Purser GJ, Patil JG. Embryonic Onset of Sexually Dimorphic Heart Rates in the Viviparous Fish, Gambusia holbrooki. Biomedicines 2021; 9:165. [PMID: 33567532 PMCID: PMC7915484 DOI: 10.3390/biomedicines9020165] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 02/01/2021] [Accepted: 02/04/2021] [Indexed: 12/12/2022] Open
Abstract
In fish, little is known about sex-specific differences in physiology and performance of the heart and whether these differences manifest during development. Here for the first time, the sex-specific heart rates during embryogenesis of Gambusia holbrooki, from the onset of the heart rates (HRs) to just prior to parturition, was investigated using light cardiogram. The genetic sex of the embryos was post-verified using a sex-specific genetic marker. Results reveal that heart rates and resting time significantly increase (p < 0.05) with progressive embryonic development. Furthermore, both ventricular and atrial frequencies of female embryos were significantly higher (p < 0.05) than those of their male sibs at the corresponding developmental stages and remained so at all later developmental stages (p < 0.05). In concurrence, the heart rate and ventricular size of the adult females were also significantly (p < 0.05) higher and larger respectively than those of males. Collectively, the results suggest that the cardiac sex-dimorphism manifests as early as late-organogenesis and persists through adulthood in this species. These findings suggest that the cardiac measurements can be employed to non-invasively sex the developing embryos, well in advance of when their phenotypic sex is discernible. In addition, G. holbrooki could serve as a better model to study comparative vertebrate cardiovascular development as well as to investigate anthropogenic and climatic impacts on heart physiology of this species, that may be sex influenced.
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Affiliation(s)
- Seyed Ehsan Mousavi
- Fisheries and Aquaculture Centre, Institute for Marine and Antarctic Studies, University of Tasmania, Taroona, TAS 7053, Australia;
| | - G. John Purser
- Fisheries and Aquaculture Centre, Institute for Marine and Antarctic Studies, University of Tasmania, Taroona, TAS 7053, Australia;
| | - Jawahar G. Patil
- Fisheries and Aquaculture Centre, Institute for Marine and Antarctic Studies, University of Tasmania, Taroona, TAS 7053, Australia;
- Inland Fisheries Service, New Norfolk, TAS 7140, Australia
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17
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Salehin N, Villarreal C, Teranikar T, Dubansky B, Lee J, Chuong CJ. Assessing Pressure-Volume Relationship in Developing Heart of Zebrafish In-Vivo. Ann Biomed Eng 2021; 49:2080-2093. [PMID: 33532949 DOI: 10.1007/s10439-021-02731-0] [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: 10/23/2020] [Accepted: 01/08/2021] [Indexed: 10/22/2022]
Abstract
During embryogenesis, the developing heart transforms from a linear peristaltic tube into a multi-chambered pulsatile pump with blood flow-regulating valves. In this work, we report how hemodynamic parameters evolve during the heart's development, leading to its rhythmic pumping and blood flow regulation as a functioning organ. We measured the time course of intra-ventricular pressure from zebrafish embryos at 3, 4, and 5 days post fertilization (dpf) using the servo null method. We also measured the ventricular volume and monitored the opening/closing activity of the AV and VB valves using 4D selective plane illumination microscopy (SPIM). Our results revealed significant increases in peak systolic pressure, stroke volume and work, cardiac output, and power generation, and a total peripheral resistance decrease from zebrafish at 4, 5 dpf versus 3 dpf. These data illustrate that the early-stage zebrafish heart's increasing efficiency is synchronous with the expected changes in valve development, chamber morphology and increasing vascular network complexity. Such physiological measurements in tractable laboratory model organisms are critical for understanding how gene variants may affect phenotype. As the zebrafish emerges as a leading biomedical model organism, the ability to effectively measure its physiology is critical to its translational relevance.
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Affiliation(s)
- Nabid Salehin
- Department of Bioengineering, University of Texas at Arlington, Arlington, TX, 76010, USA
| | - Cameron Villarreal
- Department of Bioengineering, University of Texas at Arlington, Arlington, TX, 76010, USA
| | - Tanveer Teranikar
- Department of Bioengineering, University of Texas at Arlington, Arlington, TX, 76010, USA
| | - Benjamin Dubansky
- Department of Biological Sciences, University of North Texas, Denton, TX, 76201, USA
| | - Juhyun Lee
- Department of Bioengineering, University of Texas at Arlington, Arlington, TX, 76010, USA
| | - Cheng-Jen Chuong
- Department of Bioengineering, University of Texas at Arlington, Arlington, TX, 76010, USA.
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18
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Kushwaha B, Pandey M, Das P, Joshi CG, Nagpure NS, Kumar R, Kumar D, Agarwal S, Srivastava S, Singh M, Sahoo L, Jayasankar P, Meher PK, Shah TM, Hinsu AT, Patel N, Koringa PG, Das SP, Patnaik S, Bit A, Iquebal MA, Jaiswal S, Jena J. The genome of walking catfish Clarias magur (Hamilton, 1822) unveils the genetic basis that may have facilitated the development of environmental and terrestrial adaptation systems in air-breathing catfishes. DNA Res 2021; 28:6070145. [PMID: 33416875 PMCID: PMC7934567 DOI: 10.1093/dnares/dsaa031] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 12/21/2020] [Indexed: 11/14/2022] Open
Abstract
The walking catfish Clarias magur (Hamilton, 1822) (magur) is an important catfish species inhabiting the Indian subcontinent. It is considered as a highly nutritious food fish and has the capability to walk to some distance, and survive a considerable period without water. Assembly, scaffolding and several rounds of iterations resulted in 3,484 scaffolds covering ∼94% of estimated genome with 9.88 Mb largest scaffold, and N50 1.31 Mb. The genome possessed 23,748 predicted protein encoding genes with annotation of 19,279 orthologous genes. A total of 166 orthologous groups represented by 222 genes were found to be unique for this species. The Computational Analysis of gene Family Evolution (CAFE) analysis revealed expansion of 207 gene families and 100 gene families have rapidly evolved. Genes specific to important environmental and terrestrial adaptation, viz. urea cycle, vision, locomotion, olfactory and vomeronasal receptors, immune system, anti-microbial properties, mucus, thermoregulation, osmoregulation, air-breathing, detoxification, etc. were identified and critically analysed. The analysis clearly indicated that C. magur genome possessed several unique and duplicate genes similar to that of terrestrial or amphibians’ counterparts in comparison to other teleostean species. The genome information will be useful in conservation genetics, not only for this species but will also be very helpful in such studies in other catfishes.
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Affiliation(s)
- Basdeo Kushwaha
- Molecular Biology and Biotechnology Division, ICAR-National Bureau of Fish Genetic Resources, Lucknow, Uttar Pradesh 226002, India
| | - Manmohan Pandey
- Molecular Biology and Biotechnology Division, ICAR-National Bureau of Fish Genetic Resources, Lucknow, Uttar Pradesh 226002, India
| | - Paramananda Das
- Fish Genetics and Biotechnology Division, ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar, Odisha 751002, India
| | - Chaitanya G Joshi
- Department of Animal Biotechnology, Anand Agricultural University, Anand, Gujarat 388110, India
| | - Naresh S Nagpure
- Molecular Biology and Biotechnology Division, ICAR-National Bureau of Fish Genetic Resources, Lucknow, Uttar Pradesh 226002, India
| | - Ravindra Kumar
- Molecular Biology and Biotechnology Division, ICAR-National Bureau of Fish Genetic Resources, Lucknow, Uttar Pradesh 226002, India
| | - Dinesh Kumar
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi 110012, India
| | - Suyash Agarwal
- Molecular Biology and Biotechnology Division, ICAR-National Bureau of Fish Genetic Resources, Lucknow, Uttar Pradesh 226002, India
| | - Shreya Srivastava
- Molecular Biology and Biotechnology Division, ICAR-National Bureau of Fish Genetic Resources, Lucknow, Uttar Pradesh 226002, India
| | - Mahender Singh
- Molecular Biology and Biotechnology Division, ICAR-National Bureau of Fish Genetic Resources, Lucknow, Uttar Pradesh 226002, India
| | - Lakshman Sahoo
- Fish Genetics and Biotechnology Division, ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar, Odisha 751002, India
| | - Pallipuram Jayasankar
- Fish Genetics and Biotechnology Division, ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar, Odisha 751002, India
| | - Prem K Meher
- Fish Genetics and Biotechnology Division, ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar, Odisha 751002, India
| | - Tejas M Shah
- Department of Animal Biotechnology, Anand Agricultural University, Anand, Gujarat 388110, India
| | - Ankit T Hinsu
- Department of Animal Biotechnology, Anand Agricultural University, Anand, Gujarat 388110, India
| | - Namrata Patel
- Department of Animal Biotechnology, Anand Agricultural University, Anand, Gujarat 388110, India
| | - Prakash G Koringa
- Department of Animal Biotechnology, Anand Agricultural University, Anand, Gujarat 388110, India
| | - Sofia P Das
- Fish Genetics and Biotechnology Division, ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar, Odisha 751002, India
| | - Siddhi Patnaik
- Fish Genetics and Biotechnology Division, ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar, Odisha 751002, India
| | - Amrita Bit
- Fish Genetics and Biotechnology Division, ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar, Odisha 751002, India
| | - Mir A Iquebal
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi 110012, India
| | - Sarika Jaiswal
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi 110012, India
| | - Joykrushna Jena
- Molecular Biology and Biotechnology Division, ICAR-National Bureau of Fish Genetic Resources, Lucknow, Uttar Pradesh 226002, India
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19
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Reichheld SE, Muiznieks LD, Huynh Q, Wang N, Ing C, Miao M, Sitarz EE, Pomès R, Sharpe S, Keeley FW. The evolutionary background and functional consequences of the rs2071307 polymorphism in human tropoelastin. Biopolymers 2020; 112:e23414. [PMID: 33351193 DOI: 10.1002/bip.23414] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 11/30/2020] [Accepted: 12/01/2020] [Indexed: 01/01/2023]
Abstract
Elastin is a major polymeric protein of the extracellular matrix, providing critical properties of extensibility and elastic recoil. The rs2071307 genomic polymorphism, resulting in the substitution of a serine for a glycine residue in a VPG motif in tropoelastin, has an unusually high minor allele frequency in humans. A consequence of such allelic heterozygosity would be the presence of a heterogeneous elastin polymer in up to 50% of the population, a situation which appears to be unique to Homo sapiens. VPG motifs are extremely common in hydrophobic domains of tropoelastins and are the sites of transient β-turns that are essential for maintaining the conformational flexibility required for its function as an entropic elastomer. Earlier data demonstrated that single amino acid substitutions in tropoelastin can have functional consequences for polymeric elastin, particularly when present in mixed polymers. Here, using NMR and molecular dynamics approaches, we show the rs2071307 polymorphism reduces local propensity for β-turn formation, with a consequent increase in polypeptide hydration and an expansion of the conformational ensemble manifested as an increased hydrodynamic radius, radius of gyration and asphericity. Furthermore, this substitution affects functional properties of polymeric elastin, particularly in heterogeneous polymers mimicking allelic heterozygosity. We discuss whether such effects, together with the unusually high minor allele frequency of the polymorphism, could imply some some evolutionary advantage for the heterozygous state.
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Affiliation(s)
- Sean E Reichheld
- Molecular Medicine Program, Research Institute, The Hospital for Sick Children, Toronto, Ontario, USA
| | - Lisa D Muiznieks
- Molecular Medicine Program, Research Institute, The Hospital for Sick Children, Toronto, Ontario, USA.,Elvesys Microfluidics Innovation Center, 172 rue de Charonne, 75011, Paris, France
| | - Quang Huynh
- Molecular Medicine Program, Research Institute, The Hospital for Sick Children, Toronto, Ontario, USA
| | - Nick Wang
- Molecular Medicine Program, Research Institute, The Hospital for Sick Children, Toronto, Ontario, USA.,135 W 52nd St. Apt 20A, 10019-7691, New York, New York, USA
| | - Christopher Ing
- Molecular Medicine Program, Research Institute, The Hospital for Sick Children, Toronto, Ontario, USA.,ProteinQure, Suite 304, 119 Spadina Avenue, M5V2L1, Toronto, Ontario, Canada
| | - Ming Miao
- Molecular Medicine Program, Research Institute, The Hospital for Sick Children, Toronto, Ontario, USA
| | - Eva E Sitarz
- Molecular Medicine Program, Research Institute, The Hospital for Sick Children, Toronto, Ontario, USA
| | - Régis Pomès
- Molecular Medicine Program, Research Institute, The Hospital for Sick Children, Toronto, Ontario, USA.,Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Simon Sharpe
- Molecular Medicine Program, Research Institute, The Hospital for Sick Children, Toronto, Ontario, USA.,Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Fred W Keeley
- Molecular Medicine Program, Research Institute, The Hospital for Sick Children, Toronto, Ontario, USA.,Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
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20
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Development of the ventricular myocardial trabeculae in Scyliorhinus canicula (Chondrichthyes): evolutionary implications. Sci Rep 2020; 10:14434. [PMID: 32879349 PMCID: PMC7468296 DOI: 10.1038/s41598-020-71318-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 08/05/2020] [Indexed: 12/16/2022] Open
Abstract
The development of the ventricular myocardial trabeculae occurs in three steps: emergence, trabeculation and remodeling. The whole process has been described in vertebrates with two different myocardial structural types, spongy (zebrafish) and compact (chicken and mouse). In this context, two alternative mechanisms of myocardial trabeculae emergence have been identified: (1) in chicken and mouse, the endocardial cells invade the two-layered myocardium; (2) in zebrafish, cardiomyocytes from the monolayered myocardium invaginate towards the endocardium. Currently, the process has not been studied in detail in vertebrates having a mixed type of ventricular myocardium, with an inner trabecular and an outer compact layer, which is presumptively the most primitive morphology in gnathostomes. We studied the formation of the mixed ventricular myocardium in the lesser spotted dogfish (Scyliorhinus canicula, Elasmobranchii), using light, scanning and transmission electron microscopy. Our results show that early formation of the mixed ventricular myocardium, specifically the emergence and the trabeculation steps, is driven by an endocardial invasion of the myocardium. The mechanism of trabeculation of the mixed ventricular myocardium in chondrichthyans is the one that best reproduces how this developmental process has been established from the beginning of the gnathostome radiation. The process has been apparently preserved throughout the entire group of sarcopterygians, including birds and mammals. In contrast, teleosts, at least those possessing a mostly spongy ventricular myocardium, seem to have introduced notable changes in their myocardial trabeculae development.
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21
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Parey E, Louis A, Cabau C, Guiguen Y, Roest Crollius H, Berthelot C. Synteny-Guided Resolution of Gene Trees Clarifies the Functional Impact of Whole-Genome Duplications. Mol Biol Evol 2020; 37:3324-3337. [DOI: 10.1093/molbev/msaa149] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Abstract
Whole-genome duplications (WGDs) have major impacts on the evolution of species, as they produce new gene copies contributing substantially to adaptation, isolation, phenotypic robustness, and evolvability. They result in large, complex gene families with recurrent gene losses in descendant species that sequence-based phylogenetic methods fail to reconstruct accurately. As a result, orthologs and paralogs are difficult to identify reliably in WGD-descended species, which hinders the exploration of functional consequences of WGDs. Here, we present Synteny-guided CORrection of Paralogies and Orthologies (SCORPiOs), a novel method to reconstruct gene phylogenies in the context of a known WGD event. WGDs generate large duplicated syntenic regions, which SCORPiOs systematically leverages as a complement to sequence evolution to infer the evolutionary history of genes. We applied SCORPiOs to the 320-My-old WGD at the origin of teleost fish. We find that almost one in four teleost gene phylogenies in the Ensembl database (3,394) are inconsistent with their syntenic contexts. For 70% of these gene families (2,387), we were able to propose an improved phylogenetic tree consistent with both the molecular substitution distances and the local syntenic information. We show that these synteny-guided phylogenies are more congruent with the species tree, with sequence evolution and with expected expression conservation patterns than those produced by state-of-the-art methods. Finally, we show that synteny-guided gene trees emphasize contributions of WGD paralogs to evolutionary innovations in the teleost clade.
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Affiliation(s)
- Elise Parey
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Alexandra Louis
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Cédric Cabau
- SIGENAE, GenPhySE, Université de Toulouse, INRAE, ENVT, Castanet Tolosan, France
| | | | - Hugues Roest Crollius
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Camille Berthelot
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
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22
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Yasuoka Y. Enhancer evolution in chordates: Lessons from functional analyses of cephalochordate cis‐regulatory modules. Dev Growth Differ 2020; 62:279-300. [DOI: 10.1111/dgd.12684] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 05/25/2020] [Accepted: 05/27/2020] [Indexed: 12/20/2022]
Affiliation(s)
- Yuuri Yasuoka
- Laboratory for Comprehensive Genomic Analysis RIKEN Center for Integrative Medical Sciences Tsurumi‐ku Japan
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23
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Honda A, Chigwechokha PK, Takase R, Hayasaka O, Fujimura K, Kotani T, Komatsu M, Shiozaki K. Novel Nile tilapia Neu1 sialidases: Molecular cloning and biochemical characterization of the sialidases Neu1a and Neu1b. Gene 2020; 742:144538. [DOI: 10.1016/j.gene.2020.144538] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 02/06/2020] [Accepted: 03/06/2020] [Indexed: 12/20/2022]
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24
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Conant GC. The lasting after-effects of an ancient polyploidy on the genomes of teleosts. PLoS One 2020; 15:e0231356. [PMID: 32298330 PMCID: PMC7161988 DOI: 10.1371/journal.pone.0231356] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 03/20/2020] [Indexed: 12/20/2022] Open
Abstract
The ancestor of most teleost fishes underwent a whole-genome duplication event three hundred million years ago. Despite its antiquity, the effects of this event are evident both in the structure of teleost genomes and in how the surviving duplicated genes still operate to drive form and function. I inferred a set of shared syntenic regions that survive from the teleost genome duplication (TGD) using eight teleost genomes and the outgroup gar genome (which lacks the TGD). I then phylogenetically modeled the TGD's resolution via shared and independent gene losses and applied a new simulation-based statistical test for the presence of bias toward the preservation of genes from one parental subgenome. On the basis of that test, I argue that the TGD was likely an allopolyploidy. I find that duplicate genes surviving from this duplication in zebrafish are less likely to function in early embryo development than are genes that have returned to single copy at some point in this species' history. The tissues these ohnologs are expressed in, as well as their biological functions, lend support to recent suggestions that the TGD was the source of a morphological innovation in the structure of the teleost retina. Surviving duplicates also appear less likely to be essential than singletons, despite the fact that their single-copy orthologs in mouse are no less essential than other genes.
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Affiliation(s)
- Gavin C. Conant
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, United States of America
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, United States of America
- Program in Genetics, North Carolina State University, Raleigh, NC, United States of America
- Division of Animal Sciences, University of Missouri, Columbia, MO, United States of America
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25
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Holowiecki A, Linstrum K, Ravisankar P, Chetal K, Salomonis N, Waxman JS. Pbx4 limits heart size and fosters arch artery formation by partitioning second heart field progenitors and restricting proliferation. Development 2020; 147:dev185652. [PMID: 32094112 PMCID: PMC7063670 DOI: 10.1242/dev.185652] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Accepted: 02/06/2020] [Indexed: 12/11/2022]
Abstract
Vertebrate heart development requires the integration of temporally distinct differentiating progenitors. However, few signals are understood that restrict the size of the later-differentiating outflow tract (OFT). We show that improper specification and proliferation of second heart field (SHF) progenitors in zebrafish lazarus (lzr) mutants, which lack the transcription factor Pbx4, produces enlarged hearts owing to an increase in ventricular and smooth muscle cells. Specifically, Pbx4 initially promotes the partitioning of the SHF into anterior progenitors, which contribute to the OFT, and adjacent endothelial cell progenitors, which contribute to posterior pharyngeal arches. Subsequently, Pbx4 limits SHF progenitor (SHFP) proliferation. Single cell RNA sequencing of nkx2.5+ cells revealed previously unappreciated distinct differentiation states and progenitor subpopulations that normally reside within the SHF and arterial pole of the heart. Specifically, the transcriptional profiles of Pbx4-deficient nkx2.5+ SHFPs are less distinct and display characteristics of normally discrete proliferative progenitor and anterior, differentiated cardiomyocyte populations. Therefore, our data indicate that the generation of proper OFT size and arch arteries requires Pbx-dependent stratification of unique differentiation states to facilitate both homeotic-like transformations and limit progenitor production within the SHF.
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Affiliation(s)
- Andrew Holowiecki
- Molecular Cardiovascular Biology Division and Heart Institute, Cincinnati Children's Research Foundation, Cincinnati, OH 45229, USA
| | - Kelsey Linstrum
- Molecular Cardiovascular Biology Division and Heart Institute, Cincinnati Children's Research Foundation, Cincinnati, OH 45229, USA
- Molecular Genetics Graduate Program, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Padmapriyadarshini Ravisankar
- Molecular Cardiovascular Biology Division and Heart Institute, Cincinnati Children's Research Foundation, Cincinnati, OH 45229, USA
| | - Kashish Chetal
- Bioinformatics Division, Cincinnati Children's Research Foundation, Cincinnati, OH 45229, USA
| | - Nathan Salomonis
- Bioinformatics Division, Cincinnati Children's Research Foundation, Cincinnati, OH 45229, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Joshua S Waxman
- Molecular Cardiovascular Biology Division and Heart Institute, Cincinnati Children's Research Foundation, Cincinnati, OH 45229, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
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26
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Weinberger M, Simões FC, Patient R, Sauka-Spengler T, Riley PR. Functional Heterogeneity within the Developing Zebrafish Epicardium. Dev Cell 2020; 52:574-590.e6. [PMID: 32084358 PMCID: PMC7063573 DOI: 10.1016/j.devcel.2020.01.023] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 12/07/2019] [Accepted: 01/22/2020] [Indexed: 12/31/2022]
Abstract
The epicardium is essential during cardiac development, homeostasis, and repair, and yet fundamental insights into its underlying cell biology, notably epicardium formation, lineage heterogeneity, and functional cross-talk with other cell types in the heart, are currently lacking. In this study, we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single-cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programs and distinctive spatial distribution. Perturbation of unique gene signatures uncovered specific functions associated with each subpopulation and established epicardial roles in cell adhesion, migration, and chemotaxis as a mechanism for recruitment of leukocytes into the heart. Understanding which mechanisms epicardial cells employ to establish a functional epicardium and how they communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. scRNA-seq uncovered 3 developmental epicardial subpopulations (Epi1-3) in the zebrafish Epi1-specific gene, tgm2b, regulates the cell numbers in the main epicardial sheet Epi2-specific gene, sema3fb, restricts the number of tbx18+ cells in the cardiac outflow tract Epi3-specific gene, cxcl12a, guides ptprc/CD45+ myeloid cells to the developing heart
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Affiliation(s)
- Michael Weinberger
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, Oxfordshire OX1 3PT, UK; MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, Oxfordshire OX3 9DS, UK
| | - Filipa C Simões
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, Oxfordshire OX1 3PT, UK; MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, Oxfordshire OX3 9DS, UK
| | - Roger Patient
- MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, Oxfordshire OX3 9DS, UK
| | - Tatjana Sauka-Spengler
- MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, Oxfordshire OX3 9DS, UK.
| | - Paul R Riley
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, Oxfordshire OX1 3PT, UK.
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27
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Li X, Guo B. Substantially adaptive potential in polyploid cyprinid fishes: evidence from biogeographic, phylogenetic and genomic studies. Proc Biol Sci 2020; 287:20193008. [PMID: 32075533 DOI: 10.1098/rspb.2019.3008] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Whole genome duplication (WGD) is commonly believed to play key roles in vertebrate evolution. However, nowadays polyploidy exists in a few fish, amphibian and reptile groups only, and seems to be an evolutionary dead end in vertebrates. We investigate the evolutionary significance of polyploidization in Cyprinidae-a fish family that contains more polyploid species than any other vertebrate group-with integrated biogeographic, phylogenetic and genomic analyses. First, polyploid species are found to be significantly frequent in areas of higher altitude and lower mean annual temperature compared with diploid species in Cyprinidae. Second, a polyploidy-related diversification rate shift is observed in Cyprinidae. This increased net diversification rate is only seen in three polyploid lineages, and other polyploid lineages have similar net diversification rate as well as diploid lineages in Cyprinidae. Interestingly, significant 'lag times' existed between polyploidization and radiation in Cyprinidae. Multiple polyploid lineages were established approximately 15 Ma through recurrent allopolyploidization events, but the net diversification rate did not start to increase until approximately 5 Ma-long after polyploidization events. Environmental changes associated with the continuous uplift of the Tibetan Plateau and climate change have probably promoted the initial establishment and subsequent radiation of polyploidy in Cyprinidae. Finally, the unique retention of duplicated genes in polyploid cyprinids adapted to harsh environments is found. Taken together, our results suggest that polyploidy in Cyprinidae is far more than an evolutionary dead end, but rather shows substantially adaptive potential. Polyploid cyprinids thus constitute an ideal model system for unveiling largely unexplored consequences of WGD in vertebrates, from genomic evolution to species diversification.
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Affiliation(s)
- Xinxin Li
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Baocheng Guo
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, People's Republic of China.,University of Chinese Academy of Sciences, Beijing, People's Republic of China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, People's Republic of China
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28
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Liu L, Fei F, Zhang R, Wu F, Yang Q, Wang F, Sun S, Zhao H, Li Q, Wang L, Wang Y, Gui Y, Wang X. Combinatorial genetic replenishments in myocardial and outflow tract tissues restore heart function in tnnt2 mutant zebrafish. Biol Open 2019; 8:bio.046474. [PMID: 31796423 PMCID: PMC6918781 DOI: 10.1242/bio.046474] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Cardiac muscle troponin T (Tnnt2) mediates muscle contraction in response to calcium ion dynamics, and Tnnt2 mutations are associated with multiple types of cardiomyopathy. Here, we employed a zebrafish model to investigate the genetic replenishment strategies of using conditional and inducible promoters to rescue the deficiencies in the heart. tnnt2a mutations were induced in zebrafish via the CRISPR/Cas9 technique, and the mutants displayed heart arrest and dilated cardiomyopathy-like phenotypes. We first utilized the classic myocardial promoter of the myl7 and TetOn inducible system to restore tnnt2a expression in myocardial tissue in tnnt2a mutant zebrafish. However, this attempt failed to recover normal heart function and circulation, although heart pumping was partially restored. Further analyses via both RNA-seq and immunofluorescence indicated that Tnnt2a, which was also expressed in a novel group of myl7-negative smooth muscle cells on the outflow tract (OFT), was indispensably responsible for the normal mechanical dynamics of OFT. Lastly, tnnt2 expression induced by OFT cells in addition to the myocardial cells successfully rescued heart function and circulation in tnnt2a mutant zebrafish. Together, our results reveal the significance of OFT expression of Tnnt2 for cardiac function and demonstrate zebrafish larva as a powerful and convenient in vivo platform for studying cardiomyopathy and the relevant therapeutic strategies.
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Affiliation(s)
- Lian Liu
- Department of Cardiology, Children's Hospital of Fudan University, Shanghai 201102, China
| | - Fei Fei
- Cancer Metabolism Laboratory, Cancer Institute, Fudan University Shanghai Cancer Center, Shanghai 200032, China.,Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai 230002, China
| | - Ranran Zhang
- Department of Pediatrics, the Affiliated Hospital of Qingdao University, Qingdao, Shangdong 266003, China
| | - Fang Wu
- Department of Cardiology, Children's Hospital of Fudan University, Shanghai 201102, China
| | - Qian Yang
- Department of Cardiology, Children's Hospital of Fudan University, Shanghai 201102, China
| | - Feng Wang
- Department of Cardiology, Children's Hospital of Fudan University, Shanghai 201102, China
| | - Shaoyang Sun
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai 230002, China
| | - Hui Zhao
- Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200032, China
| | - Qiang Li
- Translational Medical Center for Development and Disease, Shanghai Key Laboratory of Birth Defect, Institute of Pediatrics, Children's Hospital of Fudan University, Shanghai 201102, China
| | - Lei Wang
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai 230002, China
| | - Youhua Wang
- Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200032, China
| | - Yonghao Gui
- Department of Cardiology, Children's Hospital of Fudan University, Shanghai 201102, China
| | - Xu Wang
- Cancer Metabolism Laboratory, Cancer Institute, Fudan University Shanghai Cancer Center, Shanghai 200032, China .,Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai 230002, China
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29
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Duchemin AL, Vignes H, Vermot J. Mechanically activated piezo channels modulate outflow tract valve development through the Yap1 and Klf2-Notch signaling axis. eLife 2019; 8:44706. [PMID: 31524599 PMCID: PMC6779468 DOI: 10.7554/elife.44706] [Citation(s) in RCA: 85] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2018] [Accepted: 09/14/2019] [Indexed: 12/12/2022] Open
Abstract
Mechanical forces are well known for modulating heart valve developmental programs. Yet, it is still unclear how genetic programs and mechanosensation interact during heart valve development. Here, we assessed the mechanosensitive pathways involved during zebrafish outflow tract (OFT) valve development in vivo. Our results show that the hippo effector Yap1, Klf2, and the Notch signaling pathway are all essential for OFT valve morphogenesis in response to mechanical forces, albeit active in different cell layers. Furthermore, we show that Piezo and TRP mechanosensitive channels are important factors modulating these pathways. In addition, live reporters reveal that Piezo controls Klf2 and Notch activity in the endothelium and Yap1 localization in the smooth muscle progenitors to coordinate OFT valve morphogenesis. Together, this work identifies a unique morphogenetic program during OFT valve formation and places Piezo as a central modulator of the cell response to forces in this process.
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Affiliation(s)
- Anne-Laure Duchemin
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.,Centre National de la Recherche Scientifique, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Hélène Vignes
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.,Centre National de la Recherche Scientifique, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Julien Vermot
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.,Centre National de la Recherche Scientifique, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, Illkirch, France.,Université de Strasbourg, Illkirch, France
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30
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Gardinal MVB, Ruiz TFR, dos Santos DD, Vidal MR, Moron SE, Falleiros Junior LR, Taboga SR, Franceschini Vicentini IB, Vicentini CA. Histochemical characterization and connective fiber distribution of the cardiac outflow tract of pirarucu, Arapaima gigas (Schinz, 1822) (Osteoglossiformes, Arapaimidae). ZOOMORPHOLOGY 2019. [DOI: 10.1007/s00435-019-00459-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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31
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Versican is crucial for the initiation of cardiovascular lumen development in medaka (Oryzias latipes). Sci Rep 2019; 9:9475. [PMID: 31263118 PMCID: PMC6603046 DOI: 10.1038/s41598-019-45851-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 06/13/2019] [Indexed: 12/17/2022] Open
Abstract
Versican is an evolutionary conserved extracellular matrix proteoglycan, and versican expression loss in mice results in embryonic lethality owing to cardiovascular defects. However, the in utero development of mammals limits our understanding of the precise role of versican during cardiovascular development. Therefore, the use of evolutionarily distant species that develop ex utero is more suitable for studying the mechanistic basis of versican activity. We performed ENU mutagenesis screening to identify medaka mutants with defects in embryonic cardiovascular development. In this study, we described a recessive point mutation in the versican 3'UTR resulting in reduced versican protein expression. The fully penetrant homozygous mutant showed termination of cardiac development at the linear heart tube stage and exhibited absence of cardiac looping, a constricted outflow tract, and no cardiac jelly. Additionally, progenitor cells did not migrate from the secondary source towards the arterial pole of the linear heart tube, resulting in a constricted outflow tract. Furthermore, mutants lacked blood flow and vascular lumen despite continuous peristaltic heartbeats. These results enhance our understanding of the mechanistic basis of versican in cardiac development, and this mutant represents a novel genetic model to investigate the mechanisms of vascular tubulogenesis.
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32
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Gu L, Xia C. Cluster expansion of apolipoprotein D (ApoD) genes in teleost fishes. BMC Evol Biol 2019; 19:9. [PMID: 30621595 PMCID: PMC6325677 DOI: 10.1186/s12862-018-1323-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 12/11/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Gene and genome duplication play important roles in the evolution of gene function. Compared to individual duplicated genes, gene clusters attract particular attention considering their frequent associations with innovation and adaptation. Here, we report for the first time the expansion of the apolipoprotein D (ApoD) ligand-transporter genes in a cluster manner specific to teleost fishes. RESULTS Based on comparative genomic and transcriptomic analyses, protein 3D structure comparison, positive selection detection and breakpoints detection, the single ApoD gene in the ancestor expanded into two clusters following a dynamic evolutionary pattern in teleost fishes. Orthologous genes show conserved expression patterns, whereas lineage-specific duplicated genes show tissue-specific expression patterns and even evolve new gene expression profiles. Positive selection occurred in branches before and after gene duplication, especially for lineage-specific duplicated genes. Cluster analyses based on protein 3D structure comparisons, especially comparisons of the four loops at the opening side, show gene duplication-segregating patterns. Duplicated ApoD genes are predicted to be associated with forkhead transcription factors and MAPK genes. ApoD clusters are located next to the breakpoints of genome rearrangements. CONCLUSIONS Here, we report the expansion of ApoD genes specific to teleost fishes in a cluster manner for the first time. Neofunctionalization and subfunctionalization were observed at both the protein and expression levels after duplication. Evidence from different aspects-i.e., abnormal expression-induced disease in humans, fish-specific expansion, predicted associations with forkhead transcription factors and MAPK genes, specific expression patterns in tissues related to sexual selection and adaptation, duplicated genes under positive selection and their location next to the breakpoints of genome rearrangements-suggests the potentially advantageous roles of ApoD genes in teleost fishes. The cluster expansion of ApoD genes specific to teleost fishes provides thus an ideal evo-devo model for studying gene duplication, cluster maintenance and new gene function emergence.
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Affiliation(s)
- Langyu Gu
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing, China
- Zoological Institute, Department of Environmental Sciences, University of Basel, Basel, Switzerland
| | - Canwei Xia
- Ministry of Education Key Laboratory for Biodiversity and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, China
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33
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Katano W, Moriyama Y, Takeuchi JK, Koshiba-Takeuchi K. Cardiac septation in heart development and evolution. Dev Growth Differ 2018; 61:114-123. [PMID: 30549006 DOI: 10.1111/dgd.12580] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 11/01/2018] [Accepted: 11/01/2018] [Indexed: 01/24/2023]
Abstract
The heart is one of the vital organs and is functionalized for blood circulation from its early development. Some vertebrates have altered their living environment from aquatic to terrestrial life over the course of evolution and obtained circulatory systems well adapted to their lifestyles. The morphology of the heart has been changed together with the acquisition of a sophisticated respiratory organ, the lung. Adaptation to a terrestrial environment requires the coordination of heart and lung development due to the intake of oxygen from the air and the production of the large amount of energy needed for terrestrial life. Therefore, vertebrates developed pulmonary circulation and a septated heart (four-chambered heart) with venous and arterial blood completely separated. In this review, we summarize how vertebrates change the structures and functions of their circulatory systems according to environmental changes.
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Affiliation(s)
- Wataru Katano
- Faculty of Life Sciences, Department of Applied Biosciences, Toyo University, Ora-gun, Japan
| | - Yuuta Moriyama
- Department of Life Science and Technology, School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Jun K Takeuchi
- Department of Bio-informational Pharmacology, Medical Research Institute, Tokyo Medical and Dental University, Bunkyo, Japan
| | - Kazuko Koshiba-Takeuchi
- Faculty of Life Sciences, Department of Applied Biosciences, Toyo University, Ora-gun, Japan
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34
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Mikhaleva Y, Skinnes R, Sumic S, Thompson EM, Chourrout D. Development of the house secreting epithelium, a major innovation of tunicate larvaceans, involves multiple homeodomain transcription factors. Dev Biol 2018; 443:117-126. [DOI: 10.1016/j.ydbio.2018.09.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Revised: 07/27/2018] [Accepted: 09/05/2018] [Indexed: 01/24/2023]
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35
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Lorente-Martínez H, Agorreta A, Torres-Sánchez M, San Mauro D. Evidence of positive selection suggests possible role of aquaporins in the water-to-land transition of mudskippers. ORG DIVERS EVOL 2018. [DOI: 10.1007/s13127-018-0382-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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36
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Jensen B, H Smit T. Examples of Weak, If Not Absent, Form-Function Relations in the Vertebrate Heart. J Cardiovasc Dev Dis 2018; 5:E46. [PMID: 30205545 PMCID: PMC6162483 DOI: 10.3390/jcdd5030046] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 08/31/2018] [Accepted: 09/05/2018] [Indexed: 12/12/2022] Open
Abstract
That form and function are related is a maxim of anatomy and physiology. Yet, form-function relations can be difficult to prove. Human subjects with excessive trabeculated myocardium in the left ventricle, for example, are diagnosed with non-compaction cardiomyopathy, but the extent of trabeculations may be without relation to ejection fraction. Rather than rejecting a relation between form and function, we may ask whether the salient function is assessed. Is there a relation to electrical propagation, mean arterial blood pressure, or propensity to form blood clots? In addition, how should the extent of trabeculated muscle be assessed? While reviewing literature on trabeculated muscle, we applied Tinbergen's four types of causation-how does it work, why does it work, how is it made, and why did it evolve-to better parse what is meant by form and function. The paper is structured around cases that highlight advantages and pitfalls of applying Tinbergen's questions. It further uses the evolution of lunglessness in amphibians to argue that lung reduction impacts on chamber septation and it considers the evolution of an arterial outflow in fishes to argue that reductions in energy consumption may drive structural changes with little consequences to function. Concerning trabeculations, we argue they relate to pumping function in the embryo in the few weeks before the onset of coronary circulation. In human fetal and postnatal stages, a spectrum of trabeculated-to-compact myocardium makes no difference to cardiac function and in this period, form and function may appear unrelated.
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Affiliation(s)
- Bjarke Jensen
- Department of Medical Biology, Amsterdam Cardiovascular Sciences, University of Amsterdam, Amsterdam UMC, Meibergdreef 15, 1105AZ Amsterdam, The Netherlands.
| | - Theodoor H Smit
- Department of Medical Biology, Amsterdam Cardiovascular Sciences, University of Amsterdam, Amsterdam UMC, Meibergdreef 15, 1105AZ Amsterdam, The Netherlands.
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37
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Continuous addition of progenitors forms the cardiac ventricle in zebrafish. Nat Commun 2018; 9:2001. [PMID: 29784942 PMCID: PMC5962599 DOI: 10.1038/s41467-018-04402-6] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Accepted: 04/27/2018] [Indexed: 01/10/2023] Open
Abstract
The vertebrate heart develops from several progenitor lineages. After early-differentiating first heart field (FHF) progenitors form the linear heart tube, late-differentiating second heart field (SHF) progenitors extend the atrium and ventricle, and form inflow and outflow tracts (IFT/OFT). However, the position and migration of late-differentiating progenitors during heart formation remains unclear. Here, we track zebrafish heart development using transgenics based on the cardiopharyngeal gene tbx1. Live imaging uncovers a tbx1 reporter-expressing cell sheath that continuously disseminates from the lateral plate mesoderm towards the forming heart tube. High-speed imaging and optogenetic lineage tracing corroborates that the zebrafish ventricle forms through continuous addition from the undifferentiated progenitor sheath followed by late-phase accrual of the bulbus arteriosus (BA). FGF inhibition during sheath migration reduces ventricle size and abolishes BA formation, refining the window of FGF action during OFT formation. Our findings consolidate previous end-point analyses and establish zebrafish ventricle formation as a continuous process. Late-differentiating second heart field progenitors contribute to atrium, ventricle, and outflow tract in the zebrafish heart but how remains unclear. Here, the authors image heart formation in transgenics based on the cardiopharyngeal gene tbx1 and show that progenitors are continuously added.
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38
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Moriyama Y, Koshiba-Takeuchi K. Significance of whole-genome duplications on the emergence of evolutionary novelties. Brief Funct Genomics 2018; 17:329-338. [DOI: 10.1093/bfgp/ely007] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Yuuta Moriyama
- Institute of Science and Technology Austria (IST), Klosterneuburg, Austria
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Miller J, Dreyer TF, Bächer AS, Sinner EK, Heinrich C, Benge A, Gross E, Preis S, Rother J, Roberts A, Nelles G, Miteva T, Reuning U. Differential tumor biological role of the tumor suppressor KAI1 and its splice variant in human breast cancer cells. Oncotarget 2018; 9:6369-6390. [PMID: 29464079 PMCID: PMC5814219 DOI: 10.18632/oncotarget.23968] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Accepted: 12/23/2017] [Indexed: 01/30/2023] Open
Abstract
The tetraspanin and tumor suppressor KAI1 is downregulated or lost in many cancers which correlates with poor prognosis. KAI1 acts via physical/functional crosstalk with other membrane receptors. Also, a splice variant of KAI1 (KAI1-SP) has been identified indicative of poor prognosis. We here characterized differential effects of the two KAI1 variants on tumor biological events involving integrin (αvß3) and/or epidermal growth factor receptor (EGF-R). In MDA-MB-231 and -435 breast cancer cells, differential effects were documented on the expression levels of the tumor biologically relevant integrin αvß3 which colocalized with KAI1-WT but not with KAI1-SP. Cellular motility was assessed by video image processing, including motion detection and vector analysis for the quantification and visualization of cell motion parameters. In MDA-MB-231 cells, KAI1-SP provoked a quicker wound gap closure and higher closure rates than KAI1-WT, also reflected by different velocities and average motion amplitudes of singular cells. KAI1-SP induced highest cell motion adjacent to the wound gap borders, whereas in MDA-MB-435 cells a comparable induction of both KAI1 variants was noticed. Moreover, while KAI1-WT reduced cell growth, KAI1-SP significantly increased it going along with a pronounced EGF-R upregulation. KAI1-SP-induced cell migration and proliferation was accompanied by the activation of the focal adhesion and Src kinase. Our findings suggest that splicing of KAI1 does not only abrogate its tumor suppressive functions, but even more, promotes tumor biological effects in favor of cancer progression and metastasis.
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Affiliation(s)
- Julia Miller
- Department for Obstetrics & Gynecology, Technical University of Munich, D-81675 Munich, Germany
| | - Tobias F Dreyer
- Department for Obstetrics & Gynecology, Technical University of Munich, D-81675 Munich, Germany
| | - Anne Sophie Bächer
- Department for Obstetrics & Gynecology, Technical University of Munich, D-81675 Munich, Germany
| | - Eva-Kathrin Sinner
- BOKU, University of Natural Resources and Life Sciences, 1180 Vienna, Austria
| | - Christine Heinrich
- Department for Obstetrics & Gynecology, Technical University of Munich, D-81675 Munich, Germany
| | - Anke Benge
- Department for Obstetrics & Gynecology, Technical University of Munich, D-81675 Munich, Germany
| | - Eva Gross
- Department for Obstetrics & Gynecology, Technical University of Munich, D-81675 Munich, Germany
| | - Sarah Preis
- Department for Obstetrics & Gynecology, Technical University of Munich, D-81675 Munich, Germany
| | - Jan Rother
- Materials Science Laboratory, Sony Europe Ltd ZN Deutschland, D-70327 Stuttgart, Germany
| | - Anthony Roberts
- Materials Science Laboratory, Sony Europe Ltd ZN Deutschland, D-70327 Stuttgart, Germany
| | - Gabriele Nelles
- Materials Science Laboratory, Sony Europe Ltd ZN Deutschland, D-70327 Stuttgart, Germany
| | - Tzenka Miteva
- Materials Science Laboratory, Sony Europe Ltd ZN Deutschland, D-70327 Stuttgart, Germany
| | - Ute Reuning
- Department for Obstetrics & Gynecology, Technical University of Munich, D-81675 Munich, Germany
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Rambeau P, Faure E, Théron A, Avierinos JF, Jopling C, Zaffran S, Faucherre A. Reduced aggrecan expression affects cardiac outflow tract development in zebrafish and is associated with bicuspid aortic valve disease in humans. Int J Cardiol 2017; 249:340-343. [DOI: 10.1016/j.ijcard.2017.09.174] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Revised: 08/21/2017] [Accepted: 09/18/2017] [Indexed: 11/16/2022]
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Turetzek N, Khadjeh S, Schomburg C, Prpic NM. Rapid diversification of homothorax expression patterns after gene duplication in spiders. BMC Evol Biol 2017; 17:168. [PMID: 28709396 PMCID: PMC5513375 DOI: 10.1186/s12862-017-1013-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 07/04/2017] [Indexed: 01/09/2023] Open
Abstract
Background Gene duplications provide genetic material for the evolution of new morphological and physiological features. One copy can preserve the original gene functions while the second copy may evolve new functions (neofunctionalisation). Gene duplications may thus provide new genes involved in evolutionary novelties. Results We have studied the duplicated homeobox gene homothorax (hth) in the spider species Parasteatoda tepidariorum and Pholcus phalangioides and have compared these data with previously published data from additional spider species. We show that the expression pattern of hth1 is highly conserved among spiders, consistent with the notion that this gene copy preserves the original hth functions. By contrast, hth2 has a markedly different expression profile especially in the prosomal appendages. The pattern in the pedipalps and legs consists of several segmental rings, suggesting a possible role of hth2 in limb joint development. Intriguingly, however, the hth2 pattern is much less conserved between the species than hth1 and shows a species specific pattern in each species investigated so far. Conclusions We hypothesise that the hth2 gene has gained a new patterning function after gene duplication, but has then undergone a second phase of diversification of its new role in the spider clade. The evolution of hth2 may thus provide an interesting example for a duplicated gene that has not only contributed to genetic diversity through neofunctionalisation, but beyond that has been able to escape evolutionary conservation after neofunctionalisation thus forming the basis for further genetic diversification. Electronic supplementary material The online version of this article (doi:10.1186/s12862-017-1013-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Natascha Turetzek
- Abteilung für Entwicklungsbiologie, Johann-Friedrich-Blumenbach-Institut für Zoologie und Anthropologie, Georg-August-Universität, Göttingen, Germany.,Göttingen Center for Molecular Biosciences (GZMB), Ernst-Caspari-Haus, Göttingen, Germany.,Current address: Georg-August-Universität Göttingen, Johann-Friedrich-Blumenbach-Institut für Zoologie und Anthropologie, Abteilung Zelluläre Neurobiologie, 37077, Göttingen, Germany
| | - Sara Khadjeh
- Abteilung für Entwicklungsbiologie, Johann-Friedrich-Blumenbach-Institut für Zoologie und Anthropologie, Georg-August-Universität, Göttingen, Germany.,Göttingen Center for Molecular Biosciences (GZMB), Ernst-Caspari-Haus, Göttingen, Germany.,Present address: Clinic for Cardiology and Pneumology, University Medical Center Göttingen (UMG), Georg-August-University, Göttingen, Germany
| | - Christoph Schomburg
- Abteilung für Entwicklungsbiologie, Johann-Friedrich-Blumenbach-Institut für Zoologie und Anthropologie, Georg-August-Universität, Göttingen, Germany.,Göttingen Center for Molecular Biosciences (GZMB), Ernst-Caspari-Haus, Göttingen, Germany
| | - Nikola-Michael Prpic
- Abteilung für Entwicklungsbiologie, Johann-Friedrich-Blumenbach-Institut für Zoologie und Anthropologie, Georg-August-Universität, Göttingen, Germany. .,Göttingen Center for Molecular Biosciences (GZMB), Ernst-Caspari-Haus, Göttingen, Germany.
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The bulbus arteriosus of the holocephalan heart: gross anatomy, histomorphology, pigmentation, and evolutionary significance. ZOOLOGY 2017; 123:37-45. [PMID: 28760682 DOI: 10.1016/j.zool.2017.05.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Revised: 05/25/2017] [Accepted: 05/26/2017] [Indexed: 11/20/2022]
Abstract
This study was designed to determine whether the outflow tract of the holocephalan heart is composed of a myocardial conus arteriosus and a non-myocardial bulbus arteriosus, as is the case in elasmobranchs. This is a key issue to verify the hypothesis that these two anatomical components existed from the onset of the jawed vertebrate radiation. The Holocephali are the sister group of the elasmobranchs, sharing with them a common, still unknown Palaeozoic ancestor. The sample examined herein consisted of hearts from individuals of four species, two of them belonging to the Chimaeridae and the other two to the Rhinochimaeridae. In all specimens, the cardiac outflow tract consisted of a conus arteriosus, with myocardium in its walls and two rows of valves at its luminal side, and an intrapericardial bulbus arteriosus shorter than the conus and devoid of valves. The bulbus, mainly composed of elastin and smooth musculature, was covered by the epicardium and crossed longitudinally by coronary artery trunks. These findings give added support to the viewpoint that the outflow tract of the primitive heart of the gnathostomes was not composed of a single component, but two, the conus and the bulbus. All rabbitfish (Chimaera monstrosa) examined had pigment cells over the surface of the heart. The degree of pigmentation, which varied widely between individuals, was particularly intense in the cardiac outflow tract. Pigment cells also occurred in the bulbus arteriosus of one of the two hearts of the straightnose rabbitfish (Rhinochimaera atlantica) included in the study. The cells containing pigment, presumably derived from the neural crest, were located in the subepicardium.
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Laurent S, Salamin N, Robinson-Rechavi M. No evidence for the radiation time lag model after whole genome duplications in Teleostei. PLoS One 2017; 12:e0176384. [PMID: 28426792 PMCID: PMC5398669 DOI: 10.1371/journal.pone.0176384] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Accepted: 04/10/2017] [Indexed: 12/11/2022] Open
Abstract
The short and long term effects of polyploidization on the evolutionary fate of lineages is still unclear despite much interest. First recognized in land plants, it has become clear that polyploidization is widespread in eukaryotes, notably at the origin of vertebrates and teleost fishes. Many hypotheses have been proposed to link the species richness of lineages and whole genome duplications. For instance, the radiation time lag model suggests that paleopolyploidy would favour the apparition of new phenotypic traits, although the radiation of the lineage would not occur before a later dispersion event. Some results indicate that this model may be observed during land plant evolution. In this work, we test predictions of the radiation time lag model using both fossil data and molecular phylogenies in ancient and more recent teleost whole genome duplications. We fail to find any evidence of delayed increase of the species number after any of these events and conclude that paleopolyploidization still remains to be unambiguously linked to taxonomic diversity in teleosts.
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Affiliation(s)
- Sacha Laurent
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Nicolas Salamin
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Marc Robinson-Rechavi
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- * E-mail:
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Ryuzono S, Takase R, Kamada Y, Ikenaga T, Chigwechokha PK, Komatsu M, Shiozaki K. Suppression of Neu1 sialidase delays the absorption of yolk sac in medaka (Oryzias latipes) accompanied with the accumulation of α2-3 sialo-glycoproteins. Biochimie 2017; 135:63-71. [DOI: 10.1016/j.biochi.2017.01.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Accepted: 01/16/2017] [Indexed: 02/01/2023]
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Zoccola E, Kellie S, Barnes AC. Immune transcriptome reveals the mincle C-type lectin receptor acts as a partial replacement for TLR4 in lipopolysaccharide-mediated inflammatory response in barramundi (Lates calcarifer). Mol Immunol 2017; 83:33-45. [PMID: 28095348 DOI: 10.1016/j.molimm.2017.01.010] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Revised: 01/06/2017] [Accepted: 01/08/2017] [Indexed: 12/23/2022]
Abstract
Fish represent the most diverse and abundant extant vertebrate infraclass. They are also one of the earliest divergent phyla with adaptive immunity based on antigen recognition by MHC and immunoglobulin. The aquaculture industry, which currently provides more than half of the fish for human consumption globally, has successfully exploited the adaptive immune system of fish through mass vaccination programs. However, vaccination against highly diverse antigens, mostly carbohydrates, such as capsular polysaccharides and lipopolysaccharide (LPS) is challenging. Fish have a subdued innate response to LPS, but adaptive response is generally high and type-specific. To better understand the link between initial innate response and early onset of adaptive immunity to carbohydrate antigens in the perciform barramundi (Lates calcarifer), an immune transcriptome was prepared from pronephros and spleen following vaccination with LPS and peptidoglycan. From 163,661 transcripts derived by Illumina mRNA-Seq, most grouped in neuronal, endocrine or immune system categories, suggesting a close relationship between the three systems. Moreover, digestive enzyme transcripts in spleen appeared to be highly inducible in barramundi. Most of the known TLRs were transcribed in the barramundi spleen and HK transcriptome, with the notable exception of TLR4, which is primarily responsible for LPS recognition in mammals. Several C-type lectin receptors were also identified, including CD209, CD205, and CLEC4E (Mincle). As Mincle has been shown to bind LPS and is abundant on dendritic cells, its role in response to LPS in barramundi was further investigated. A high dose of LPS induced TNF-alpha expression via Mincle. However, IL-6 regulation, whilst still regulated in response to LPS, did not depend upon the Mincle pathway, suggesting other routes of activation. This study thus suggests that Mincle acts as a partial substitute for TLR4 in barramundi in the processing of LPS.
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Affiliation(s)
- Emmanuelle Zoccola
- School of Biological Sciences, The University of Queensland, St. Lucia, QLD 4072, Australia
| | - Stuart Kellie
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD 4072, Australia; Institute for Molecular Biosciences, The University of Queensland, St. Lucia, QLD 4072, Australia; Australian Institute for Infectious Diseases, The University of Queensland, St. Lucia, QLD 4072, Australia
| | - Andrew C Barnes
- School of Biological Sciences, The University of Queensland, St. Lucia, QLD 4072, Australia.
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Grant MG, Patterson VL, Grimes DT, Burdine RD. Modeling Syndromic Congenital Heart Defects in Zebrafish. Curr Top Dev Biol 2017; 124:1-40. [DOI: 10.1016/bs.ctdb.2016.11.010] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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47
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Higashiyama H, Hirasawa T, Oisi Y, Sugahara F, Hyodo S, Kanai Y, Kuratani S. On the vagal cardiac nerves, with special reference to the early evolution of the head-trunk interface. J Morphol 2016; 277:1146-58. [PMID: 27216138 DOI: 10.1002/jmor.20563] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Revised: 04/28/2016] [Accepted: 05/02/2016] [Indexed: 12/11/2022]
Abstract
The vagus nerve, or the tenth cranial nerve, innervates the heart in addition to other visceral organs, including the posterior visceral arches. In amniotes, the anterior and posterior cardiac branches arise from the branchial and intestinal portions of the vagus nerve to innervate the arterial and venous poles of the heart, respectively. The evolution of this innervation pattern has yet to be elucidated, due mainly to the lack of morphological data on the vagus in basal vertebrates. To investigate this topic, we observed the vagus nerves of the lamprey (Lethenteron japonicum), elephant shark (Callorhinchus milii), and mouse (Mus musculus), focusing on the embryonic patterns of the vagal branches in the venous pole. In the lamprey, no vagus branch was found in the venous pole throughout development, whereas the arterial pole was innervated by a branch from the branchial portion. In contrast, the vagus innervated the arterial and venous poles in the mouse and elephant shark. Based on the morphological patterns of these branches, the venous vagal branches of the mouse and elephant shark appear to belong to the intestinal part of the vagus, implying that the cardiac nerve pattern is conserved among crown gnathostomes. Furthermore, we found a topographical shift of the structures adjacent to the venous pole (i.e., the hypoglossal nerve and pronephros) between the extant gnathostomes and lamprey. Phylogenetically, the lamprey morphology is likely to be the ancestral condition for vertebrates, suggesting that the evolution of the venous branch occurred early in the gnathostome lineage, in parallel with the remodeling of the head-trunk interfacial domain during the acquisition of the neck. J. Morphol. 277:1146-1158, 2016. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Hiroki Higashiyama
- Department of Biology, Graduate School of Science, Kobe University, Kobe, 657-8501, Japan.,Evolutionary Morphology Laboratory, RIKEN, Kobe, 650-0047, Japan.,Laboratory of Veterinary Anatomy, the University of Tokyo, Tokyo, 113-8657, Japan
| | - Tatsuya Hirasawa
- Evolutionary Morphology Laboratory, RIKEN, Kobe, 650-0047, Japan
| | - Yasuhiro Oisi
- Evolutionary Morphology Laboratory, RIKEN, Kobe, 650-0047, Japan.,Development and Function of Inhibitory Neural Circuits, Max Planck Florida Institute for Neuroscience, Jupiter, Florida 33458, USA
| | - Fumiaki Sugahara
- Evolutionary Morphology Laboratory, RIKEN, Kobe, 650-0047, Japan.,Division of Biology, Hyogo College of Medicine, Nishinomiya, Hyogo, 663-8501, Japan
| | - Susumu Hyodo
- Laboratory of Physiology, Atmosphere and Ocean Research Institute, the University of Tokyo, Chiba, 277-8564, Japan
| | - Yoshiakira Kanai
- Laboratory of Veterinary Anatomy, the University of Tokyo, Tokyo, 113-8657, Japan
| | - Shigeru Kuratani
- Evolutionary Morphology Laboratory, RIKEN, Kobe, 650-0047, Japan
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The Asian arowana (Scleropages formosus) genome provides new insights into the evolution of an early lineage of teleosts. Sci Rep 2016; 6:24501. [PMID: 27089831 PMCID: PMC4835728 DOI: 10.1038/srep24501] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Accepted: 03/30/2016] [Indexed: 11/09/2022] Open
Abstract
The Asian arowana (Scleropages formosus), one of the world's most expensive cultivated ornamental fishes, is an endangered species. It represents an ancient lineage of teleosts: the Osteoglossomorpha. Here, we provide a high-quality chromosome-level reference genome of a female golden-variety arowana using a combination of deep shotgun sequencing and high-resolution linkage mapping. In addition, we have also generated two draft genome assemblies for the red and green varieties. Phylogenomic analysis supports a sister group relationship between Osteoglossomorpha (bonytongues) and Elopomorpha (eels and relatives), with the two clades together forming a sister group of Clupeocephala which includes all the remaining teleosts. The arowana genome retains the full complement of eight Hox clusters unlike the African butterfly fish (Pantodon buchholzi), another bonytongue fish, which possess only five Hox clusters. Differential gene expression among three varieties provides insights into the genetic basis of colour variation. A potential heterogametic sex chromosome is identified in the female arowana karyotype, suggesting that the sex is determined by a ZW/ZZ sex chromosomal system. The high-quality reference genome of the golden arowana and the draft assemblies of the red and green varieties are valuable resources for understanding the biology, adaptation and behaviour of Asian arowanas.
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