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Zimmer AM. Ammonia excretion by the fish gill: discoveries and ideas that shaped our current understanding. J Comp Physiol B 2024:10.1007/s00360-024-01561-5. [PMID: 38849577 DOI: 10.1007/s00360-024-01561-5] [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: 12/15/2023] [Revised: 03/06/2024] [Accepted: 05/15/2024] [Indexed: 06/09/2024]
Abstract
The fish gill serves many physiological functions, among which is the excretion of ammonia, the primary nitrogenous waste in most fishes. Although it is the end-product of nitrogen metabolism, ammonia serves many physiological functions including acting as an acid equivalent and as a counter-ion in mechanisms of ion regulation. Our current understanding of the mechanisms of ammonia excretion have been influenced by classic experimental work, clever mechanistic approaches, and modern molecular and genetic techniques. In this review, I will overview the history of the study of ammonia excretion by the gills of fishes, highlighting the important advancements that have shaped this field with a nearly 100-year history. The developmental and evolutionary implications of an ammonia and gill-dominated nitrogen regulation strategy in most fishes will also be discussed. Throughout the review, I point to areas in which more work is needed to push forward this field of research that continues to produce novel insights and discoveries that will undoubtedly shape our overall understanding of fish physiology.
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Affiliation(s)
- Alex M Zimmer
- Department of Biological Sciences, University of New Brunswick, 100 Tucker Park Road, Saint John, Saint John, New Brunswick, E2L 4L5, Canada.
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Abstract
The use of multiple species to model complex human psychiatric disorders, such as ADHD, can give important insights into conserved evolutionary patterns underlying multidomain behaviors (e.g., locomotion, attention, and impulsivity). Here we discuss the advantages and challenges in modelling ADHD-like phenotypes in zebrafish (Danio rerio), a vertebrate species that has been widely used in neuroscience and behavior research. Moreover, multiple behavioral tasks can be used to model the core symptoms of ADHD and its comorbidities. We present a critical review of current ADHD studies in zebrafish, and how this species might be used to accelerate the discovery of new drug treatments for this disorder.
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Affiliation(s)
- Barbara D Fontana
- Brain and Behaviour Laboratory, School of Pharmacy and Biomedical Sciences, University of Portsmouth, Portsmouth, UK
| | - William H J Norton
- Department of Neuroscience, Psychology and Behaviour, College of Medicine, Biological Sciences and Psychology, University of Leicester, Leicester, UK.
- Department of Genetics, Institute of Biology, ELTE Eötvös Loránd University, Budapest, Hungary.
| | - Matthew O Parker
- Brain and Behaviour Laboratory, School of Pharmacy and Biomedical Sciences, University of Portsmouth, Portsmouth, UK.
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3
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Zimmer AM, Goss GG, Glover CN. Reductionist approaches to the study of ionoregulation in fishes. Comp Biochem Physiol B Biochem Mol Biol 2021; 255:110597. [PMID: 33781928 DOI: 10.1016/j.cbpb.2021.110597] [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: 01/05/2021] [Revised: 03/15/2021] [Accepted: 03/22/2021] [Indexed: 10/21/2022]
Abstract
The mechanisms underlying ionoregulation in fishes have been studied for nearly a century, and reductionist methods have been applied at all levels of biological organization in this field of research. The complex nature of ionoregulatory systems in fishes makes them ideally suited to reductionist methods and our collective understanding has been dramatically shaped by their use. This review provides an overview of the broad suite of techniques used to elucidate ionoregulatory mechanisms in fishes, from the whole-animal level down to the gene, discussing some of the advantages and disadvantages of these methods. We provide a roadmap for understanding and appreciating the work that has formed the current models of organismal, endocrine, cellular, molecular, and genetic regulation of ion balance in fishes and highlight the contribution that reductionist techniques have made to some of the fundamental leaps forward in the field throughout its history.
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Affiliation(s)
- Alex M Zimmer
- Department of Biological Sciences, CW 405, Biological Sciences Bldg., University of Alberta, Edmonton, AB T6G 2E9, Canada.
| | - Greg G Goss
- Department of Biological Sciences, CW 405, Biological Sciences Bldg., University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Chris N Glover
- Department of Biological Sciences, CW 405, Biological Sciences Bldg., University of Alberta, Edmonton, AB T6G 2E9, Canada; Faculty of Science and Technology and Athabasca River Basin Research Institute, Athabasca University, Athabasca, AB T9S 3A3, Canada
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4
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Fontana BD, Müller TE, Cleal M, de Abreu MS, Norton WHJ, Demin KA, Amstislavskaya TG, Petersen EV, Kalueff AV, Parker MO, Rosemberg DB. Using zebrafish (Danio rerio) models to understand the critical role of social interactions in mental health and wellbeing. Prog Neurobiol 2021; 208:101993. [PMID: 33440208 DOI: 10.1016/j.pneurobio.2021.101993] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 11/24/2020] [Accepted: 01/05/2021] [Indexed: 02/07/2023]
Abstract
Social behavior represents a beneficial interaction between conspecifics that is critical for maintaining health and wellbeing. Dysfunctional or poor social interaction are associated with increased risk of physical (e.g., vascular) and psychiatric disorders (e.g., anxiety, depression, and substance abuse). Although the impact of negative and positive social interactions is well-studied, their underlying mechanisms remain poorly understood. Zebrafish have well-characterized social behavior phenotypes, high genetic homology with humans, relative experimental simplicity and the potential for high-throughput screens. Here, we discuss the use of zebrafish as a candidate model organism for studying the fundamental mechanisms underlying social interactions, as well as potential impacts of social isolation on human health and wellbeing. Overall, the growing utility of zebrafish models may improve our understanding of how the presence and absence of social interactions can differentially modulate various molecular and physiological biomarkers, as well as a wide range of other behaviors.
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Affiliation(s)
- Barbara D Fontana
- Brain and Behaviour Laboratory, School of Pharmacy and Biomedical Sciences, University of Portsmouth, UK.
| | - Talise E Müller
- Graduate Program in Biological Sciences: Toxicological Biochemistry, Natural and Exact Sciences Center, Federal University of Santa Maria, Santa Maria, RS, Brazil; Laboratory of Experimental Neuropscychobiology, Department of Biochemistry and Molecular Biology, Natural and Exact Sciences Center, Federal University of Santa Maria, Santa Maria, RS, Brazil
| | - Madeleine Cleal
- Brain and Behaviour Laboratory, School of Pharmacy and Biomedical Sciences, University of Portsmouth, UK
| | - Murilo S de Abreu
- Bioscience Institute, University of Passo Fundo, Passo Fundo, Brazil
| | - William H J Norton
- Department of Neuroscience, Psychology and Behaviour, College of Medicine, Biological Sciences and Psychology, University of Leicester, Leicester, UK; The International Zebrafish Neuroscience Research Consortium (ZNRC), Slidell, LA, USA
| | - Konstantin A Demin
- Institute of Experimental Medicine, Almazov National Medical Research Center, St. Petersburg, Russia; Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia; Scientific Research Center of Radiology and Surgical Technologies, St. Petersburg, Russia
| | | | - Elena V Petersen
- Laboratory of Molecular Biology, Neuroscience and Bioscreening, Moscow Institute of Physics and Technology, Moscow, Russia
| | - Allan V Kalueff
- School of Pharmacy, Southwest University, Beibei, Chongqing, China; Ural Federal University, Ekaterinburg, Russia
| | - Matthew O Parker
- Brain and Behaviour Laboratory, School of Pharmacy and Biomedical Sciences, University of Portsmouth, UK; The International Zebrafish Neuroscience Research Consortium (ZNRC), Slidell, LA, USA
| | - Denis B Rosemberg
- Graduate Program in Biological Sciences: Toxicological Biochemistry, Natural and Exact Sciences Center, Federal University of Santa Maria, Santa Maria, RS, Brazil; Laboratory of Experimental Neuropscychobiology, Department of Biochemistry and Molecular Biology, Natural and Exact Sciences Center, Federal University of Santa Maria, Santa Maria, RS, Brazil; The International Zebrafish Neuroscience Research Consortium (ZNRC), Slidell, LA, USA.
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5
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Ichino N, Serres MR, Urban RM, Urban MD, Treichel AJ, Schaefbauer KJ, Greif LE, Varshney GK, Skuster KJ, McNulty MS, Daby CL, Wang Y, Liao HK, El-Rass S, Ding Y, Liu W, Anderson JL, Wishman MD, Sabharwal A, Schimmenti LA, Sivasubbu S, Balciunas D, Hammerschmidt M, Farber SA, Wen XY, Xu X, McGrail M, Essner JJ, Burgess SM, Clark KJ, Ekker SC. Building the vertebrate codex using the gene breaking protein trap library. eLife 2020; 9:54572. [PMID: 32779569 PMCID: PMC7486118 DOI: 10.7554/elife.54572] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 08/07/2020] [Indexed: 12/14/2022] Open
Abstract
One key bottleneck in understanding the human genome is the relative under-characterization of 90% of protein coding regions. We report a collection of 1200 transgenic zebrafish strains made with the gene-break transposon (GBT) protein trap to simultaneously report and reversibly knockdown the tagged genes. Protein trap-associated mRFP expression shows previously undocumented expression of 35% and 90% of cloned genes at 2 and 4 days post-fertilization, respectively. Further, investigated alleles regularly show 99% gene-specific mRNA knockdown. Homozygous GBT animals in ryr1b, fras1, tnnt2a, edar and hmcn1 phenocopied established mutants. 204 cloned lines trapped diverse proteins, including 64 orthologs of human disease-associated genes with 40 as potential new disease models. Severely reduced skeletal muscle Ca2+ transients in GBT ryr1b homozygous animals validated the ability to explore molecular mechanisms of genetic diseases. This GBT system facilitates novel functional genome annotation towards understanding cellular and molecular underpinnings of vertebrate biology and human disease.
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Affiliation(s)
- Noriko Ichino
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, United States
| | - MaKayla R Serres
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, United States
| | - Rhianna M Urban
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, United States
| | - Mark D Urban
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, United States
| | - Anthony J Treichel
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, United States
| | - Kyle J Schaefbauer
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, United States
| | - Lauren E Greif
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, United States
| | - Gaurav K Varshney
- Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, United States.,Functional & Chemical Genomics Program, Oklahoma Medical Research Foundation, Oklahoma City, United States
| | - Kimberly J Skuster
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, United States
| | - Melissa S McNulty
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, United States
| | - Camden L Daby
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, United States
| | - Ying Wang
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, United States
| | - Hsin-Kai Liao
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, United States
| | - Suzan El-Rass
- Zebrafish Centre for Advanced Drug Discovery & Keenan Research Centre for Biomedical Science, Li Ka Shing Knowledge Institute, St. Michael's Hospital, Unity Health Toronto & University of Toronto, Toronto, Canada
| | - Yonghe Ding
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, United States.,Department of Cardiovascular Medicine, Mayo Clinic, Rochester, United States
| | - Weibin Liu
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, United States.,Department of Cardiovascular Medicine, Mayo Clinic, Rochester, United States
| | - Jennifer L Anderson
- Department of Embryology, Carnegie Institution for Science, Baltimore, United States
| | - Mark D Wishman
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, United States
| | - Ankit Sabharwal
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, United States
| | - Lisa A Schimmenti
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, United States.,Department of Clinical Genomics, Mayo Clinic, Rochester, United States.,Department of Otorhinolaryngology, Mayo Clinic, Rochester, United States
| | - Sridhar Sivasubbu
- Genomics and Molecular Medicine Unit, CSIR-Institute of Genomics and Integrative Biology, Delhi, India
| | - Darius Balciunas
- Department of Biology, Temple University, Philadelphia, United States
| | - Matthias Hammerschmidt
- Institute of Zoology, Developmental Biology Unit, University of Cologne, Cologne, Germany
| | - Steven Arthur Farber
- Department of Embryology, Carnegie Institution for Science, Baltimore, United States
| | - Xiao-Yan Wen
- Zebrafish Centre for Advanced Drug Discovery & Keenan Research Centre for Biomedical Science, Li Ka Shing Knowledge Institute, St. Michael's Hospital, Unity Health Toronto & University of Toronto, Toronto, Canada
| | - Xiaolei Xu
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, United States.,Department of Cardiovascular Medicine, Mayo Clinic, Rochester, United States
| | - Maura McGrail
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, United States
| | - Jeffrey J Essner
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, United States
| | - Shawn M Burgess
- Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, United States
| | - Karl J Clark
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, United States
| | - Stephen C Ekker
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, United States
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Carrington B, Weinstein RN, Sood R. BE4max and AncBE4max Are Efficient in Germline Conversion of C:G to T:A Base Pairs in Zebrafish. Cells 2020; 9:cells9071690. [PMID: 32674364 PMCID: PMC7407168 DOI: 10.3390/cells9071690] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 07/06/2020] [Accepted: 07/10/2020] [Indexed: 12/12/2022] Open
Abstract
The ease of use and robustness of genome editing by CRISPR/Cas9 has led to successful use of gene knockout zebrafish for disease modeling. However, it still remains a challenge to precisely edit the zebrafish genome to create single-nucleotide substitutions, which account for ~60% of human disease-causing mutations. Recently developed base editing nucleases provide an excellent alternate to CRISPR/Cas9-mediated homology dependent repair for generation of zebrafish with point mutations. A new set of cytosine base editors, termed BE4max and AncBE4max, demonstrated improved base editing efficiency in mammalian cells but have not been evaluated in zebrafish. Therefore, we undertook this study to evaluate their efficiency in converting C:G to T:A base pairs in zebrafish by somatic and germline analysis using highly active sgRNAs to twist and ntl genes. Our data demonstrated that these improved BE4max set of plasmids provide desired base substitutions at similar efficiency and without any indels compared to the previously reported BE3 and Target-AID plasmids in zebrafish. Our data also showed that AncBE4max produces fewer incorrect and bystander edits, suggesting that it can be further improved by codon optimization of its components for use in zebrafish.
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Zimmer AM, Perry SF. The Rhesus glycoprotein Rhcgb is expendable for ammonia excretion and Na + uptake in zebrafish (Danio rerio). Comp Biochem Physiol A Mol Integr Physiol 2020; 247:110722. [PMID: 32437959 DOI: 10.1016/j.cbpa.2020.110722] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 05/01/2020] [Accepted: 05/01/2020] [Indexed: 11/27/2022]
Abstract
In zebrafish (Danio rerio), the ammonia-transporting Rhesus glycoprotein Rhcgb is implicated in mechanisms of ammonia excretion and Na+ uptake. In particular, Rhcgb is thought to play an important role in maintaining ammonia excretion in response to alkaline conditions and high external ammonia (HEA) exposure, in addition to facilitating Na+ uptake via a functional metabolon with the Na+/H+-exchanger Nhe3b, specifically under low Na+ conditions. In the present study, we hypothesized that CRISPR/Cas9 knockout of rhcgb would reduce ammonia excretion and Na+ uptake capacity, particularly under the conditions listed above that have elicited increases in Rhcgb-mediated ammonia excretion and/or Na+ uptake. Contrary to this hypothesis, however, larval and juvenile rhcgb knockout (KO) mutants showed no reductions in ammonia excretion or Na+ uptake under any of the conditions tested in our study. In fact, under control conditions, rhcgb KO mutants generally displayed an increase in ammonia excretion, potentially due to increased transcript abundance of another rh gene, rhbg. Under alkaline conditions, rhcgb KO mutants were also able to maintain ammonia excretion, similar to wild-type fish, and stimulation of ammonia excretion after HEA exposure also was not affected by rhcgb KO. Surprisingly, ammonia excretion and Na+ uptake were unaffected by rhcgb or nhe3b KO in juvenile zebrafish acclimated to normal (800 μmol/L) or low (10 μmol/L) Na+ conditions. These results demonstrate that Rhcgb is expendable for ammonia excretion and Na+ uptake in zebrafish, highlighting the plasticity and flexibility of these physiological systems in this species.
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Affiliation(s)
- Alex M Zimmer
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada; Department of Biology, University of Ottawa, Ottawa, Ontario, Canada.
| | - Steve F Perry
- Department of Biology, University of Ottawa, Ottawa, Ontario, Canada
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8
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Zhang T, Peterson RT. Modeling Lysosomal Storage Diseases in the Zebrafish. Front Mol Biosci 2020; 7:82. [PMID: 32435656 PMCID: PMC7218095 DOI: 10.3389/fmolb.2020.00082] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Accepted: 04/08/2020] [Indexed: 12/13/2022] Open
Abstract
Lysosomal storage diseases (LSDs) are a family of 70 metabolic disorders characterized by mutations in lysosomal proteins that lead to storage material accumulation, multiple-organ pathologies that often involve neurodegeneration, and early mortality in a significant number of patients. Along with the necessity for more effective therapies, there exists an unmet need for further understanding of disease etiology, which could uncover novel pathways and drug targets. Over the past few decades, the growth in knowledge of disease-associated pathways has been facilitated by studies in model organisms, as advancements in mutagenesis techniques markedly improved the efficiency of model generation in mammalian and non-mammalian systems. In this review we highlight non-mammalian models of LSDs, focusing specifically on the zebrafish, a vertebrate model organism that shares remarkable genetic and metabolic similarities with mammals while also conferring unique advantages such as optical transparency and amenability toward high-throughput applications. We examine published zebrafish LSD models and their reported phenotypes, address organism-specific advantages and limitations, and discuss recent technological innovations that could provide potential solutions.
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Affiliation(s)
- T Zhang
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Utah, Salt Lake City, UT, United States
| | - R T Peterson
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Utah, Salt Lake City, UT, United States
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9
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Sun Y, Zhu Z. Designing future farmed fishes using genome editing. SCIENCE CHINA-LIFE SCIENCES 2019; 62:420-422. [DOI: 10.1007/s11427-018-9467-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 01/16/2019] [Indexed: 12/16/2022]
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10
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Genome Editing in Zebrafish Using CRISPR-Cas9: Applications for Developmental Toxicology. Methods Mol Biol 2019; 1965:235-250. [PMID: 31069679 DOI: 10.1007/978-1-4939-9182-2_16] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Environment-gene interactions have a powerful impact on embryo development. The ability to precisely edit the genome makes it possible to address questions concerning the specific roles that genes or variants play in modulating the response to environmental challenges. In this chapter, we provide a simplified protocol using CRISPR-Cas9 ribonucleoproteins for genome editing in the zebrafish model organism. The genetic manipulation can then be coupled with chemical screens to identify and understand the mechanism behind toxicants or compounds that modulate development.
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Zimmer AM, Shir-Mohammadi K, Kwong RWM, Perry SF. Reassessing the contribution of the Na+/H+ exchanger Nhe3b to Na+ uptake in zebrafish (Danio rerio) using CRISPR/Cas9 gene editing. J Exp Biol 2019; 223:jeb.215111. [DOI: 10.1242/jeb.215111] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 12/10/2019] [Indexed: 12/14/2022]
Abstract
Freshwater fishes absorb Na+ from their dilute environment using ion-transporting cells. In larval zebrafish (Danio rerio), Na+ uptake is coordinated by (1) Na+/H+-exchanger 3b (Nhe3b) and (2) H+-ATPase-powered electrogenic uptake in H+-ATPase-rich (HR) cells and by (3) Na+-Cl−-cotransporter (Ncc) expressed in NCC cells. The present study aimed to better understand the roles of these 3 proteins in Na+ uptake by larval zebrafish under ‘normal’ (800 µmol/L) and ‘low’ (10 µmol/L) Na+ conditions. We hypothesized that Na+ uptake would be reduced by CRISPR/Cas9 knockout (KO) of slc9a3.2 (encoding Nhe3b), particularly in low Na+ where Nhe3b is believed to play a dominant role. Contrary to this hypothesis, Na+ uptake was sustained in nhe3b KO larvae under both Na+ conditions, which led to the exploration of whether compensatory regulation of H+-ATPase or Ncc was responsible for maintaining Na+ uptake in nhe3b KO larvae. mRNA expression of the genes encoding H+-ATPase and Ncc were not altered in nhe3b KO. Moreover, morpholino knockdown of H+-ATPase, which significantly reduced H+ flux by HR cells, did not reduce Na+ uptake in nhe3b KO larvae, nor did rearing larvae in chloride-free conditions, thereby eliminating any driving force for Na+-Cl−-cotransport via Ncc. Finally, simultaneously treating nhe3b KO larvae with H+-ATPase morpholino and chloride-free conditions did not reduce Na+ uptake under normal or low Na+. These findings highlight the flexibility of the Na+ uptake system and demonstrate that Nhe3b is expendable to Na+ uptake in zebrafish and that our understanding of Na+ uptake mechanisms in this species is incomplete.
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Affiliation(s)
- Alex M. Zimmer
- Department of Biology, University of Ottawa, Ottawa, Ontario, Canada
| | | | | | - Steve F. Perry
- Department of Biology, University of Ottawa, Ottawa, Ontario, Canada
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Ramanagoudr-Bhojappa R, Carrington B, Ramaswami M, Bishop K, Robbins GM, Jones M, Harper U, Frederickson SC, Kimble DC, Sood R, Chandrasekharappa SC. Multiplexed CRISPR/Cas9-mediated knockout of 19 Fanconi anemia pathway genes in zebrafish revealed their roles in growth, sexual development and fertility. PLoS Genet 2018; 14:e1007821. [PMID: 30540754 PMCID: PMC6328202 DOI: 10.1371/journal.pgen.1007821] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Revised: 01/10/2019] [Accepted: 11/08/2018] [Indexed: 11/28/2022] Open
Abstract
Fanconi Anemia (FA) is a genomic instability syndrome resulting in aplastic anemia, developmental abnormalities, and predisposition to hematological and other solid organ malignancies. Mutations in genes that encode proteins of the FA pathway fail to orchestrate the repair of DNA damage caused by DNA interstrand crosslinks. Zebrafish harbor homologs for nearly all known FA genes. We used multiplexed CRISPR/Cas9-mediated mutagenesis to generate loss-of-function mutants for 17 FA genes: fanca, fancb, fancc, fancd1/brca2, fancd2, fance, fancf, fancg, fanci, fancj/brip1, fancl, fancm, fancn/palb2, fanco/rad51c, fancp/slx4, fancq/ercc4, fanct/ube2t, and two genes encoding FA-associated proteins: faap100 and faap24. We selected two indel mutations predicted to cause premature truncations for all but two of the genes, and a total of 36 mutant lines were generated for 19 genes. Generating two independent mutant lines for each gene was important to validate their phenotypic consequences. RT-PCR from homozygous mutant fish confirmed the presence of transcripts with indels in all genes. Interestingly, 4 of the indel mutations led to aberrant splicing, which may produce a different protein than predicted from the genomic sequence. Analysis of RNA is thus critical in proper evaluation of the consequences of the mutations introduced in zebrafish genome. We used fluorescent reporter assay, and western blots to confirm loss-of-function for several mutants. Additionally, we developed a DEB treatment assay by evaluating morphological changes in embryos and confirmed that homozygous mutants from all the FA genes that could be tested (11/17), displayed hypersensitivity and thus were indeed null alleles. Our multiplexing strategy helped us to evaluate 11 multiple gene knockout combinations without additional breeding. Homozygous zebrafish for all 19 single and 11 multi-gene knockouts were adult viable, indicating FA genes in zebrafish are generally not essential for early development. None of the mutant fish displayed gross developmental abnormalities except for fancp-/- fish, which were significantly smaller in length than their wildtype clutch mates. Complete female-to-male sex reversal was observed in knockouts for 12/17 FA genes, while partial sex reversal was seen for the other five gene knockouts. All adult females were fertile, and among the adult males, all were fertile except for the fancd1 mutants and one of the fancj mutants. We report here generation and characterization of zebrafish knockout mutants for 17 FA disease-causing genes, providing an integral resource for understanding the pathophysiology associated with the disrupted FA pathway. Deficiencies in repair of DNA damage can cause diseases such as Fanconi anemia (FA), which is characterized by birth defects, bone marrow failure, anemia, leukemia and other cancers. A set of proteins constitute the FA pathway and together orchestrate the DNA repair process. Inactivation of one or more gene(s) encoding the proteins of the DNA repair pathway in an animal model would enable us to study the functions of these proteins in maintenance of normal cellular functions and the overall health of an individual in the absence of function. We systematically targeted the FA pathway in zebrafish using CRISPR/Cas9. We generated 36 fish lines with loss-of-function mutations in 19 FA pathway genes and showed that all survive to adulthood. We did not notice obvious morphological changes except in fancp gene-inactivated fish, which were smaller in length. However, all mutant fish were either exclusively or in majority male. Unlike reduced fertility among FA patients, all adult mutant fish were fertile, except for the fancd1 and fancj knockout males. These mutant zebrafish will serve as a huge resource for the scientific community to study the role of FA proteins in fish development, DNA repair, and as models for FA disease.
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Affiliation(s)
- Ramanagouda Ramanagoudr-Bhojappa
- Cancer Genomics Unit, Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Blake Carrington
- Zebrafish Core, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Mukundhan Ramaswami
- Cancer Genomics Unit, Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Kevin Bishop
- Zebrafish Core, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Gabrielle M. Robbins
- Zebrafish Core, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - MaryPat Jones
- Genomics Core, Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Ursula Harper
- Genomics Core, Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Stephen C. Frederickson
- Zebrafish Core, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Danielle C. Kimble
- Cancer Genomics Unit, Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Raman Sood
- Zebrafish Core, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Settara C. Chandrasekharappa
- Cancer Genomics Unit, Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
- Genomics Core, Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
- * E-mail:
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Grajevskaja V, Camerota D, Bellipanni G, Balciuniene J, Balciunas D. Analysis of a conditional gene trap reveals that tbx5a is required for heart regeneration in zebrafish. PLoS One 2018; 13:e0197293. [PMID: 29933372 PMCID: PMC6014646 DOI: 10.1371/journal.pone.0197293] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Accepted: 04/30/2018] [Indexed: 01/27/2023] Open
Abstract
The ability to conditionally inactivate genes is instrumental for fine genetic analysis of all biological processes, but is especially important for studies of biological events, such as regeneration, which occur late in ontogenesis or in adult life. We have constructed and tested a fully conditional gene trap vector, and used it to inactivate tbx5a in the cardiomyocytes of larval and adult zebrafish. We observe that loss of tbx5a function significantly impairs the ability of zebrafish hearts to regenerate after ventricular resection, indicating that Tbx5a plays an essential role in the transcriptional program of heart regeneration.
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Affiliation(s)
- Viktorija Grajevskaja
- Department of Biology, College of Science and Technology, Temple University, Philadelphia, PA, United States of America
- Department of Zoology, Faculty of Natural Sciences, Vilnius University, Vilnius, Lithuania
| | - Diana Camerota
- Department of Biology, College of Science and Technology, Temple University, Philadelphia, PA, United States of America
| | - Gianfranco Bellipanni
- Department of Biology, College of Science and Technology, Temple University, Philadelphia, PA, United States of America
| | - Jorune Balciuniene
- Department of Biology, College of Science and Technology, Temple University, Philadelphia, PA, United States of America
| | - Darius Balciunas
- Department of Biology, College of Science and Technology, Temple University, Philadelphia, PA, United States of America
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Zebrafish Models of Rare Hereditary Pediatric Diseases. Diseases 2018; 6:diseases6020043. [PMID: 29789451 PMCID: PMC6023479 DOI: 10.3390/diseases6020043] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 05/17/2018] [Accepted: 05/19/2018] [Indexed: 12/12/2022] Open
Abstract
Recent advances in sequencing technologies have made it significantly easier to find the genetic roots of rare hereditary pediatric diseases. These novel methods are not panaceas, however, and they often give ambiguous results, highlighting multiple possible causative mutations in affected patients. Furthermore, even when the mapping results are unambiguous, the affected gene might be of unknown function. In these cases, understanding how a particular genotype can result in a phenotype also needs carefully designed experimental work. Model organism genetics can offer a straightforward experimental setup for hypothesis testing. Containing orthologs for over 80% of the genes involved in human diseases, zebrafish (Danio rerio) has emerged as one of the top disease models over the past decade. A plethora of genetic tools makes it easy to create mutations in almost any gene of the zebrafish genome and these mutant strains can be used in high-throughput preclinical screens for active molecules. As this small vertebrate species offers several other advantages as well, its popularity in biomedical research is bound to increase, with “aquarium to bedside” drug development pipelines taking a more prevalent role in the near future.
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