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Zajic DE, Podrabsky JE. GABA metabolism is crucial for long-term survival of anoxia in annual killifish embryos. J Exp Biol 2020; 223:jeb229716. [PMID: 32859669 DOI: 10.1242/jeb.229716] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 08/24/2020] [Indexed: 08/25/2023]
Abstract
In most vertebrates, a lack of oxygen quickly leads to irreparable damages to vital organs, such as the brain and heart. However, there are some vertebrates that have evolved mechanisms to survive periods of no oxygen (anoxia). The annual killifish (Austrofundulus limnaeus) survives in ephemeral ponds in the coastal deserts of Venezuela and their embryos have the remarkable ability to tolerate anoxia for months. When exposed to anoxia, embryos of A. limnaeus respond by producing significant amounts of γ-aminobutyric acid (GABA). This study aims to understand the role of GABA in supporting the metabolic response to anoxia. To explore this, we investigated four developmentally distinct stages of A. limnaeus embryos that vary in their anoxia tolerance. We measured GABA and lactate concentrations across development in response to anoxia and aerobic recovery. We then inhibited enzymes responsible for the production and degradation of GABA and observed GABA and lactate concentrations, as well as embryo mortality. Here, we show for the first time that GABA metabolism affects anoxia tolerance in A. limnaeus embryos. Inhibition of enzymes responsible for GABA production (glutamate decarboxylase) and degradation (GABA-transaminase and succinic acid semialdehyde dehydrogenase) led to increased mortality, supporting a role for GABA as an intermediate product and not a metabolic end-product. We propose multiple roles for GABA during anoxia and aerobic recovery in A. limnaeus embryos, serving as a neurotransmitter, an energy source, and an anti-oxidant.
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Affiliation(s)
- Daniel E Zajic
- Department of Biology, Portland State University, PO Box 751, Portland, OR 97207, USA
- Health, Human Performance, and Athletics Department, Linfield University, 900 SE Baker, McMinnville, OR 97128, USA
| | - Jason E Podrabsky
- Department of Biology, Portland State University, PO Box 751, Portland, OR 97207, USA
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Wagner JT, Knapp MJ, Podrabsky JE. Antioxidant capacity and anoxia-tolerance in Austrofundulus limnaeus embryos. J Exp Biol 2019; 222:jeb.204347. [DOI: 10.1242/jeb.204347] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 05/28/2019] [Indexed: 12/19/2022]
Abstract
Embryos of Austrofundulus limnaeus can tolerate extreme environmental stresses by entering into a state of metabolic and developmental arrest known as diapause. Oxidative stress is ubiquitous in aerobic organisms and the unique biology and ecology of A. limnaeus likely results in frequent and repeated exposures to oxidative stress during development. Antioxidant capacity of A. limnaeus was explored during development by measuring antioxidant capacity due to small molecules and several enzymatic antioxidant systems. Diapause II embryos can survive for several days in 1% hydrogen peroxide without indications of negative effects. Surprisingly, both small and large molecule antioxidant systems are highest during early development and may be due to maternal provisioning. Antioxidant capacity is largely invested in small molecules during early development and in enzymatic systems during late development. The switch in antioxidant mechanisms and decline in small molecule antioxidants during development correlates with the loss of extreme anoxia tolerance.
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Affiliation(s)
- Josiah T. Wagner
- Department of Biology, Portland State University, P.O. Box 751, Portland, OR 97207, USA
- Knight Cancer Institute Cancer Early Detection Advanced Research Center, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Mailcode: KR-CEDR, Portland, OR 97239, USA
| | - Michael J. Knapp
- Department of Biology, Portland State University, P.O. Box 751, Portland, OR 97207, USA
| | - Jason E. Podrabsky
- Department of Biology, Portland State University, P.O. Box 751, Portland, OR 97207, USA
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Wagner JT, Singh PP, Romney AL, Riggs CL, Minx P, Woll SC, Roush J, Warren WC, Brunet A, Podrabsky JE. The genome of Austrofundulus limnaeus offers insights into extreme vertebrate stress tolerance and embryonic development. BMC Genomics 2018; 19:155. [PMID: 29463212 PMCID: PMC5819677 DOI: 10.1186/s12864-018-4539-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Accepted: 02/12/2018] [Indexed: 11/21/2022] Open
Abstract
Background The annual killifish Austrofundulus limnaeus inhabits ephemeral ponds in northern Venezuela, South America, and is an emerging extremophile model for vertebrate diapause, stress tolerance, and evolution. Embryos of A. limnaeus regularly experience extended periods of desiccation and anoxia as a part of their natural history and have unique metabolic and developmental adaptations. Currently, there are limited genomic resources available for gene expression and evolutionary studies that can take advantage of A. limnaeus as a unique model system. Results We describe the first draft genome sequence of A. limnaeus. The genome was assembled de novo using a merged assembly strategy and was annotated using the NCBI Eukaryotic Annotation Pipeline. We show that the assembled genome has a high degree of completeness in genic regions that is on par with several other teleost genomes. Using RNA-seq and phylogenetic-based approaches, we identify several candidate genes that may be important for embryonic stress tolerance and post-diapause development in A. limnaeus. Several of these genes include heat shock proteins that have unique expression patterns in A. limnaeus embryos and at least one of these may be under positive selection. Conclusion The A. limnaeus genome is the first South American annual killifish genome made publicly available. This genome will be a valuable resource for comparative genomics to determine the genetic and evolutionary mechanisms that support the unique biology of annual killifishes. In a broader context, this genome will be a valuable tool for exploring genome-environment interactions and their impacts on vertebrate physiology and evolution. Electronic supplementary material The online version of this article (10.1186/s12864-018-4539-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Josiah T Wagner
- Department of Biology, Center for Life in Extreme Environments, Portland State University, Portland, Oregon, USA. .,Knight Cancer Early Detection Advanced Research Center, Oregon Health and Science University, Portland, Oregon, USA.
| | - Param Priya Singh
- Department of Genetics, Stanford University, Stanford, California, USA
| | - Amie L Romney
- Department of Biology, Center for Life in Extreme Environments, Portland State University, Portland, Oregon, USA
| | - Claire L Riggs
- Department of Biology, Center for Life in Extreme Environments, Portland State University, Portland, Oregon, USA
| | - Patrick Minx
- McDonnell Genome Institute at Washington University, St Louis, Missouri, USA
| | - Steven C Woll
- Department of Biology, Center for Life in Extreme Environments, Portland State University, Portland, Oregon, USA
| | - Jake Roush
- Department of Biology, Center for Life in Extreme Environments, Portland State University, Portland, Oregon, USA
| | - Wesley C Warren
- McDonnell Genome Institute at Washington University, St Louis, Missouri, USA
| | - Anne Brunet
- Department of Genetics, Stanford University, Stanford, California, USA.,Glenn Center for the Biology of Aging, Stanford, California, USA
| | - Jason E Podrabsky
- Department of Biology, Center for Life in Extreme Environments, Portland State University, Portland, Oregon, USA
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Wagner JT, Herrejon Chavez F, Podrabsky JE. Mitochondrial DNA Sequence and Lack of Response to Anoxia in the Annual Killifish Austrofundulus limnaeus. Front Physiol 2016; 7:379. [PMID: 27630577 PMCID: PMC5005410 DOI: 10.3389/fphys.2016.00379] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2016] [Accepted: 08/17/2016] [Indexed: 12/14/2022] Open
Abstract
The annual killifish Austrofundulus limnaeus inhabits ephemeral ponds in regions of Venezuela, South America. Permanent populations of A. limnaeus are maintained by production of stress-tolerant embryos that are able to persist in the desiccated sediment. Previous work has demonstrated that A. limnaeus have a remarkable ability to tolerate extended periods of anoxia and desiccating conditions. After considering temperature, A. limnaeus embryos have the highest known tolerance to anoxia when compared to any other vertebrate yet studied. Oxygen is completely essential for the process of oxidative phosphorylation by mitochondria, the intracellular organelle responsible for the majority of adenosine triphosphate production. Thus, understanding the unique properties of A. limnaeus mitochondria is of great interest. In this work, we describe the first complete mitochondrial genome (mtgenome) sequence of a single adult A. limnaeus individual and compare both coding and non-coding regions to several other closely related fish mtgenomes. Mitochondrial features were predicted using MitoAnnotator and polyadenylation sites were predicted using RNAseq mapping. To estimate the responsiveness of A. limnaeus mitochondria to anoxia treatment, we measure relative mitochondrial DNA copy number and total citrate synthase activity in both relatively anoxia-tolerant and anoxia-sensitive embryonic stages. Our cross-species comparative approach identifies unique features of ND1, ND5, ND6, and ATPase-6 that may facilitate the unique phenotype of A. limnaeus embryos. Additionally, we do not find evidence for mitochondrial degradation or biogenesis during anoxia/reoxygenation treatment in A. limnaeus embryos, suggesting that anoxia-tolerant mitochondria do not respond to anoxia in a manner similar to anoxia-sensitive mitochondria.
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Affiliation(s)
- Josiah T Wagner
- Department of Biology, Center for Life in Extreme Environments, Portland State University Portland, OR, USA
| | - Florisela Herrejon Chavez
- Department of Biology, Center for Life in Extreme Environments, Portland State University Portland, OR, USA
| | - Jason E Podrabsky
- Department of Biology, Center for Life in Extreme Environments, Portland State University Portland, OR, USA
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Podrabsky JE, Wilson NE. Hypoxia and Anoxia Tolerance in the Annual Killifish Austrofundulus limnaeus. Integr Comp Biol 2016; 56:500-9. [PMID: 27507238 DOI: 10.1093/icb/icw092] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Embryos of the annual killifish Austrofundulus limnaeus are routinely exposed to oxygen limitation during development and are extremely tolerant of anoxia. Importantly, tolerance of anoxia is not strictly associated with entrance into metabolic dormancy associated with diapause II, but rather any embryo will respond to anoxia by entering into a state of anoxia-induced quiescence. Hypoxia causes a reduction in the rate of development, reduced heart rates, and reduced capacities for metabolic enzyme activity in both aerobic and anaerobic pathways. Embryos of A. limnaeus begin life as oxyconformers, and transition into oxyregulators near the completion of embryonic development. As this transition occurs, extreme anoxia tolerance is lost. The rate of early development is independent of oxygen partial pressure, despite the fact that the embryos are oxyconformers. This suggests a contribution from anaerobic pathways to support early development. However, the specific pathways supporting this metabolism are unknown. The response of A. limnaeus embryos to hypoxia and anoxia is unique compared to other fishes and most other vertebrates, and thus future studies on this species may lend insight into novel mechanisms that support survival during prolonged oxygen limitation.
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Affiliation(s)
- Jason E Podrabsky
- Department of Biology, Portland State University, PO Box 751, Portland, OR 97207, USA
| | - Natalie E Wilson
- Department of Biology, Portland State University, PO Box 751, Portland, OR 97207, USA
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Podrabsky JE, Hand SC. Physiological strategies during animal diapause: lessons from brine shrimp and annual killifish. ACTA ACUST UNITED AC 2016; 218:1897-906. [PMID: 26085666 DOI: 10.1242/jeb.116194] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Diapause is a programmed state of developmental arrest that typically occurs as part of the natural developmental progression of organisms that inhabit seasonal environments. The brine shrimp Artemia franciscana and annual killifish Austrofundulus limnaeus share strikingly similar life histories that include embryonic diapause as a means to synchronize the growth and reproduction phases of their life history to favorable environmental conditions. In both species, respiration rate is severely depressed during diapause and thus alterations in mitochondrial physiology are a key component of the suite of characters associated with cessation of development. Here, we use these two species to illustrate the basic principles of metabolic depression at the physiological and biochemical levels. It is clear that these two species use divergent molecular mechanisms to achieve the same physiological and ecological outcomes. This pattern of convergent physiological strategies supports the importance of biochemical and physiological adaptations to cope with extreme environmental stress and suggests that inferring mechanism from transcriptomics or proteomics or metabolomics alone, without rigorous follow-up at the biochemical and physiological levels, could lead to erroneous conclusions.
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Affiliation(s)
- Jason E Podrabsky
- Department of Biology, Portland State University, P.O. Box 751, Portland, OR 97207-0751, USA
| | - Steven C Hand
- Department of Biological Sciences, Division of Cellular, Integrative and Comparative Biology, Louisiana State University, Baton Rouge, LA 70803, USA
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Hand SC, Denlinger DL, Podrabsky JE, Roy R. Mechanisms of animal diapause: recent developments from nematodes, crustaceans, insects, and fish. Am J Physiol Regul Integr Comp Physiol 2016; 310:R1193-211. [PMID: 27053646 PMCID: PMC4935499 DOI: 10.1152/ajpregu.00250.2015] [Citation(s) in RCA: 140] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Accepted: 03/11/2016] [Indexed: 01/22/2023]
Abstract
Life cycle delays are beneficial for opportunistic species encountering suboptimal environments. Many animals display a programmed arrest of development (diapause) at some stage(s) of their development, and the diapause state may or may not be associated with some degree of metabolic depression. In this review, we will evaluate current advancements in our understanding of the mechanisms responsible for the remarkable phenotype, as well as environmental cues that signal entry and termination of the state. The developmental stage at which diapause occurs dictates and constrains the mechanisms governing diapause. Considerable progress has been made in clarifying proximal mechanisms of metabolic arrest and the signaling pathways like insulin/Foxo that control gene expression patterns. Overlapping themes are also seen in mechanisms that control cell cycle arrest. Evidence is emerging for epigenetic contributions to diapause regulation via small RNAs in nematodes, crustaceans, insects, and fish. Knockdown of circadian clock genes in selected insect species supports the importance of clock genes in the photoperiodic response that cues diapause. A large suite of chaperone-like proteins, expressed during diapause, protects biological structures during long periods of energy-limited stasis. More information is needed to paint a complete picture of how environmental cues are coupled to the signal transduction that initiates the complex diapause phenotype, as well as molecular explanations for how the state is terminated. Excellent examples of molecular memory in post-dauer animals have been documented in Caenorhabditis elegans It is clear that a single suite of mechanisms does not regulate diapause across all species and developmental stages.
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Affiliation(s)
- Steven C Hand
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana;
| | - David L Denlinger
- Departments of Entomology and Evolution, Ecology and Organismal Biology, Ohio State University, Columbus, Ohio
| | - Jason E Podrabsky
- Department of Biology, Portland State University, Portland, Oregon; and
| | - Richard Roy
- Department of Biology, McGill University, Montréal, Québec, Canada
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8
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Insights into Sex Chromosome Evolution and Aging from the Genome of a Short-Lived Fish. Cell 2016; 163:1527-38. [PMID: 26638077 DOI: 10.1016/j.cell.2015.10.071] [Citation(s) in RCA: 183] [Impact Index Per Article: 22.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Revised: 08/11/2015] [Accepted: 10/21/2015] [Indexed: 01/16/2023]
Abstract
The killifish Nothobranchius furzeri is the shortest-lived vertebrate that can be bred in the laboratory. Its rapid growth, early sexual maturation, fast aging, and arrested embryonic development (diapause) make it an attractive model organism in biomedical research. Here, we report a draft sequence of its genome that allowed us to uncover an intra-species Y chromosome polymorphism representing-in real time-different stages of sex chromosome formation that display features of early mammalian XY evolution "in action." Our data suggest that gdf6Y, encoding a TGF-β family growth factor, is the master sex-determining gene in N. furzeri. Moreover, we observed genomic clustering of aging-related genes, identified genes under positive selection, and revealed significant similarities of gene expression profiles between diapause and aging, particularly for genes controlling cell cycle and translation. The annotated genome sequence is provided as an online resource (http://www.nothobranchius.info/NFINgb).
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Nathaniel TI, Williams-Hernandez A, Hunter AL, Liddy C, Peffley DM, Umesiri FE, Imeh-Nathaniel A. Tissue hypoxia during ischemic stroke: adaptive clues from hypoxia-tolerant animal models. Brain Res Bull 2015; 114:1-12. [PMID: 25738761 DOI: 10.1016/j.brainresbull.2015.02.006] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2014] [Revised: 02/12/2015] [Accepted: 02/19/2015] [Indexed: 10/23/2022]
Abstract
The treatment and prevention of hypoxic/ischemic brain injury in stroke patients remain a severe and global medical issue. Numerous clinical studies have resulted in a failure to develop chemical neuroprotection for acute, ischemic stroke. Over 150 estimated clinical trials of ischemic stroke treatments have been done, and more than 200 drugs and combinations of drugs for ischemic and hemorrhagic strokes have been developed. Billions of dollars have been invested for new scientific breakthroughs with only limited success. The revascularization of occluded cerebral arteries such as anti-clot treatments of thrombolysis has proven effective, but it can only be used in a 3-4.5h time frame after the onset of a stroke, and not for every patient. This review is about novel insights on how to resist tissue hypoxia from unconventional animal models. Ability to resist tissue hypoxia is an extraordinary ability that is not common in many laboratory animals such as rat and mouse models. For example, we can learn from a naked mole-rat, Chrysemys picta, how to actively regulate brain metabolic activity to defend the brain against fluctuating oxygen tension and acute bouts of oxidative stress following the onset of a stroke. Additionally, a euthermic arctic ground squirrel can teach us how the brain of a stroke patient can remain well oxygenated during tissue hypoxia with no evidence of cellular stress. In this review, we discuss how these animals provide us with a system to gain insight into the possible mechanisms of tissue hypoxia/ischemia. This issue is of clinical significance to stroke patients. We describe specific physiological and molecular adaptations employed by different animals' models of hypoxia tolerance in aquatic and terrestrial environments. We highlight how these adaptations might provide potential clues on strategies to adapt for the clinical management of tissue hypoxia during conditions such as stroke where oxygen demand fails to match the supply.
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Affiliation(s)
- Thomas I Nathaniel
- University of South Carolina School of Medicine-Greenville, 701 Grove Road, Greenville, SC 29605, United States.
| | - Ashley Williams-Hernandez
- University of South Carolina School of Medicine-Greenville, 701 Grove Road, Greenville, SC 29605, United States
| | - Anan L Hunter
- University of South Carolina School of Medicine-Greenville, 701 Grove Road, Greenville, SC 29605, United States
| | - Caroline Liddy
- University of South Carolina School of Medicine-Greenville, 701 Grove Road, Greenville, SC 29605, United States
| | - Dennis M Peffley
- University of South Carolina School of Medicine-Greenville, 701 Grove Road, Greenville, SC 29605, United States
| | - Francis E Umesiri
- Chemistry department, John Brown University, 2000 W. University Street, Siloam Springs, AR 72761, United States
| | - Adebobola Imeh-Nathaniel
- Department of Biology, North Greenville University, 7801 North Tigerville Road, Tigerville, SC 29688, United States
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Wagner JT, Podrabsky JE. Extreme tolerance and developmental buffering of UV-C induced DNA damage in embryos of the annual killifish Austrofundulus limnaeus. ACTA ACUST UNITED AC 2014; 323:10-30. [PMID: 25387429 DOI: 10.1002/jez.1890] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2014] [Revised: 07/16/2014] [Accepted: 08/15/2014] [Indexed: 11/09/2022]
Abstract
Free-living aquatic embryos are often at risk of exposure to ultraviolet radiation (UV-R). Successful completion of embryonic development depends on efficient removal of DNA lesions, and thus many aquatic embryos have mechanisms to reverse DNA lesions induced by UV-R. However, little is known of how embryos that are able to enter embryonic dormancy may respond to UV-R exposure and subsequent DNA damage. Embryos of the annual killifish Austrofundulus limnaeus are unique among vertebrates because their normal embryonic development includes (1) a complete dispersion of embryonic blastomeres prior to formation of the definitive embryonic axis, and (2) entry into a state of metabolic depression and developmental arrest termed diapause. Here, we show that developing and diapausing embryos of A. limnaeus have exceptional tolerance of UV-C radiation and can successfully complete embryonic development after receiving substantial doses of UV-C, especially if allowed to recover in full-spectrum light. Recovery in full-spectrum light permits efficient removal of the most common type of DNA lesion induced by UV-R: cyclobutane pyrimidine dimers. Interestingly, whole-mount embryo TUNEL assays suggest that apoptosis may not be a major contributor to cell death in embryos UV-C irradiated during dispersion/reaggregation or diapause. We also observed embryo mortality to be significantly delayed by several weeks in diapausing embryos irradiated and allowed to recover in the dark. These atypical responses to UV-R induced DNA damage may be due to the unique annual killifish life history and provide insight into DNA damage repair and recognition mechanisms during embryonic dormancy.
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Affiliation(s)
- Josiah T Wagner
- Department of Biology, Portland State University, Portland, Oregon
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