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Ingelson-Filpula WA, Kadamani KL, Ojaghi M, Pamenter ME, Storey KB. Hypoxia-induced downregulation of RNA m 6A protein machinery in the naked mole-rat heart. Biochimie 2024; 225:125-132. [PMID: 38788827 DOI: 10.1016/j.biochi.2024.05.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 05/15/2024] [Accepted: 05/21/2024] [Indexed: 05/26/2024]
Abstract
Naked mole-rats, Heterocephalus glaber, are champion hypoxia-tolerant rodents that live under low oxygen conditions in their subterranean burrows. Detrimental effects of low oxygen can be mitigated through metabolic rate depression (MRD), metabolic reorganization, and global downregulation of nonessential cellular processes. Recent research has progressively implicated epigenetic modifications - rapid, reversible changes to gene expression that do not alter the DNA sequence itself - as major players in implementing and maintaining MRD. N6-adenosine (m6A) methylation is the most prevalent mammalian RNA modification and is responsible for pre-mRNA processing and mRNA export from the nucleus. Hence, m6A -mediated conformational changes alter the cellular fate of transcripts. The present study investigated the role of m6A RNA methylation responses to 24 h of hypoxia exposure in H. glaber cardiac tissue. Total protein levels of m6A writers/readers/erasers, m6A demethylase activity, and total m6A quantification were measured under normoxic vs. hypoxic conditions in H. glaber heart. While there was no change in either demethylase activity or total m6A content, many proteins of the m6A pathway were downregulated during hypoxia. Overall, m6A may not be a signature hypoxia-responsive characteristic in H. glaber heart, but downregulation of the protein machinery involved in m6A cycling points to an alternate biological involvement. Further research will explore other forms of RNA modifications and other epigenetic mechanisms to determine the controls on hypoxia endurance in this subterranean mammal.
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Affiliation(s)
- W Aline Ingelson-Filpula
- Affiliation: Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, Ontario, Canada, K1S 5B6.
| | - Karen L Kadamani
- Biology Department, University of Ottawa, Marie-Curie Pvt, Ottawa, Ontario, K1N 9A7, Canada
| | - Mohammad Ojaghi
- Biology Department, University of Ottawa, Marie-Curie Pvt, Ottawa, Ontario, K1N 9A7, Canada
| | - Matthew E Pamenter
- Biology Department, University of Ottawa, Marie-Curie Pvt, Ottawa, Ontario, K1N 9A7, Canada; Brain and Mind Research Institute, University of Ottawa, Ottawa, Ontario, Canada
| | - Kenneth B Storey
- Affiliation: Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, Ontario, Canada, K1S 5B6
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Niu Y, Zhang X, Men S, Xu T, Zhang H, Li X, Storey KB, Chen Q. Effects of hibernation on two important contractile tissues in tibetan frogs, Nanorana parkeri: a perspective from transcriptomics and metabolomics approaches. BMC Genomics 2024; 25:454. [PMID: 38720264 PMCID: PMC11080311 DOI: 10.1186/s12864-024-10357-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 04/26/2024] [Indexed: 05/12/2024] Open
Abstract
BACKGROUND In response to seasonal cold and food shortage, the Xizang plateau frogs, Nanorana parkeri (Anura: Dicroglossidae), enter a reversible hypometabolic state where heart rate and oxygen consumption in skeletal muscle are strongly suppressed. However, the effect of winter hibernation on gene expression and metabolic profiling in these two tissues remains unknown. In the present study, we conducted transcriptomic and metabolomic analyses of heart and skeletal muscle from summer- and winter-collected N. parkeri to explore mechanisms involved in seasonal hibernation. RESULTS We identified 2407 differentially expressed genes (DEGs) in heart and 2938 DEGs in skeletal muscle. Enrichment analysis showed that shared DEGs in both tissues were enriched mainly in translation and metabolic processes. Of these, the expression of genes functionally categorized as "response to stress", "defense mechanisms", or "muscle contraction" were particularly associated with hibernation. Metabolomic analysis identified 24 and 22 differentially expressed metabolites (DEMs) in myocardium and skeletal muscle, respectively. In particular, pathway analysis showed that DEMs in myocardium were involved in the pentose phosphate pathway, glycerolipid metabolism, pyruvate metabolism, citrate cycle (TCA cycle), and glycolysis/gluconeogenesis. By contrast, DEMs in skeletal muscle were mainly involved in amino acid metabolism. CONCLUSIONS In summary, natural adaptations of myocardium and skeletal muscle in hibernating N. parkeri involved transcriptional alterations in translation, stress response, protective mechanisms, and muscle contraction processes as well as metabolic remodeling. This study provides new insights into the transcriptional and metabolic adjustments that aid winter survival of high-altitude frogs N. parkeri.
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Affiliation(s)
- Yonggang Niu
- School of Life Sciences, Dezhou University, Dezhou, 253023, Shandong, China.
- School of Life Sciences, Lanzhou University, Lanzhou, 730000, Gansu, China.
| | - Xuejing Zhang
- School of Life Sciences, Lanzhou University, Lanzhou, 730000, Gansu, China
| | - Shengkang Men
- School of Life Sciences, Lanzhou University, Lanzhou, 730000, Gansu, China
| | - Tisen Xu
- School of Life Sciences, Dezhou University, Dezhou, 253023, Shandong, China
| | - Haiying Zhang
- School of Life Sciences, Dezhou University, Dezhou, 253023, Shandong, China
| | - Xiangyong Li
- School of Life Sciences, Dezhou University, Dezhou, 253023, Shandong, China
| | - Kenneth B Storey
- Department of Biology, Carleton University, Ottawa, ON, K1S 5B6, Canada
| | - Qiang Chen
- School of Life Sciences, Lanzhou University, Lanzhou, 730000, Gansu, China.
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Ingelson-Filpula WA, Storey KB. Hibernation-Induced microRNA Expression Promotes Signaling Pathways and Cell Cycle Dysregulation in Ictidomys tridecemlineatus Cardiac Tissue. Metabolites 2023; 13:1096. [PMID: 37887421 PMCID: PMC10608741 DOI: 10.3390/metabo13101096] [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: 08/30/2023] [Revised: 10/05/2023] [Accepted: 10/16/2023] [Indexed: 10/28/2023] Open
Abstract
The thirteen-lined ground squirrel Ictidomys tridecemlineatus is a rodent that lives throughout the United States and Canada and uses metabolic rate depression to facilitate circannual hibernation which helps it survive the winter. Metabolic rate depression is the reorganization of cellular physiology and molecular biology to facilitate a global downregulation of nonessential genes and processes, which conserves endogenous fuel resources and prevents the buildup of waste byproducts. Facilitating metabolic rate depression requires a complex interplay of regulatory approaches, including post-transcriptional modes such as microRNA. MicroRNA are short, single-stranded RNA species that bind to mRNA transcripts and target them for degradation or translational suppression. Using next-generation sequencing, we analyzed euthermic vs. hibernating cardiac tissue in I. tridecemlineatus to predict seven miRNAs (let-7e-5p, miR-122-5p, miR-2355-3p, miR-6715b-3p, miR-378i, miR-9851-3p, and miR-454-3p) that may be differentially regulated during hibernation. Gene ontology and KEGG pathway analysis suggested that these miRNAs cause a strong activation of ErbB2 signaling which causes downstream effects, including the activation of MAPK and PI3K/Akt signaling and concurrent decreases in p53 signaling and cell cycle-related processes. Taken together, these results predict critical miRNAs that may change during hibernation in the hearts of I. tridecemlineatus and identify key signaling pathways that warrant further study in this species.
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Affiliation(s)
| | - Kenneth B. Storey
- Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, ON K1S 5B6, Canada;
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James RS, Seebacher F, Tallis J. Can animals tune tissue mechanics in response to changing environments caused by anthropogenic impacts? J Exp Biol 2023; 226:287009. [PMID: 36779312 DOI: 10.1242/jeb.245109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/14/2023]
Abstract
Anthropogenic climate change and pollution are impacting environments across the globe. This Review summarises the potential impact of such anthropogenic effects on animal tissue mechanics, given the consequences for animal locomotor performance and behaviour. More specifically, in light of current literature, this Review focuses on evaluating the acute and chronic effects of temperature on the mechanical function of muscle tissues. For ectotherms, maximal muscle performance typically occurs at temperatures approximating the natural environment of the species. However, species vary in their ability to acclimate to chronic changes in temperature, which is likely to have longer-term effects on species range. Some species undergo periods of dormancy to avoid extreme temperature or drought. Whilst the skeletal muscle of such species generally appears to be adapted to minimise muscle atrophy and maintain performance for emergence from dormancy, the increased occurrence of extreme climatic conditions may reduce the survival of individuals in such environments. This Review also considers the likely impact of anthropogenic pollutants, such as hormones and heavy metals, on animal tissue mechanics, noting the relative paucity of literature directly investigating this key area. Future work needs to determine the direct effects of anthropogenic environmental changes on animal tissues and related changes in locomotor performance and behaviour, including accounting for currently unknown interactions between environmental factors, e.g. temperature and pollutants.
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Affiliation(s)
- Rob S James
- Faculty of Life Sciences, University of Bradford, Bradford BD7 1DP, UK
| | - Frank Seebacher
- School of Life and Environmental Sciences A08, University of Sydney, Sydney, NSW 2006, Australia
| | - Jason Tallis
- Research Centre for Sport, Exercise and Life Sciences, Coventry University, Priory Street, Coventry CV1 5FB, UK
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Ingelson-Filpula WA, Hadj-Moussa H, Storey KB. MicroRNA transcriptomics in liver of the freeze-tolerant gray tree frog (Dryophytes versicolor) indicates suppression of energy-expensive pathways. Cell Biochem Funct 2023; 41:309-320. [PMID: 36823992 DOI: 10.1002/cbf.3783] [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: 12/15/2022] [Revised: 02/06/2023] [Accepted: 02/14/2023] [Indexed: 02/25/2023]
Abstract
The rapid and reversible nature of microRNA (miRNA) transcriptional regulation is ideal for implementing global changes to cellular processes and metabolism, a necessary asset for the freeze-tolerant gray tree frog (Dryophytes versicolor). D. versicolor can freeze up to 42% of its total body water during the winter and then thaw completely upon more favorable conditions of spring. Herein, we examined the freeze-specific miRNA responses in the gray tree frog using RBiomirGS, a bioinformatic tool designed for the analysis of miRNA-seq transcriptomics in non-genome sequenced organisms. We identified 11 miRNAs differentially regulated during freezing (miR-140-3p, miR-181a-5p, miR-206-3p, miR-451a, miR-19a-3p, miR-101-3p, miR-30e-5p, miR-142-3p and -5p, miR-21-5p, and miR-34a-5p). Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis suggests these miRNAs play roles in downregulating signaling pathways, apoptosis, and nuclear processes while enhancing ribosomal biogenesis. Overall, these findings point towards miRNA inducing a state of energy conservation by downregulating energy-expensive pathways, while ribosomal biogenesis may lead to prioritization of critical processes for freeze-tolerance survival.
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Affiliation(s)
| | | | - Kenneth B Storey
- Department of Biology, Institute of Biochemistry, Carleton University, Ottawa, Ontario, Canada
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Ingelson-Filpula WA, Cheng H, Eaton L, Pamenter ME, Storey KB. Small RNA sequencing in hypoxic naked mole-rat hearts suggests microRNA regulation of RNA- and translation-related processes. FEBS Lett 2022; 596:2821-2833. [PMID: 36120811 DOI: 10.1002/1873-3468.14499] [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: 08/25/2022] [Revised: 09/09/2022] [Accepted: 09/12/2022] [Indexed: 11/09/2022]
Abstract
The naked mole-rat (Heterocephalus glaber) regularly endures intermittent periods of hypoxia in its burrows, surviving in part due to metabolic rate depression (MRD)-a strategy of conserving cellular resources by downregulating nonessential gene expression and reorganizing cellular processes. MicroRNA (miRNA) are short, noncoding RNAs already implicated for their roles in numerous models of extreme environmental stress; given their rapid, reversible nature, they are ideal for implementing MRD. We performed small RNA sequencing on cardiac tissue from normoxic vs. 24 h hypoxic naked mole-rats, and used bioinformatics to predict eighteen miRNAs which may be differentially regulated during hypoxia. Gene Ontology and KEGG pathway mapping further suggest these miRNAs play roles in largely translation-related functions, including RNA processing and catabolism.
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Affiliation(s)
- W Aline Ingelson-Filpula
- Institute of Biochemistry and Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, Ontario, K1S 5B6, Canada
| | - Hang Cheng
- Biology Department, University of Ottawa, Marie-Curie Pvt, Ottawa, Ontario, K1N 9A7, Canada
| | - Liam Eaton
- Biology Department, University of Ottawa, Marie-Curie Pvt, Ottawa, Ontario, K1N 9A7, Canada
| | - Matthew E Pamenter
- Biology Department, University of Ottawa, Marie-Curie Pvt, Ottawa, Ontario, K1N 9A7, Canada.,Brain and Mind Research Institute, University of Ottawa, Ottawa, Ontario, Canada
| | - Kenneth B Storey
- Institute of Biochemistry and Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, Ontario, K1S 5B6, Canada
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