1
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Ren X, Zhao J, Hu J. Non-concordant epigenetic and transcriptional responses to acute thermal stress in western mosquitofish (Gambusia affinis). Mol Ecol 2024:e17332. [PMID: 38529738 DOI: 10.1111/mec.17332] [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: 07/17/2023] [Revised: 02/28/2024] [Accepted: 03/18/2024] [Indexed: 03/27/2024]
Abstract
Climate change is intensifying the frequency and severity of extreme temperatures. Understanding the molecular mechanisms underlying the ability to cope with acute thermal stress is key for predicting species' responses to extreme temperature events. While many studies have focused on the individual roles of gene expression, post-transcriptional processes and epigenetic modifications in response to acute thermal stress, the relative contribution of these molecular mechanisms remains unclear. The wide range of thermal limits of western mosquitofish (Gambusia affinis) provides an opportunity to explore this interplay. Here, we quantified changes in gene expression, alternative splicing, DNA methylation and microRNA (miRNA) expression in muscle tissue dissected from mosquitofish immediately after reaching high (CTmax) or low thermal limit (CTmin). Although the numbers of genes showing expression and splicing changes in response to acute temperature stress were small, we found a possibly larger and non-redundant role of splicing compared to gene expression, with more genes being differentially spliced (DSGs) than differentially expressed (DEGs), and little overlap between DSGs and DEGs. We also identified a small proportion of CpGs showing significant methylation change (i.e. differentially methylated cytosines, DMCs) in fish at thermal limits; however, there was no overlap between DEGs and genes annotated with DMCs in both CTmax and CTmin experiments. The weak interplay between epigenetic modifications and gene expression was further supported by our discoveries of no differentially expressed miRNAs. These findings provide novel insights into the relative role of different molecular mechanisms underlying immediate responses to extreme temperatures and demonstrate non-concordant responses of epigenetic and transcriptional mechanisms to acute temperature stress.
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Affiliation(s)
- Xingyue Ren
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, P. R. China
| | - Junjie Zhao
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, P. R. China
| | - Juntao Hu
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, P. R. China
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2
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Amaro F, González D, Gutiérrez JC. MicroRNAs in Tetrahymena thermophila: An epigenetic regulatory mechanism in the response to cadmium stress. Microbiol Res 2024; 280:127565. [PMID: 38160574 DOI: 10.1016/j.micres.2023.127565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 11/15/2023] [Accepted: 12/01/2023] [Indexed: 01/03/2024]
Abstract
Among the epigenetic mechanisms based on non-coding RNA are microRNAs (miRNAs) that are involved in the post-transcriptional regulation of mRNAs. In many organisms, the expression of genes involved in the cellular response to biotic or abiotic stress depends on the regulation, generally inhibitory, performed by miRNAs. For the first time in the eukaryotic microorganism (ciliate-model) Tetrahymena thermophila, miRNAs involved in the post-transcriptional regulation of transcripts linked to the response to cadmium have been isolated and analyzed. Forty de novo miRNAs (we named tte-miRNAs) have been isolated from control and Cd-treated populations (1 or 24 h exposures). An exhaustive comparative analysis of the features of these mature tte-miRNAs and their precursor sequences (pre-tte-miRNAs) confirms that they are true miRNAs. In addition to the three types of miRNA isoforms previously described in other organisms, two new types are also described among the tte-miRNAs studied. A certain percentage of the pre-tte-miRNA sequences are in introns from genes with many introns, and have been defined as 5', 3'-tailed mirtrons. A qRT-PCR analysis of selected tte-miRNAs together with some of their targets has validated them. Cd is one of the most toxic metals for the cell, which must defend itself against its toxicity by various mechanisms, such as expulsion by membrane pumps, chelation by metallothioneins, among others. Like other toxic metals, Cd also causes a well-known series of cellular effects such as intense proteotoxicity. Many of the targets that are regulated by the tte-miRNAs are transcripts encoding proteins that fit into these defense mechanisms and toxic metal effects.
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Affiliation(s)
- Francisco Amaro
- Department of Genetics, Physiology and Microbiology, Faculty of Biology, Complutense University of Madrid, 28040 Madrid. Spain
| | - David González
- Department of Genetics, Physiology and Microbiology, Faculty of Biology, Complutense University of Madrid, 28040 Madrid. Spain
| | - Juan-Carlos Gutiérrez
- Department of Genetics, Physiology and Microbiology, Faculty of Biology, Complutense University of Madrid, 28040 Madrid. Spain.
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3
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Han L, Hao P, Wang W, Wu Y, Ruan S, Gao C, Tian W, Tian Y, Li X, Wang L, Zhang W, Wang H, Chang Y, Ding J. Molecular mechanisms that regulate the heat stress response in sea urchins (Strongylocentrotus intermedius) by comparative heat tolerance performance and whole-transcriptome RNA sequencing. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 901:165846. [PMID: 37541492 DOI: 10.1016/j.scitotenv.2023.165846] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 06/07/2023] [Accepted: 07/26/2023] [Indexed: 08/06/2023]
Abstract
In the context of climate change and extreme high temperature, the commercially important sea urchin Strongylocentrotus intermedius suffers high mortality during summer in Northern China. How sea urchins respond to high temperatures is of great concern to academia and industry. How to understand the heat tolerance of sea urchin from the whole transcriptome level. In this study, the heat-resistant S. intermedius bred by our team and its control group were used as the research objects, then we applied whole-transcriptome RNA sequencing to detect differentially expressed mRNAs, microRNAs, long noncoding RNAs that respond to heat stress in the heat-resistant and control S. intermedius. A competitive endogenous RNA (ceRNA) regulatory network was constructed with predicted pairs of differentially expressed mRNAs and noncoding RNAs and revealed the molecular regulatory mechanisms in S. intermedius responding to heat stress. A functional analysis suggested that the ceRNAs were involved in basal metabolism, calcium ion transport, endoplasmic reticulum stress, and apoptosis. This is the whole-transcriptomic analysis of S. intermedius under heat stress to propose ceRNA networks that will provide a basis for studying the potential functions of long noncoding RNAs and miRNAs in the heat stress response in S. intermedius and provide a theoretical basis for the study of the molecular mechanism of sea urchins in response to environmental changes.
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Affiliation(s)
- Lingshu Han
- Key Laboratory of Northern Aquatic Germplasm Resources and Genetic Breeding in Liaoning Province, Dalian 116023, China; Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning, 116023, China; School of Marine Sciences, Ningbo University, Ningbo 315211, China
| | - Pengfei Hao
- Key Laboratory of Northern Aquatic Germplasm Resources and Genetic Breeding in Liaoning Province, Dalian 116023, China; Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning, 116023, China
| | - Wenpei Wang
- Key Laboratory of Northern Aquatic Germplasm Resources and Genetic Breeding in Liaoning Province, Dalian 116023, China; Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning, 116023, China
| | - Yanglei Wu
- Key Laboratory of Northern Aquatic Germplasm Resources and Genetic Breeding in Liaoning Province, Dalian 116023, China; Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning, 116023, China
| | - Shuchao Ruan
- Key Laboratory of Northern Aquatic Germplasm Resources and Genetic Breeding in Liaoning Province, Dalian 116023, China; Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning, 116023, China
| | - Chuang Gao
- Key Laboratory of Northern Aquatic Germplasm Resources and Genetic Breeding in Liaoning Province, Dalian 116023, China; Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning, 116023, China
| | - Wanrong Tian
- Key Laboratory of Northern Aquatic Germplasm Resources and Genetic Breeding in Liaoning Province, Dalian 116023, China; Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning, 116023, China
| | - Ye Tian
- Key Laboratory of Northern Aquatic Germplasm Resources and Genetic Breeding in Liaoning Province, Dalian 116023, China; Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning, 116023, China
| | - Xiaonan Li
- Key Laboratory of Northern Aquatic Germplasm Resources and Genetic Breeding in Liaoning Province, Dalian 116023, China; Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning, 116023, China
| | - Luo Wang
- Key Laboratory of Northern Aquatic Germplasm Resources and Genetic Breeding in Liaoning Province, Dalian 116023, China; Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning, 116023, China
| | - Weijie Zhang
- Key Laboratory of Northern Aquatic Germplasm Resources and Genetic Breeding in Liaoning Province, Dalian 116023, China; Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning, 116023, China
| | - Heng Wang
- Key Laboratory of Northern Aquatic Germplasm Resources and Genetic Breeding in Liaoning Province, Dalian 116023, China; Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning, 116023, China
| | - Yaqing Chang
- Key Laboratory of Northern Aquatic Germplasm Resources and Genetic Breeding in Liaoning Province, Dalian 116023, China; Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning, 116023, China
| | - Jun Ding
- Key Laboratory of Northern Aquatic Germplasm Resources and Genetic Breeding in Liaoning Province, Dalian 116023, China; Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning, 116023, China.
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Xu P, Zhang W, Wang X, Zhu Y, Liang W, He Y, Yu X. Multiomics analysis reveals a link between Brassica-specific miR1885 and rapeseed tolerance to low temperature. PLANT, CELL & ENVIRONMENT 2023; 46:3405-3419. [PMID: 37564020 DOI: 10.1111/pce.14690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 06/26/2023] [Accepted: 08/01/2023] [Indexed: 08/12/2023]
Abstract
Brassica crops include various edible vegetable and plant oil crops, and their production is limited by low temperature beyond their tolerant capability. The key regulators of low-temperature resistance in Brassica remain largely unexplored. To identify posttranscriptional regulators of plant response to low temperature, we performed small RNA profiling, and found that 16 known miRNAs responded to cold treatment in Brassica rapa. The cold response of seven of those miRNAs were further confirmed by qRT-PCR and/or northern blot analyses. In parallel, a genome-wide association study of 220 accessions of Brassica napus identified four candidate MIRNA genes, all of which were cold-responsive, at the loci associated with low-temperature resistance. Specifically, these large-scale data analyses revealed a link between miR1885 and the plant response to low temperature in both B. rapa and B. napus. Using 5' rapid amplification of cDNA ends approach, we validated that miR1885 can cleave its putative target gene transcripts, Bn.TIR.A09 and Bn.TNL.A03, in B. napus. Furthermore, overexpression of miR1885 in Semiwinter type B. napus decreased the mRNA abundance of Bn.TIR.A09 and Bn.TNL.A03 and resulted in increased sensitivity to low temperature. Knocking down of miR1885 in Spring type B. napus led to increased mRNA abundance of its targets and improved rapeseed tolerance to low temperature. Together, our results suggested that the loci of miR1885 and its targets could be potential candidates for the molecular breeding of low temperature-tolerant Spring type Brassica crops.
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Affiliation(s)
- Pengfei Xu
- Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Wenting Zhang
- Guangdong Provincial Key Laboratory of Crops Genetics & Improvement, Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Xuan Wang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Yantao Zhu
- Hybrid Rape Research Center of Shaanxi Province, Yangling, Shaanxi, China
| | - Wanqi Liang
- Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Yuke He
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Xiang Yu
- Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
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5
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Zhao G, Liu Z, Quan J, Sun J, Li L, Lu J. Potential role of miR-8159-x in heat stress response in rainbow trout (Oncorhynchus mykiss). Comp Biochem Physiol B Biochem Mol Biol 2023; 268:110877. [PMID: 37356566 DOI: 10.1016/j.cbpb.2023.110877] [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: 03/10/2023] [Revised: 06/05/2023] [Accepted: 06/22/2023] [Indexed: 06/27/2023]
Abstract
Rainbow trout (Oncorhynchus mykiss) is a representative species of cold-water fish. Elevated temperatures during summer often result in significant high mortality rates. MicroRNAs (miRNAs) are class of small non-coding RNAs that play a crucial role as post-transcriptional regulators in various biological processes. Emerging evidence suggests that miRNAs are important regulators role during heat stress. Analyzing previously obtained miRNA-sequencing data, we observed substantial down regulation of miR-8159-x in the liver tissue of heat stressed rainbow trout. In this study, we conducted a dual luciferase reporter assay to validate that miR-8159-x target, a key gene involved in heat stress in rainbow trout. By examining the expression patterns of miR-8159-x and hsp90a1 in the liver tissue at 18 °C (CG) and 24 °C (HS) groups, we propose that miR-8159-x may negatively regulate hsp90a1. Furthermore, in vitro hepatocyte assay, transfection with miR-8159-x mimics significantly reduced the expression level of hsp90a1, whereas transfection with a miR-8159-x inhibitor yielded the opposite effect. Additionally, overexpression of miR-8159-x inhibited cell proliferation and induced apoptosis in normal rainbow trout hepatocytes. We further investigated the effects of miR-8159-x overexpression or inhibition on the mRNA and protein levels of the target gene hsp90a1 under heat stress conditions. In conclusion, our findings suggest that miR-8159-x participates in the biological response to heat stress by targeting hsp90a1. These results contribute to a better understanding of the molecular mechanisms underlying heat stress in rainbow trout and provide valuable insights for future research.
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Affiliation(s)
- Guiyan Zhao
- College of Animal Science & Technology, Gansu Agricultural University, Lanzhou 730070, PR China.
| | - Zhe Liu
- College of Animal Science & Technology, Gansu Agricultural University, Lanzhou 730070, PR China.
| | - Jinqiang Quan
- College of Animal Science & Technology, Gansu Agricultural University, Lanzhou 730070, PR China.
| | - Jun Sun
- College of Animal Science & Technology, Gansu Agricultural University, Lanzhou 730070, PR China.
| | - Lanlan Li
- College of Animal Science & Technology, Gansu Agricultural University, Lanzhou 730070, PR China.
| | - Junhao Lu
- College of Animal Science & Technology, Gansu Agricultural University, Lanzhou 730070, PR China.
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6
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Breedon SA, Varma A, Quintero-Galvis JF, Gaitán-Espitia JD, Mejías C, Nespolo RF, Storey KB. Torpor-responsive microRNAs in the heart of the Monito del monte, Dromiciops gliroides. Biofactors 2023; 49:1061-1073. [PMID: 37219063 DOI: 10.1002/biof.1976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 05/14/2023] [Indexed: 05/24/2023]
Abstract
The marsupial Monito del monte (Dromiciops gliroides) utilizes both daily and seasonal bouts of torpor to preserve energy and prolong survival during periods of cold and unpredictable food availability. Torpor involves changes in cellular metabolism, including specific changes to gene expression that is coordinated in part, by the posttranscriptional gene silencing activity of microRNAs (miRNA). Previously, differential miRNA expression has been identified in D. gliroides liver and skeletal muscle; however, miRNAs in the heart of Monito del monte remained unstudied. In this study, the expression of 82 miRNAs was assessed in the hearts of active and torpid D. gliroides, finding that 14 were significantly differentially expressed during torpor. These 14 miRNAs were then used in bioinformatic analyses to identify Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways that were predicted to be most affected by these differentially expressed miRNAs. Overexpressed miRNAs were predicted to primarily regulate glycosaminoglycan biosynthesis, along with various signaling pathways such as Phosphoinositide-3-kinase/protein kinase B and transforming growth factor-β. Similarly, signaling pathways including phosphatidylinositol and Hippo were predicted to be regulated by the underexpression of miRNAs during torpor. Together, these results suggest potential molecular adaptations that protect against irreversible tissue damage and enable continued cardiac and vascular function despite hypothermia and limited organ perfusion during torpor.
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Affiliation(s)
- Sarah A Breedon
- Department of Biology and Institute of Biochemistry, Carleton University, Ottawa, Ontario, Canada
| | - Anchal Varma
- Department of Biology and Institute of Biochemistry, Carleton University, Ottawa, Ontario, Canada
| | - Julian F Quintero-Galvis
- Facultad de Ciencias, Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Valdivia, Chile
| | - Juan Diego Gaitán-Espitia
- The Swire Institute of Marine Science and School of Biological Sciences, The University of Hong Kong, Hong Kong, China
| | - Carlos Mejías
- Facultad de Ciencias, Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Valdivia, Chile
- Millenium Nucleus of Limit of Life (LiLi), Valdivia, Chile
| | - Roberto F Nespolo
- Facultad de Ciencias, Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Valdivia, Chile
- Millenium Nucleus of Limit of Life (LiLi), Valdivia, Chile
| | - Kenneth B Storey
- Department of Biology and Institute of Biochemistry, Carleton University, Ottawa, Ontario, Canada
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Selvaraju S, Ramya L, Swathi D, Archana SS, Lavanya M, Krishnappa B, Binsila BK, Mahla AS, Arangasamy A, Andonissamy J, Kumar P, Sharma RK. Cryostress induces fragmentation and alters the abundance of sperm transcripts associated with fertilizing competence and reproductive processes in buffalo. Cell Tissue Res 2023:10.1007/s00441-023-03764-8. [PMID: 37079096 DOI: 10.1007/s00441-023-03764-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 03/09/2023] [Indexed: 04/21/2023]
Abstract
The study aimed to assess the influence of cryostress on RNA integrity and functional significance in sperm fertilizing ability. The fresh and post-thawed buffalo sperm (n = 6 each) samples were evaluated for their functional attributes, and sperm total RNA was subjected to transcriptome sequencing followed by validation using real-time PCR and dot blot. Overall, 6911 genes had an expression of FPKM > 1, and among these 431 genes were abundantly expressed (FPKM > 20) in buffalo sperm. These abundantly expressed genes regulate reproductive functions such as sperm motility (TEKT2, SPEM1, and PRM3, FDR = 1.10E-08), fertilization (EQTN, PLCZ1, and SPESP1, FDR = 7.25E-06) and the developmental process involved in reproduction (SPACA1, TNP1, and YBX2, FDR = 7.21E-06). Cryopreservation significantly (p < 0.05) affected the structural and functional membrane integrities of sperm. The expression levels of transcripts that regulate the metabolic activities and fertility-related functions were compromised during cryopreservation. Interestingly, cryostress induces the expression of genes involved (p < 0.05) in chemokine signaling (CX3CL1, CCL20, and CXCR4), G-protein coupled receptor binding (ADRB1, EDN1, and BRS3), translation (RPS28, MRPL28, and RPL18A), oxidative phosphorylation (ND1, ND2, and COX2), response to reactive oxygen species (GLRX2, HYAL2, and EDN1), and immune responses (CX3CL1, CCL26, and TBXA2R). These precociously expressed genes during cryopreservation alter the signaling mechanisms that govern sperm functional competence and can impact fertilization and early embryonic development.
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Affiliation(s)
- Sellappan Selvaraju
- Reproductive Physiology Laboratory, ICAR-National Institute of Animal Nutrition and Physiology, Adugodi, Bengaluru, 560030, India.
| | - Laxman Ramya
- Reproductive Physiology Laboratory, ICAR-National Institute of Animal Nutrition and Physiology, Adugodi, Bengaluru, 560030, India
| | - Divakar Swathi
- Reproductive Physiology Laboratory, ICAR-National Institute of Animal Nutrition and Physiology, Adugodi, Bengaluru, 560030, India
| | | | - Maharajan Lavanya
- Reproductive Physiology Laboratory, ICAR-National Institute of Animal Nutrition and Physiology, Adugodi, Bengaluru, 560030, India
| | - Balaganur Krishnappa
- Reproductive Physiology Laboratory, ICAR-National Institute of Animal Nutrition and Physiology, Adugodi, Bengaluru, 560030, India
| | - Bala Krishnan Binsila
- Reproductive Physiology Laboratory, ICAR-National Institute of Animal Nutrition and Physiology, Adugodi, Bengaluru, 560030, India
| | - Ajit Singh Mahla
- Reproductive Physiology Laboratory, ICAR-National Institute of Animal Nutrition and Physiology, Adugodi, Bengaluru, 560030, India
- Physiology and Biochemistry Division, ICAR-Central Sheep and Wool Research Institute, Avikanagar, Rajasthan, 304501, India
| | - Arunachalam Arangasamy
- Reproductive Physiology Laboratory, ICAR-National Institute of Animal Nutrition and Physiology, Adugodi, Bengaluru, 560030, India
| | - Jerome Andonissamy
- Animal Physiology and Reproduction Division, ICAR-Central Institute for Research on Buffaloes, Hisar, Haryana, 125001, India
| | - Pradeep Kumar
- Animal Physiology and Reproduction Division, ICAR-Central Institute for Research on Buffaloes, Hisar, Haryana, 125001, India
| | - Rakesh Kumar Sharma
- Animal Physiology and Reproduction Division, ICAR-Central Institute for Research on Buffaloes, Hisar, Haryana, 125001, India
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TXNIP shuttling - a key molecular link in regulating inflammation and mitochondrial dysfunction in freeze tolerant wood frogs. Gene 2023; 857:147184. [PMID: 36627089 DOI: 10.1016/j.gene.2023.147184] [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: 08/19/2022] [Revised: 11/27/2022] [Accepted: 01/04/2023] [Indexed: 01/09/2023]
Abstract
Amphibians such as the wood frogs,Rana sylvatica, are a primary example of a freeze-tolerant vertebrate that undergoes whole body freezing. Multiple adaptations including sequestering 65-70% of total body water as extracellular/extra organ ice and producing massive amounts of glucose as a cryoprotectant support this. Interestingly, the high glucose levels induced in response to freezing can amplify oxidative stress's effects (reactive oxygen species, ROS) and induce inflammation and mitochondrial dysfunction. Since both freezing and dehydration stress (independent of freezing) can render wood frogs hyperglycemic, this study focussed on these two stresses to elucidate the role of a scaffold protein thioredoxin interacting protein (TXNIP), which localizes in multiple compartments inside the cell under hyperglycemic conditions and mediate diverse stress responses. The results from this study suggest a stress-specific response of TXNIP in inducing the cell-damaging pathway of inflammasome activation via its cytoplasmic localization during freezing. Interestingly, mitochondrial localization of TXNIP did not leads to increase in its binding to thioredoxin 2 (TRX-2) and activating the dysfunction of this organelle by releasing a mitochondrial protein cytochrome c (Cyt c) in cytoplasm under both freezing and dehydration stresses. Post-translational modifications of TXNIP hinted on changes in the regulating proteins involved in the inflammasome and mitochondrial dysfunction pathways, whereas sequential differences (cytosine residues) of amphibian TXNIP (compared to mammalian) assessed via 3D-modeling attributed to its weak binding to TRX-2. Overall, this study summarizes differential role of proteins activated under freeze and dehydration induced hyperglycemic response in freeze tolerant wood frogs.
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Varma A, Breedon SA, Storey KB. Sub-zero microRNA expression in the liver of the frozen hatchling painted turtle, Chrysemys picta marginata. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 857:159304. [PMID: 36220468 DOI: 10.1016/j.scitotenv.2022.159304] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 09/09/2022] [Accepted: 10/04/2022] [Indexed: 06/16/2023]
Abstract
The Midland painted turtle (Chrysemys picta marginata) are the highest known vertebrate species to experience and survive freezing and sub-zero temperatures. Painted turtles typically hatch from their eggs in the fall and remain underground in their nests until the following spring. While in these nests over the winter, hatchling turtles withstand over 50 % of their total extracellular body water freezing. Herein, the expression of microRNAs (miRNAs) was investigated in response to freezing stress in the hatchling painted turtle liver. A total of 204 known miRNAs were identified to be expressed in turtles, with 17 being upregulated and 13 being downregulated during freezing. KEGG and GO analyses suggested that upregulated miRNAs inhibit genes of cell cycle and Focal adhesion and Adherens junction, suggesting their role in downregulation of central metabolic processes necessary for metabolic rate depression (MRD) and maintaining the tissue homeostasis. Only 9 of the 36 enriched KEGG pathways were less targeted by miRNAs during freezing, including linoleic acid metabolism and multiple signaling pathways. These predicted upregulated pathways likely promote homeoviscous adaptation and expression of pro-survival/protective proteins for metabolic adaptations necessary for defence of liver during MRD. Overall, miRNA-seq analysis of liver revealed a strong role of miRNA in the adaptive strategy that not only enables hatchlings to substantially suppress their nonessential energy needs but also makes them flexible enough to restore and protect their basal organ functions by activating pro-survival processes.
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Affiliation(s)
- Anchal Varma
- Institute of Biochemistry & Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, Ontario K1S 5B6, Canada
| | - Sarah A Breedon
- Institute of Biochemistry & Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, Ontario K1S 5B6, Canada
| | - Kenneth B Storey
- Institute of Biochemistry & Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, Ontario K1S 5B6, Canada.
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Villalobos-Escobedo JM, Martínez-Hernández JP, Pelagio-Flores R, González-De la Rosa PM, Carreras-Villaseñor N, Abreu-Goodger C, Herrera-Estrella AH. Trichoderma atroviride hyphal regeneration and conidiation depend on cell-signaling processes regulated by a microRNA-like RNA. Microb Genom 2022; 8. [PMID: 36239595 DOI: 10.1099/mgen.0.000869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The ability to respond to injury is essential for the survival of an organism and involves analogous mechanisms in animals and plants. Such mechanisms integrate coordinated genetic and metabolic reprogramming events requiring regulation by small RNAs for adequate healing of the wounded area. We have previously reported that the response to injury of the filamentous fungus Trichoderma atroviride involves molecular mechanisms closely resembling those of plants and animals that lead to the formation of new hyphae (regeneration) and the development of asexual reproduction structures (conidiophores). However, the involvement of microRNAs in this process has not been investigated in fungi. In this work, we explore the participation of microRNA-like RNAs (milRNAs) molecules by sequencing messenger and small RNAs during the injury response of the WT strain and RNAi mutants. We found that Dcr2 appears to play an important role in hyphal regeneration and is required to produce the majority of sRNAs in T. atroviride. We also determined that the three main milRNAs produced via Dcr2 are induced during the damage-triggered developmental process. Importantly, elimination of a single milRNA phenocopied the main defects observed in the dcr2 mutant. Our results demonstrate the essential role of milRNAs in hyphal regeneration and asexual development by post-transcriptionally regulating cellular signalling processes involving phosphorylation events. These observations allow us to conclude that fungi, like plants and animals, in response to damage activate fine-tuning regulatory mechanisms.
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Affiliation(s)
- José M Villalobos-Escobedo
- Laboratorio Nacional de Genómica para la Biodiversidad-Unidad de Genómica Avanzada, Cinvestav. Km 9.6 Libramiento Norte Carretera Irapuato-León, 36824, Irapuato, Gto, Mexico
| | - J Pedro Martínez-Hernández
- Laboratorio Nacional de Genómica para la Biodiversidad-Unidad de Genómica Avanzada, Cinvestav. Km 9.6 Libramiento Norte Carretera Irapuato-León, 36824, Irapuato, Gto, Mexico
| | - Ramón Pelagio-Flores
- Laboratorio Nacional de Genómica para la Biodiversidad-Unidad de Genómica Avanzada, Cinvestav. Km 9.6 Libramiento Norte Carretera Irapuato-León, 36824, Irapuato, Gto, Mexico.,Present address: Facultad de Químico Farmacobiología, Universidad Michoacana de San Nicolás de Hidalgo, C.P. 58030 Morelia, Michoacán, Mexico
| | - Pablo M González-De la Rosa
- Laboratorio Nacional de Genómica para la Biodiversidad-Unidad de Genómica Avanzada, Cinvestav. Km 9.6 Libramiento Norte Carretera Irapuato-León, 36824, Irapuato, Gto, Mexico.,Present address: Tree of Life, Wellcome Sanger Institute, Cambridge CB10 1SA, UK
| | - Nohemí Carreras-Villaseñor
- Laboratorio Nacional de Genómica para la Biodiversidad-Unidad de Genómica Avanzada, Cinvestav. Km 9.6 Libramiento Norte Carretera Irapuato-León, 36824, Irapuato, Gto, Mexico.,Present address: Red de Estudios Moleculares Avanzados, Instituto de Ecología A.C. C.P. 91070 Xalapa, Veracruz, Mexico
| | - Cei Abreu-Goodger
- Laboratorio Nacional de Genómica para la Biodiversidad-Unidad de Genómica Avanzada, Cinvestav. Km 9.6 Libramiento Norte Carretera Irapuato-León, 36824, Irapuato, Gto, Mexico.,Present address: Institute of Ecology and Evolution, University of Edinburgh, Edinburgh, UK
| | - Alfredo H Herrera-Estrella
- Laboratorio Nacional de Genómica para la Biodiversidad-Unidad de Genómica Avanzada, Cinvestav. Km 9.6 Libramiento Norte Carretera Irapuato-León, 36824, Irapuato, Gto, Mexico
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11
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Tang L, Huang F, You W, Poetsch A, Nóbrega RH, Power DM, Zhu T, Liu K, Wang HY, Wang Q, Xu X, Feng B, Schartl M, Shao C. ceRNA crosstalk mediated by ncRNAs is a novel regulatory mechanism in fish sex determination and differentiation. Genome Res 2022; 32:1502-1515. [PMID: 35961776 PMCID: PMC9435745 DOI: 10.1101/gr.275962.121] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 06/29/2022] [Indexed: 11/25/2022]
Abstract
Competing endogenous RNAs (ceRNAs) are vital regulators of gene networks in mammals. The involvement of noncoding RNAs (ncRNAs) as ceRNA in genotypic sex determination (GSD) and environmental sex determination (ESD) in fish is unknown. The Chinese tongue sole, which has both GSD and ESD mechanisms, was used to map the dynamic expression pattern of ncRNAs and mRNA in gonads during sex determination and differentiation. Transcript expression patterns shift during the sex differentiation phase, and ceRNA modulation occurs through crosstalk of differentially expressed long ncRNAs (lncRNAs), circular RNAs (circRNAs), microRNAs (miRNAs), and sex-related genes in fish. Of note was the significant up-regulation of a circRNA from the sex-determining gene dmrt1 (circular RNA dmrt1) and a lncRNA, called AMSDT (which stands for associated with male sex differentiation of tongue sole) in Chinese tongue sole testis. These two ncRNAs both share the same miRNA response elements with gsdf, which has an up-regulated expression when they bind to miRNA cse-miR-196 and concurrent down-regulated female sex-related genes to facilitate testis differentiation. This is the first demonstration in fish that ceRNA crosstalk mediated by ncRNAs modulates sexual development and unveils a novel regulatory mechanism for sex determination and differentiation.
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Affiliation(s)
- Lili Tang
- Key Lab of Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong, 266071, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, Shandong, 266237, China
| | - Fei Huang
- Genosys, Incorporated, Shenzhen, Guangdong, 518000, China
| | - Wuxin You
- NCU-QMUL Joint Research Institute of Precision Medical Sciences, Queen Mary School, Nanchang University, Nanchang, 330036, China
| | - Ansgar Poetsch
- College of Marine Life Science, Ocean University of China, Qingdao, Shandong, 266003, China
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, Shandong, 266237, China
- Department of Plant Biochemistry, Ruhr University Bochum, Bochum, North Rhine-Westphalia, 44801, Germany
| | - Rafael Henrique Nóbrega
- Institute of Biosciences Department of Structural and Functional Biology Division Morphology Reproductive and Molecular Biology Group, São Paulo State University, Botucatu, São Paulo, 01049-010, Brazil
| | - Deborah Mary Power
- Comparative Endocrinology and Integrative Biology, Centre of Marine Sciences, Universidade do Algarve, Campus de Gambelas, Faro, Algarve, 8005-139, Portugal
| | - Tengfei Zhu
- Key Lab of Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong, 266071, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, Shandong, 266237, China
| | - Kaiqiang Liu
- Key Lab of Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong, 266071, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, Shandong, 266237, China
| | - Hong-Yan Wang
- Key Lab of Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong, 266071, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, Shandong, 266237, China
| | - Qian Wang
- Key Lab of Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong, 266071, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, Shandong, 266237, China
| | - Xiwen Xu
- Key Lab of Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong, 266071, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, Shandong, 266237, China
| | - Bo Feng
- Key Lab of Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong, 266071, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, Shandong, 266237, China
| | - Manfred Schartl
- Developmental Biochemistry, Biocenter, University of Würzburg, Würzburg, Bayern, 97074, Germany
- The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, San Marcos, Texas 78666, USA
| | - Changwei Shao
- Key Lab of Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong, 266071, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, Shandong, 266237, China
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12
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DNA Hypomethylation May Contribute to Metabolic Recovery of Frozen Wood Frog Brains. EPIGENOMES 2022; 6:epigenomes6030017. [PMID: 35893013 PMCID: PMC9326605 DOI: 10.3390/epigenomes6030017] [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: 05/19/2022] [Revised: 06/14/2022] [Accepted: 07/07/2022] [Indexed: 02/04/2023] Open
Abstract
Transcriptional suppression is characteristic of extreme stress responses, speculated to preserve energetic resources in the maintenance of hypometabolism. In recent years, epigenetic regulation has become heavily implicated in stress adaptation of many animals, including supporting freeze tolerance of the wood frog (Rana sylvatica). However, nervous tissues are frequently lacking in these multi-tissue analyses which warrants investigation. The present study examines the role of DNA methylation, a core epigenetic mechanism, in the response of wood frog brains to freezing. We use immunoblot analysis to track the relative expression of DNA methyltransferases (DNMT), methyl-CpG-binding domain (MBD) proteins and ten-eleven-translocation (TET) demethylases across the freeze-thaw cycle in R. sylvatica brain, including selected comparisons to freeze-associated sub-stresses (anoxia and dehydration). Global methyltransferase activities and 5-hmC content were also assessed. The data show coordinated evidence for DNA hypomethylation in wood frog brains during freeze-recovery through the combined roles of depressed DNMT3A/3L expression driving lowered DNMT activity and increased TET2/3 levels leading to elevated 5-hmC genomic content (p < 0.05). Raised levels of DNMT1 during high dehydration were also noteworthy. The above suggest that alleviation of transcriptionally repressive 5-mC DNA methylation is a necessary component of the wood frog freeze-thaw cycle, potentially facilitating the resumption of a normoxic transcriptional state as frogs thaw and resume normal metabolic activities.
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13
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Saiyed AN, Vasavada AR, Johar SRK. Recent trends in miRNA therapeutics and the application of plant miRNA for prevention and treatment of human diseases. FUTURE JOURNAL OF PHARMACEUTICAL SCIENCES 2022; 8:24. [PMID: 35382490 PMCID: PMC8972743 DOI: 10.1186/s43094-022-00413-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 03/21/2022] [Indexed: 02/17/2023] Open
Abstract
Background Researchers now have a new avenue to investigate when it comes to miRNA-based therapeutics. miRNAs have the potential to be valuable biomarkers for disease detection. Variations in miRNA levels may be able to predict changes in normal physiological processes. At the epigenetic level, miRNA has been identified as a promising candidate for distinguishing and treating various diseases and defects. Main body In recent pharmacology, plants miRNA-based drugs have demonstrated a potential role in drug therapeutics. The purpose of this review paper is to discuss miRNA-based therapeutics, the role of miRNA in pharmacoepigenetics modulations, plant miRNA inter-kingdom regulation, and the therapeutic value and application of plant miRNA for cross-kingdom approaches. Target prediction and complementarity with host genes, as well as cross-kingdom gene interactions with plant miRNAs, are also revealed by bioinformatics research. We also show how plant miRNA can be transmitted from one species to another by crossing kingdom boundaries in this review. Despite several unidentified barriers to plant miRNA cross-transfer, plant miRNA-based gene regulation in trans-kingdom gene regulation may soon be valued as a possible approach in plant-based drug therapeutics. Conclusion This review summarised the biochemical synthesis of miRNAs, pharmacoepigenetics, drug therapeutics and miRNA transkingdom transfer.
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Affiliation(s)
- Atiyabanu N. Saiyed
- Department of Cell and Molecular Biology, Iladevi Cataract and IOL Research Centre, Ahmedabad, Gujarat India
- Ph.D. scholar of Manipal Academy of Higher Education, Manipal, Karnataka India
| | - Abhay R. Vasavada
- Department of Cell and Molecular Biology, Iladevi Cataract and IOL Research Centre, Ahmedabad, Gujarat India
| | - S. R. Kaid Johar
- Department of Zoology, BMTC, Human Genetics, USSC, Gujarat University, Ahmedabad, Gujarat India
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14
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Zhang D, Pan J, Liu C, Meng F, Zhang Y, Cao J, Cao Y, Zhou H. Identification of sodium homeostasis genes in Camelus bactrianus by whole transcriptome sequencing. FEBS Open Bio 2022; 12:864-876. [PMID: 35147292 PMCID: PMC8972041 DOI: 10.1002/2211-5463.13380] [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: 12/15/2021] [Revised: 01/25/2022] [Accepted: 02/09/2022] [Indexed: 11/20/2022] Open
Abstract
Salt dietary intake is tightly coupled to human health, and excessive sodium can cause strokes and cardiovascular diseases. Research into the renal medulla of camels exhibiting high salt resistance may aid identification of the mechanisms governing resistance to high salinity. In this study, we used RNA sequencing (RNA‐seq) to show that in the renal medulla of camels under salt stress, 22 mRNAs, 2 long noncoding RNAs (lncRNAs), and 31 microRNAs (miRNAs) exhibited differential expression compared with the free salt‐intake diet group. Using fluorescence in situ hybridization and dual‐luciferase reporter assays, we demonstrated that the lncRNA LNC003834 can bind miRNA‐34a and thereby relieve suppression of the salt‐absorption‐inhibiting SLC14A1 mRNA from miRNA‐34a, suggesting that the above lncRNA‐miRNA‐mRNA act as competing endogenous RNAs (ceRNAs). We subsequently performed short hairpin RNA and small RNA interference and reactive oxygen species (ROS) detection assays to show that SLC6A1, PCBP2, and PEX5L can improve the antioxidation capacity of renal medulla cells of camel by decreasing ROS levels. Our data suggest that camels achieve sodium homeostasis through regulating the expression of salt‐reabsorption‐related genes in the renal medulla, and this involves ceRNAs (SLC14A1 mRNA, LNC003834, and miRNA‐34a) and antioxidant genes (SLC6A1, PCBP2, and PEX5L). These data may assist in the development of treatments for diseases induced by high salt diets.
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Affiliation(s)
- Dong Zhang
- Inner Mongolia Key Laboratory of Bio-manufacture, Inner Mongolia Agricultural University, Hohhot, China.,College of Life Sciences, Inner Mongolia Agricultural University, Hohhot, China
| | - Jing Pan
- Inner Mongolia Key Laboratory of Bio-manufacture, Inner Mongolia Agricultural University, Hohhot, China.,College of Life Sciences, Inner Mongolia Agricultural University, Hohhot, China.,Department of Reproductive Medicine, Inner Mongolia Maternal and Child Health Care Hospital, Hohhot, China
| | - Chunxia Liu
- Inner Mongolia Key Laboratory of Bio-manufacture, Inner Mongolia Agricultural University, Hohhot, China.,College of Life Sciences, Inner Mongolia Agricultural University, Hohhot, China
| | - Fanhua Meng
- Inner Mongolia Key Laboratory of Bio-manufacture, Inner Mongolia Agricultural University, Hohhot, China.,College of Life Sciences, Inner Mongolia Agricultural University, Hohhot, China
| | - Yanru Zhang
- Inner Mongolia Key Laboratory of Bio-manufacture, Inner Mongolia Agricultural University, Hohhot, China.,College of Life Sciences, Inner Mongolia Agricultural University, Hohhot, China
| | - Junwei Cao
- Inner Mongolia Key Laboratory of Bio-manufacture, Inner Mongolia Agricultural University, Hohhot, China.,College of Life Sciences, Inner Mongolia Agricultural University, Hohhot, China
| | - Yu Cao
- Inner Mongolia Key Laboratory of Bio-manufacture, Inner Mongolia Agricultural University, Hohhot, China.,College of Life Sciences, Inner Mongolia Agricultural University, Hohhot, China.,Institute of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Huanmin Zhou
- Inner Mongolia Key Laboratory of Bio-manufacture, Inner Mongolia Agricultural University, Hohhot, China.,College of Life Sciences, Inner Mongolia Agricultural University, Hohhot, China
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15
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Turning Data to Knowledge: Online Tools, Databases, and Resources in microRNA Research. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1385:133-160. [DOI: 10.1007/978-3-031-08356-3_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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16
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MicroRNA Cues from Nature: A Roadmap to Decipher and Combat Challenges in Human Health and Disease? Cells 2021; 10:cells10123374. [PMID: 34943882 PMCID: PMC8699674 DOI: 10.3390/cells10123374] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 11/22/2021] [Accepted: 11/27/2021] [Indexed: 12/15/2022] Open
Abstract
MicroRNAs are small non-coding RNA (18–24 nt long) that fine-tune gene expression at the post-transcriptional level. With the advent of “multi-omics” analysis and sequencing approaches, they have now been implicated in every facet of basic molecular networks, including metabolism, homeostasis, and cell survival to aid cellular machinery in adapting to changing environmental cues. Many animals must endure harsh environmental conditions in nature, including cold/freezing temperatures, oxygen limitation (anoxia/hypoxia), and food or water scarcity, often requiring them to revamp their metabolic organization, frequently on a seasonal or life stage basis. MicroRNAs are important regulatory molecules in such processes, just as they are now well-known to be involved in many human responses to stress or disease. The present review outlines the role of miRNAs in natural animal models of environmental stress and adaptation including torpor/hibernation, anoxia/hypoxia tolerance, and freeze tolerance. We also discuss putative medical applications of advances in miRNA biology including organ preservation for transplant, inflammation, ageing, metabolic disorders (e.g., obesity), mitochondrial dysfunction (mitoMirs) as well as specialized miRNA subgroups respective to low temperature (CryomiRs) and low oxygen (OxymiRs). The review also covers differential regulation of conserved and novel miRNAs involved at cell, tissue, and stress specific levels across multiple species and their roles in survival. Ultimately, the species-specific comparison and conserved miRNA responses seen in evolutionarily disparate animal species can help us to understand the complex miRNA network involved in regulating and reorganizing metabolism to achieve diverse outcomes, not just in nature, but in human health and disease.
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17
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Yu D, Peng Z, Wu H, Zhang X, Ji C, Peng X. Stress responses in expressions of microRNAs in mussel Mytilus galloprovincialis exposed to cadmium. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2021; 212:111927. [PMID: 33508712 DOI: 10.1016/j.ecoenv.2021.111927] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 01/06/2021] [Accepted: 01/10/2021] [Indexed: 06/12/2023]
Abstract
MicroRNAs (miRNAs) are known to have complicated functions in aquatic species, but little is known about the role of miRNAs in mollusk species under environmental stress. In this study, we performed small RNA sequencing to characterize the differentially expressed miRNAs in different tissues (whole tissues, digestive glands, gills, and gonads) of blue mussels (Mytilus galloprovincialis) exposed to cadmium (Cd). In summary, 107 known miRNAs and 32 novel miRNAs were significantly (p < 0.01) differentially expressed after Cd exposure. The peak size of miRNAs was 22 nucleotides. Target genes of these differentially expressions of miRNAs related to immune defense, apoptosis, lipid and xenobiotic metabolism showed significant changes under Cd stress. These findings provide the first characterization of miRNAs in mussel M. galloprovincialis and expressions of many target genes in response to Cd stress.
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Affiliation(s)
- Deliang Yu
- Center for Biomedical Optics and Photonics (CBOP) & College of Physics and Optoelectronic Engineering, Key Laboratory of Optoelectronic Devices and Systems, Shenzhen University, Shenzhen 518060, PR China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, PR China; Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, PR China
| | - Zheng Peng
- Center for Biomedical Optics and Photonics (CBOP) & College of Physics and Optoelectronic Engineering, Key Laboratory of Optoelectronic Devices and Systems, Shenzhen University, Shenzhen 518060, PR China
| | - Huifeng Wu
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, PR China; Shandong Key Laboratory of Coastal Environmental Processes, YICCAS, Yantai 264003, PR China; CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research (YIC), Chinese Academy of Sciences (CAS), YICCAS, Yantai 264003, PR China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, PR China.
| | - Xiaoying Zhang
- AstraZeneca-Shenzhen University Joint Institute of Nephrology, Department of Physiology, Shenzhen University Health Science Center, Shenzhen University, Shenzhen 518060, PR China
| | - Chenglong Ji
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, PR China; Shandong Key Laboratory of Coastal Environmental Processes, YICCAS, Yantai 264003, PR China; CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research (YIC), Chinese Academy of Sciences (CAS), YICCAS, Yantai 264003, PR China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, PR China
| | - Xiao Peng
- Center for Biomedical Optics and Photonics (CBOP) & College of Physics and Optoelectronic Engineering, Key Laboratory of Optoelectronic Devices and Systems, Shenzhen University, Shenzhen 518060, PR China.
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18
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Wijenayake S, Storey KB. Oxidative Damage? Not a Problem! The Characterization of Humanin-like Mitochondrial Peptide in Anoxia Tolerant Freshwater Turtles. Protein J 2021; 40:87-107. [PMID: 33387248 DOI: 10.1007/s10930-020-09944-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/25/2020] [Indexed: 11/30/2022]
Abstract
Mitochondria was long thought to be an "end function" organelle that regulated the metabolic flux and apoptosis in the cell. However, with the discovery of the mitochondrial peptide (MDP) humanin (HN/MTRNR2), the cytoprotective and pro-survival applications of MDPs have taken the forefront of therapeutic and diagnostic research. However, the regulation of humanin-like MDPs in natural model systems that can tolerate lethal environmental and cytotoxic insults remains to be investigated. Red-eared sliders are champion anaerobes that can withstand three continuous months of anoxia followed by rapid bouts of oxygen reperfusion without incurring cellular damage. Freshwater turtles employ extensive physiological and biochemical strategies to combat anoxia, with metabolic rate depression and a global enhancement of antioxidant and cytoprotective pathways being the two most important contributors. The main aim of this study was to uncover and characterize the humanin-homologue in freshwater turtles as well as investigate the differential regulation of humanin in response to short and long-term oxygen deprivation. In this study we have used de novo and homology-based protein modelling to elucidate the putative structure of humanin in red-eared sliders as well as an ELISA and western immunoblotting to confirm the protein abundance in the turtle brain and six peripheral tissues during control, 5 h, and 20 h anoxia (n = 4/group). We found that a humanin-homologue (TSE-humanin) is present in red-eared sliders and it may play a cytoprotective role against oxidative damage.
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Affiliation(s)
- Sanoji Wijenayake
- Department of Biology, Institute of Biochemistry, Carleton University, Ottawa, ON, Canada.,Department of Biological Sciences and Center for Environmental Epigenetics and Development, University of Toronto, Toronto, ON, Canada
| | - Kenneth B Storey
- Department of Biology, Institute of Biochemistry, Carleton University, Ottawa, ON, Canada. .,Department of Chemistry, Institute of Biochemistry, 1125 Colonel By Drive, Ottawa, ON, K1S 5B6, Canada.
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19
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Dynamic regulation of histone H3 lysine (K) acetylation and deacetylation during prolonged oxygen deprivation in a champion anaerobe. Mol Cell Biochem 2020; 474:229-241. [PMID: 32729004 DOI: 10.1007/s11010-020-03848-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 07/20/2020] [Indexed: 12/14/2022]
Abstract
Trachemys scripta elegans can survive up to three months of absolute anoxia at 3 °C and recover with minimal cellular damage. Red-eared sliders employ various physiological and biochemical adaptations to survive anoxia with metabolic rate depression (MRD) being the most prominent adaptation. MRD is mediated by epigenetic, transcriptional, post-transcriptional, and post-translational mechanisms aimed at shutting down cellular processes that are not needed for anoxia survival, while reprioritizing ATP towards cell processes that are vital for anaerobiosis. Histone acetylation/deacetylation are epigenetic modifications that maintain a proper balance between permissive chromatin and restricted chromatin, yet very little is known about protein regulation and enzymatic activity of the writers and erasers of acetylation during natural anoxia tolerance. As such, this study explored the interplay between transcriptional activators, histone acetyltransferases (HATs), and transcriptional repressors, sirtuins (SIRTs), along with three prominent acetyl-lysine (K) moieties of histone H3 in the liver of red-eared sliders. Western immunoblotting was used to measure acetylation levels of H3-K14, H3-K18, and H3-K56, as well as protein levels of histone H3-total, HATs, and nuclear SIRTs in the liver in response to 5 h and 20 h anoxia. Global and nuclear enzymatic activity of HATs and enzymatic activity of nuclear SIRTs were also measured. Overall, a strong suppression of HATs-mediated H3 acetylation and SIRT-mediated deacetylation was evident in the liver of red-eared sliders that could play an important role in ATP conservation as part of the overall reduction in metabolic rate.
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20
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Song X, Yang T, Yan X, Zheng F, Xu X, Zhou C. Comparison of microsatellite distribution patterns in twenty-nine beetle genomes. Gene 2020; 757:144919. [PMID: 32603771 DOI: 10.1016/j.gene.2020.144919] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Revised: 06/15/2020] [Accepted: 06/20/2020] [Indexed: 01/20/2023]
Abstract
Simple sequence repeats (SSRs) represent an important source of genetic variation that provides a basis for adaptation to different environments in organisms. In this study, we examined the distribution patterns of SSRs in twenty-nine beetle genomes and carried out Gene Ontology (GO) analysis of CDSs embedded with perfect SSRs (P-SSRs). The results demonstrated that imperfect SSRs (I-SSRs) represented the most abundant SSR category in beetle genomes and in different genomic regions (CDS, exon, and intron regions). The numbers of P-SSRs, I-SSRs, compound SSRs, and variable number tandem repeats were positively correlated with beetle genome size, whereas neither the frequency nor the density of the SSRs was correlated with genome size. Moreover, our results demonstrated that common genomic features of P-SSRs within the same suborder or family of Coleoptera were rare. Mono-, di-, tri-, or tetranucleotide SSRs were the most abundant P-SSR categories in beetle genomes. The preferred predominant repeat motif among the mononucleotide P-SSRs was (A)n, but the most frequent repeat motifs for other length classes varied differentially among these genomes. Furthermore, the P-SSR type with the highest GC content differed in the beetle genomes and in different genomic regions. CV (coefficient of variability) analysis demonstrated that the repeat copy numbers of P-SSRs presented relatively higher variation in introns than in CDSs and exons. The GO terms of CDSs containing P-SSRs for molecular functions were mainly enriched in "binding" and "transcription". Our findings will be useful for studying the functional roles of microsatellite heterogeneity in beetle adaptation.
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Affiliation(s)
- Xuhao Song
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong 637009, Sichuan Province, China.
| | - Tingbang Yang
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong 637009, Sichuan Province, China
| | - Xianghui Yan
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong 637009, Sichuan Province, China
| | - Fake Zheng
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong 637009, Sichuan Province, China
| | - Xiaoqin Xu
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong 637009, Sichuan Province, China
| | - Caiquan Zhou
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong 637009, Sichuan Province, China.
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Kim TW, Lee YS, Yun NH, Shin CH, Hong HK, Kim HH, Cho YB. MicroRNA-17-5p regulates EMT by targeting vimentin in colorectal cancer. Br J Cancer 2020; 123:1123-1130. [PMID: 32546833 PMCID: PMC7524803 DOI: 10.1038/s41416-020-0940-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 04/27/2020] [Accepted: 05/28/2020] [Indexed: 01/29/2023] Open
Abstract
Background Epithelial–mesenchymal transition (EMT) is the most common cause of death in colorectal cancer (CRC). In this study, we investigated the functional roles of miRNA-17-5p in EMT of CRC cells. Methods In order to determine if miRNA-17-5p regulated EMT, the precursors and inhibitors of miR-17-5p were transduced into four CRC cells. To evaluate the regulatory mechanism, we performed argonaute 2 (Ago2) immunoprecipitation (IP) and luciferase assay. In addition, we used an intra-splenic injection mouse model of BALB/c nude mice to investigate the metastatic potential of miRNA-17-5p in vivo. Results The miRNA-17-5p expression was lower in primary CRC tissues with metastasis than in primary CRC tissues without metastasis in our RNA sequencing data of patient tissue. Real-time quantitative PCR revealed that miRNA-17-5p was inversely correlated with that of vimentin in five CRC cell lines. Over-expression of miRNA-17-5p decreased vimentin expression and inhibited cell migration and invasion in both LoVo and HT29 cells. However, inhibition of miRNA-17-5p showed the opposite effect. Ago2 IP and luciferase assay revealed that miRNA-17-5p directly bound to the 3′UTR of VIM mRNA. Furthermore, miRNA-17-5p inhibited the metastasis of CRC into liver in vivo. Conclusions Our results demonstrated that miRNA-17-5p regulates vimentin expression, thereby regulating metastasis of CRC.
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Affiliation(s)
- Tae Won Kim
- Department of Health Sciences and Technology, SAIHST, Sungkyunkwan University, Seoul, Republic of Korea
| | - Yeo Song Lee
- Sungkyunkwan University School of Medicine, Seoul, Republic of Korea.,Institute for Future Medicine, Samsung Medical Center, Seoul, Republic of Korea
| | - Nak Hyeon Yun
- Department of Health Sciences and Technology, SAIHST, Sungkyunkwan University, Seoul, Republic of Korea
| | - Chang Hoon Shin
- Department of Health Sciences and Technology, SAIHST, Sungkyunkwan University, Seoul, Republic of Korea
| | - Hye Kyung Hong
- Institute for Future Medicine, Samsung Medical Center, Seoul, Republic of Korea
| | - Hyeon Ho Kim
- Department of Health Sciences and Technology, SAIHST, Sungkyunkwan University, Seoul, Republic of Korea. .,Institute for Future Medicine, Samsung Medical Center, Seoul, Republic of Korea.
| | - Yong Beom Cho
- Department of Health Sciences and Technology, SAIHST, Sungkyunkwan University, Seoul, Republic of Korea. .,Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea.
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22
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Brites D. Regulatory function of microRNAs in microglia. Glia 2020; 68:1631-1642. [PMID: 32463968 DOI: 10.1002/glia.23846] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 04/14/2020] [Accepted: 05/04/2020] [Indexed: 12/11/2022]
Abstract
Microglia are CNS-resident cells involved in immune surveillance and maintenance of intercellular homeostasis, while also contributing to neurologic pathologies. MicroRNAs (miRNAs) are a class of small (~22 nucleotides) single-stranded noncoding RNAs that participate in gene regulation at the post-transcriptional level. miRNAs typically bind to the untranslated region (3' UTR) of RNAs. It has been shown that miRNAs are important players in controlling inflammation and that their abnormal expression is linked to cancer and ageing, and to the onset and progression of neurodegenerative disease. Furthermore, miRNAs participate in intercellular trafficking. Thus, miRNAs are released from cells in a free form, bound to proteins or packaged within extracellular vesicles (EVs), exerting paracrine and long distance signaling. In this review, recent findings on the role of miRNAs as drivers of microglia phenotypic changes and their cotribution in neurological disease are addressed. MAIN POINTS: miRNAs have a key role in microglia function/dysfunction, polarization, and restoration. Microglia are both a source and recipient of extracellular vesicles (EVs) containing miRNAs. Extracellular miRNAs may be found as soluble (free and EV cargo) and protein complexes.
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Affiliation(s)
- Dora Brites
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal.,Department of Biochemistry and Human Biology, Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal
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A Unique Energy-Saving Strategy during Hibernation Revealed by Multi-Omics Analysis in the Chinese Alligator. iScience 2020; 23:101202. [PMID: 32534442 PMCID: PMC7298530 DOI: 10.1016/j.isci.2020.101202] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 04/16/2020] [Accepted: 05/22/2020] [Indexed: 12/11/2022] Open
Abstract
Many ectotherms hibernate in face of the harsh winter conditions to improve their survival rate. However, the molecular mechanism underlying this process remains unclear. Here, we explored the hibernation mechanism of Chinese alligator using integrative multi-omics analysis. We revealed that (1) the thyroid hormone biosynthesis, nutrition absorption and metabolism, muscle contraction, urinary excretion and immunity function pathways are overall downregulated during hibernation; (2) the fat catabolism is completely suppressed, contrasting with the upregulation of hepatic fatty-acid-transporter CPT1A, suggesting a unique energy-saving strategy that differs from that in hibernating mammals; (3) the hibernation-related genes are not only directly regulated by DNA methylation but also controlled by methylation-dependent transcription networks. In addition, we identified and compared tissue-specific, species-specific, and conserved season-biased miRNAs, demonstrating complex post-transcriptional regulation during hibernation. Our study revealed the genetic and epigenetic mechanisms underlying hibernation in the Chinese alligator and provided molecular insights into the evolution of hibernation regulation.
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Hadj-Moussa H, Storey KB. The OxymiR response to oxygen limitation: a comparative microRNA perspective. J Exp Biol 2020; 223:223/10/jeb204594. [DOI: 10.1242/jeb.204594] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
ABSTRACT
From squid at the bottom of the ocean to humans at the top of mountains, animals have adapted to diverse oxygen-limited environments. Surviving these challenging conditions requires global metabolic reorganization that is orchestrated, in part, by microRNAs that can rapidly and reversibly target all biological functions. Herein, we review the involvement of microRNAs in natural models of anoxia and hypoxia tolerance, with a focus on the involvement of oxygen-responsive microRNAs (OxymiRs) in coordinating the metabolic rate depression that allows animals to tolerate reduced oxygen levels. We begin by discussing animals that experience acute or chronic periods of oxygen deprivation at the ocean's oxygen minimum zone and go on to consider more elevated environments, up to mountain plateaus over 3500 m above sea level. We highlight the commonalities and differences between OxymiR responses of over 20 diverse animal species, including invertebrates and vertebrates. This is followed by a discussion of the OxymiR adaptations, and maladaptations, present in hypoxic high-altitude environments where animals, including humans, do not enter hypometabolic states in response to hypoxia. Comparing the OxymiR responses of evolutionarily disparate animals from diverse environments allows us to identify species-specific and convergent microRNA responses, such as miR-210 regulation. However, it also sheds light on the lack of a single unified response to oxygen limitation. Characterizing OxymiRs will help us to understand their protective roles and raises the question of whether they can be exploited to alleviate the pathogenesis of ischemic insults and boost recovery. This Review takes a comparative approach to addressing such possibilities.
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Affiliation(s)
- Hanane Hadj-Moussa
- Institute of Biochemistry and Department of Biology, Carleton University, Ottawa, ON, Canada, K1S 5B6
| | - Kenneth B. Storey
- Institute of Biochemistry and Department of Biology, Carleton University, Ottawa, ON, Canada, K1S 5B6
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25
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Storey KB, Storey JM. Mitochondria, metabolic control and microRNA: Advances in understanding amphibian freeze tolerance. Biofactors 2020; 46:220-228. [PMID: 31026112 DOI: 10.1002/biof.1511] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/03/2019] [Revised: 03/27/2019] [Accepted: 04/02/2019] [Indexed: 01/08/2023]
Abstract
Winter survival for many animal species depends freeze tolerance, a capacity to endure the conversion of as much as 65-70% of total body water into extracellular ice while reorganizing metabolism to provide cells with cryoprotection against insults that include prolonged ischemia and hyperosmotic stress. Natural freeze tolerance involves not just de novo preservation mechanisms such as synthesis of high levels of cryoprotectants or novel proteins that manage ice formation, but also requires attention to and co-ordination of many cellular processes. The present review examines recent studies of the freeze-tolerant wood frog (Rana sylvatica) that probed previously unexplored areas of metabolic adaptation for freezing survival, with a particular emphasis on mitochondria. Post-translational controls on enzyme function play a prominent role in resculpting metabolic responses of the wood frog to freezing including reversible phosphorylation control over fuel processing at the pyruvate dehydrogenase locus and modulation of antioxidant defense enzymes (Mn-SOD, catalase). Enzymes involved in mitochondrial nitrogen metabolism (glutamate dehydrogenase, carbamoyl phosphate synthetase) are also differentially regulated during freezing but by different post-translational modifications including ADP-ribosylation, lysine acetylation or glutarylation. The action of microRNAs in mediating post-translational controls on gene expression aid the suppression of energy-expensive (cell cycle) or destructive (apoptosis) processes in the frozen state while also providing storage of transcripts that will be immediately available for repair or reactivation of metabolic processes after thawing. The effects of low temperature in strengthening mRNA-microRNA interactions can also provide a passive mechanism of metabolic suppression in the frozen state.
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Affiliation(s)
- Kenneth B Storey
- Department of Biology, Carleton University, Ottawa, Ontario, Canada
| | - Janet M Storey
- Department of Biology, Carleton University, Ottawa, Ontario, Canada
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26
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Protein lysine methylation in the regulation of anoxia tolerance in the red eared slider turtle, Trachemys scripta elegans. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2020; 34:100660. [PMID: 32066095 DOI: 10.1016/j.cbd.2020.100660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 01/29/2020] [Accepted: 01/30/2020] [Indexed: 11/23/2022]
Abstract
The red eared slider turtle (Trachemys scripta elegans) is a champion vertebrate facultative anaerobe, capable of surviving for several months under conditions of exceptionally low oxygen availability. The ability of the turtle to facilitate this impressive tolerance to oxygen restriction is accomplished through a dramatic reduction in non-essential cellular processes. This is done in an attempt to conserve limited ATP stores and match demand in the anoxic state, with ATP supplied primarily through anaerobic glycolysis. Determining both the non-essential and the essential cellular processes that are deemed to be anoxia-responsive in the turtle has been an intense area of study over the past few decades. As a result, recent advancements have established the influence of global metabolic controls, such as post-transcriptional and post-translational regulation of gene expression in anoxia adaptation. A remaining question is whether or not epigenetic-level regulatory mechanisms are also utilized to allow for local control over gene expression. Recently, research has begun to document lysine methylation as an anoxia-responsive post-translational histone modification, as the activities of a number of methyl-lysine regulatory enzymes are extraordinarily sensitive to oxygen availability. As a result, oxygen-dependent methyl-lysine regulatory enzymes have been of particular interest to several recent studies of animal oxygen sensitivity, including the freshwater turtle. This review will introduce the concept of lysine methylation as an oxygen-sensitive protein modification as well as a prospectus on how this modification may contribute to anoxia tolerance in the turtle.
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Hawkins LJ, Storey KB. Advances and applications of environmental stress adaptation research. Comp Biochem Physiol A Mol Integr Physiol 2019; 240:110623. [PMID: 31778815 DOI: 10.1016/j.cbpa.2019.110623] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 11/19/2019] [Accepted: 11/21/2019] [Indexed: 02/06/2023]
Abstract
Evolution has produced animals that survive extreme fluctuations in environmental conditions including freezing temperatures, anoxia, desiccating conditions, and prolonged periods without food. For example, the wood frog survives whole-body freezing every winter, arresting all gross physiological functions, but recovers functions upon thawing in the spring. Likewise, many small mammals hibernate for months at a time with minimal metabolic activity, organ perfusion, and movement, yet do not suffer significant muscle atrophy upon arousal. These conditions and the biochemical adaptations employed to deal with them can be viewed as Nature's answer to problems that humans wish to answer, particularly in a biomedical context. This review focuses on recent advances in the field of animal environmental stress adaptation, starting with an emphasis on new areas of research such as epigenetics and microRNA. We then examine new and emerging technologies such as genome editing, novel sequencing applications, and single cell analysis and how these can push us closer to a deeper understanding of biochemical adaptation. Next, evaluate the potential contributions of new high-throughput technologies (e.g. next-generation sequencing, mass spectrometry proteomics) to better understanding the adaptations that support these extreme phenotypes. Concluding, we examine some of the human applications that can be gained from understanding the principles of biochemical adaptation including organ preservation and treatments for conditions such as ischemic stroke and muscle disuse atrophy.
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Affiliation(s)
- Liam J Hawkins
- Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, ON K1S 5B6, Canada
| | - Kenneth B Storey
- Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, ON K1S 5B6, Canada.
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28
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Biggar KK, Storey KB. Functional impact of microRNA regulation in models of extreme stress adaptation. J Mol Cell Biol 2019; 10:93-101. [PMID: 29206937 DOI: 10.1093/jmcb/mjx053] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2017] [Accepted: 11/30/2017] [Indexed: 01/12/2023] Open
Abstract
When confronted with severe environmental stress, some animals are able to undergo a substantial reorganization of their cellular environment that enables long-term survival. One molecular mechanism of adaptation that has received considerable attention in recent years has been the action of reversible transcriptome regulation by microRNA. The implementation of new computational and high-throughput experimental approaches has started to uncover the vital contributions of microRNA towards stress adaptation. Indeed, recent studies have suggested that microRNA may have a major regulatory influence over a number of cellular processes that are essential to prolonged environmental stress survival. To date, a number of studies have highlighted the role of microRNA in the regulation of a metabolically depressed state, documenting stress-responsive microRNA expression during mammalian hibernation, frog and insect freeze tolerance, and turtle and marine snail anoxia tolerance. These studies collectively indicate a conserved principle of microRNA stress response across phylogeny. As we are on the verge of dissecting the role of microRNA in environmental stress adaptation, this review summarizes recent research advances and the hallmark expression patterns that facilitate stress survival.
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Affiliation(s)
- Kyle K Biggar
- Institute of Biochemistry & Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada
| | - Kenneth B Storey
- Institute of Biochemistry & Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada
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29
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The expression of genes involved in excitatory and inhibitory neurotransmission in turtle (Trachemys scripta) brain during anoxic submergence at 21 °C and 5 °C reveals the importance of cold as a preparatory cue for anoxia survival. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2019; 30:55-70. [DOI: 10.1016/j.cbd.2018.12.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Accepted: 12/27/2018] [Indexed: 11/20/2022]
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30
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Stefanovic B, Spasojevic N, Jovanovic P, Dronjak S. Melatonin treatment affects changes in adrenal gene expression of catecholamine biosynthesizing enzymes and norepinephrine transporter in the rat model of chronic-stress-induced depression. Can J Physiol Pharmacol 2019; 97:685-690. [PMID: 30773040 DOI: 10.1139/cjpp-2018-0612] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
This study investigated the effects of melatonin treatment on adrenal catecholamine content, synthesis, uptake, and vesicular transport induced by the chronic unpredictable mild stress (CUMS) model of depression in rats. This entailed quantifying the norepinephrine, epinephrine, mRNA, and protein levels of tyrosine hydroxylase (TH), dopamine-β-hydroxylase (DBH), phenylethanolamine N-methyltransferase (PNMT), norepinephrine transporter (NET), and vesicular monoamine transporter 2 (VMAT2) in the adrenal medulla. CUMS caused a significant depletion of norepinephrine stores and protein levels of TH, DBH, and NET, whereas the gene expression of PNMT was increased. It was observed that melatonin treatment in the CUMS rats prevented the stress-induced decrease in norepinephrine content and the protein expression of TH, DBH, and NET in the adrenal medulla of chronically stressed rats. The present study demonstrates the stimulatory effect of melatonin on adrenomedullary synthesis, the uptake and content of catecholamine in the rat model of chronic stress-induced depression.
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Affiliation(s)
- Bojana Stefanovic
- a Department of Molecular Biology and Endocrinology, Institute of Nuclear Sciences "Vinca", University of Belgrade, Belgrade, Serbia
| | - Natasa Spasojevic
- a Department of Molecular Biology and Endocrinology, Institute of Nuclear Sciences "Vinca", University of Belgrade, Belgrade, Serbia
| | - Predrag Jovanovic
- a Department of Molecular Biology and Endocrinology, Institute of Nuclear Sciences "Vinca", University of Belgrade, Belgrade, Serbia.,b CEDARS-SINAI, Center for Neural Science and Medicine, 8700 Beverly Blvd., Los Angeles, CA 90048, USA
| | - Sladjana Dronjak
- a Department of Molecular Biology and Endocrinology, Institute of Nuclear Sciences "Vinca", University of Belgrade, Belgrade, Serbia
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Goodale BC, Hampton TH, Ford EN, Jackson CE, Shaw JR, Stanton BA, King BL. Profiling microRNA expression in Atlantic killifish (Fundulus heteroclitus) gill and responses to arsenic and hyperosmotic stress. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2019; 206:142-153. [PMID: 30476744 PMCID: PMC6298807 DOI: 10.1016/j.aquatox.2018.11.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Revised: 11/09/2018] [Accepted: 11/09/2018] [Indexed: 06/09/2023]
Abstract
The Atlantic killifish (Fundulus heteroclitus), native to estuarine areas of the Atlantic coast of the United States, has become a valuable ecotoxicological model as a result of its ability to acclimate to rapid environmental changes and adapt to polluted habitats. MicroRNAs (miRNAs) are highly conserved small RNAs that regulate gene expression and play critical roles in stress responses in a variety of organisms. Global miRNA expression in killifish and the potential roles miRNA have in environmental acclimation have yet to be characterized. Accordingly, we profiled miRNA expression in killifish gill for the first time and identified a small group of highly expressed, well-conserved miRNAs as well as 16 novel miRNAs not yet identified in other organisms. Killifish respond to large fluctuations in salinity with rapid changes in gene expression and protein trafficking to maintain osmotic balance, followed by a secondary phase of gene and protein expression changes that enable remodeling of the gills. Arsenic, a major environmental toxicant, was previously shown to inhibit gene expression responses in killifish gill, as well the ability of killifish to acclimate to a rapid increase in salinity. Thus, we examined the individual and combined effects of salinity and arsenic on miRNA expression in killifish gill. Using small RNA sequencing, we identified 270 miRNAs expressed in killifish, and found that miR-135b was differentially expressed in response to arsenic and at 24 h following transfer to salt water. Predicted targets of miR-135b are involved in ion transport, cell motility and migration, GTPase mediated signal transduction and organelle assembly. Consistent with previous studies of these two environmental stressors, we found a significant interaction (i.e., arsenic dependent salinity effect), whereby killifish exposed to arsenic exhibited an opposite response in miR-135b expression at 24 h post hyperosmotic challenge compared to controls. By examining mRNA expression of predicted miRNA targets during salinity acclimation and arsenic exposure, we found that miR-135b targets were significantly more likely to decrease during salinity acclimation than non-targets. Our identification of a significant interaction effect of arsenic and salinity on miR-135b expression supports the hypothesis that arsenic alters upstream regulators of stress response networks, which may adversely affect the killifish response to osmotic stress. The characterization of miRNAs in this ecotoxicological model will be a valuable resource for future studies investigating the role of miRNAs in response to environmental stress.
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Affiliation(s)
- Britton C Goodale
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, United States.
| | - Thomas H Hampton
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, United States
| | - Emily N Ford
- Department of Physical and Biological Sciences, Western New England University, Springfield, MA 01119, United States
| | - Craig E Jackson
- School of Public and Environmental Affairs, Indiana University, Bloomington, IN 47405, United States
| | - Joseph R Shaw
- School of Public and Environmental Affairs, Indiana University, Bloomington, IN 47405, United States
| | - Bruce A Stanton
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, United States
| | - Benjamin L King
- Department of Molecular and Biomedical Sciences, University of Maine, Orono, ME 04469, United States
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Fernandez-Marrero Y, Bachmann D, Lauber E, Kaufmann T. Negative Regulation of BOK Expression by Recruitment of TRIM28 to Regulatory Elements in Its 3' Untranslated Region. iScience 2018; 9:461-474. [PMID: 30471638 PMCID: PMC6260365 DOI: 10.1016/j.isci.2018.11.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Revised: 10/23/2018] [Accepted: 11/01/2018] [Indexed: 02/07/2023] Open
Abstract
BCL-2-related ovarian killer (BOK) is a pro-apoptotic BAX-like member of the BCL-2 family with suggested tumor suppressor activity. The molecular mechanisms regulating BOK expression are poorly understood and fail to explain a frequent lack of concordance between protein and transcript levels. Here, we describe a potent post-transcriptional mechanism that negatively regulates BOK expression mediated by conserved (AU/U)-rich elements within its 3’ UTR. Using proteomics approaches we identified TRIM28 as a key component associating with U-rich elements in the human BOK 3’ UTR, resulting in a dramatic reduction of BOK expression. TRIM28 is overexpressed in several cancers, correlating with poor patient outcome, whereas the BOK locus is frequently deleted or its expression downregulated in human cancers. Data mining indicated that, for certain cancers, high TRIM28 and low BOK expression are significantly correlated in the stratum of patients with the worst survival, suggesting that this mechanism might be of potential therapeutic value. BOK mRNA is destabilized by AU-(mouse) or U-rich (human) elements within its 3’ UTR Mutation of these ARE/URE sequences results in increased BOK RNA and protein levels TRIM28 represses BOK expression by associating with the UREs of human BOK mRNA Inverse correlation of TRIM28 and BOK levels predicts survival in selected cancers
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Affiliation(s)
- Yuniel Fernandez-Marrero
- Institute of Pharmacology, Faculty of Medicine, University of Bern, Inselspital, INO-F, 3010 Bern, Switzerland
| | - Daniel Bachmann
- Institute of Pharmacology, Faculty of Medicine, University of Bern, Inselspital, INO-F, 3010 Bern, Switzerland
| | - Emanuel Lauber
- Institute of Pharmacology, Faculty of Medicine, University of Bern, Inselspital, INO-F, 3010 Bern, Switzerland
| | - Thomas Kaufmann
- Institute of Pharmacology, Faculty of Medicine, University of Bern, Inselspital, INO-F, 3010 Bern, Switzerland.
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Costanzo JP. Overwintering adaptations and extreme freeze tolerance in a subarctic population of the wood frog, Rana sylvatica. J Comp Physiol B 2018; 189:1-15. [PMID: 30390099 DOI: 10.1007/s00360-018-1189-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 10/21/2018] [Accepted: 10/29/2018] [Indexed: 12/12/2022]
Abstract
The terrestrially hibernating wood frog (Rana sylvatica) is well-known for its iconic freeze tolerance, an overwintering adaptation that has received considerable investigation over the past 35 years. Virtually, all of this research has concerned frogs indigenous to the temperate regions of its broad range within North America. However, recent investigations have shown that frogs of subarctic populations are extremely cold hardy, being capable of surviving freezing for longer periods and at much lower temperatures as compared to conspecifics from temperate regions. Their exceptional freeze tolerance is partly supported by an enhanced cryoprotectant system that uses very high levels of urea and glucose to limit ice formation, regulate metabolism, and protect macromolecules and cellular structures from freezing/thawing stresses. In the weeks before they begin hibernating, northern frogs undertake radical physiological transitions, such as depletion of fat stores and catabolism of muscle protein, that prime the cryoprotectant system by accruing urea and stockpiling glycogen from which glucose is mobilized during freezing. Concentrations of cryoprotectants ultimately achieved in Alaskan frogs when freezing occurs vary among tissues but generally are higher than those of frogs inhabiting milder climates. This review summarizes the molecular, biochemical, and physiological adaptations permitting this northern phenotype to survive the long and harsh winters of the region.
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Affiliation(s)
- Jon P Costanzo
- Department of Biology, Miami University, 45056, Oxford, OH, USA.
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Biggar K, Luu B, Wu C, Pifferi F, Perret M, Storey K. Identification of novel and conserved microRNA and their expression in the gray mouse lemur, Microcebus murinus, a primate capable of daily torpor. Gene 2018; 677:332-339. [DOI: 10.1016/j.gene.2018.08.014] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Revised: 07/10/2018] [Accepted: 08/04/2018] [Indexed: 12/13/2022]
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35
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Zheng J, Cao J, Mao Y, Su Y, Wang J. Identification of microRNAs with heat stress responsive and immune properties in Marsupenaeus japonicus based on next-generation sequencing and bioinformatics analysis: Essential regulators in the heat stress-host interactions. FISH & SHELLFISH IMMUNOLOGY 2018; 81:390-398. [PMID: 29778844 DOI: 10.1016/j.fsi.2018.05.030] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2018] [Revised: 05/09/2018] [Accepted: 05/16/2018] [Indexed: 06/08/2023]
Abstract
Summer mortality syndrome is one of the most serious issue for Marsupenaeus japonicus aquaculture in China. Since it causes massive economic loss and threatens sustainability of M. japonicus aquaculture industry, thus, there is an urgent desire to reveal the heat stress-host interactions mechanisms that lead to mass mortalities of M. japonicus in hot summer months. MicroRNAs (miRNAs) are small noncoding RNAs that involved in regulation of diverse biological processes, including stress and immune response, and might serve as potential regulators in the heat stress-host interactions. In the present study, miRNAs with heat stress responsive and immune properties were identified and characterized in M. japonicus by small RNA sequencing and bioinformatics analysis. In total, 79 host miRNAs were identified, among which 15 miRNAs were differentially expressed in response to heat stress. Target genes prediction and function annotation revealed that a variety of host cellular processes, such as signal transduction, transcription, anti-stress response, ribosomal biogenesis, lipid metabolism, cytoskeleton, etc, were potentially subject to miRNA-mediated regulation in response to heat stress. Furthermore, a total of 30 host miRNAs that potentially involved in interaction with white spot syndrome virus (WSSV) were obtained via predicting and analyzing the target genes from WSSV. The results showed that a batch of WSSV genes that code for structural proteins and enzymes that are essential for WSSV infection and proliferation, such as envelope proteins, capsid proteins, immediate-early proteins, collagen-like protein, protein kinase, thymidylate synthetase, TATA-box bind protein, etc, were predicted to be targeted by host miRNAs. Several of the host miRNAs with predicted antiviral capacity were down-regulated under heat stress, indicating a repression of host miRNA-mediated antiviral immune response. This study highlighted the essential roles of host miRNAs in the heat stress-host interactions and provided valuable information for further investigation on the mechanism of miRNA-mediated heat stress and immune response of shrimp.
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Affiliation(s)
- Jinbin Zheng
- College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Jiawen Cao
- College of the Environment and Ecology, Xiamen University, Xiamen 361102, China
| | - Yong Mao
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361102, China; College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China.
| | - Yongquan Su
- College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Jun Wang
- College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
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36
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Li C, Xu D. Understanding microRNAs regulation in heat shock response in the sea cucumber Apostichopus japonicus. FISH & SHELLFISH IMMUNOLOGY 2018; 81:214-220. [PMID: 30016683 DOI: 10.1016/j.fsi.2018.07.034] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 07/11/2018] [Accepted: 07/13/2018] [Indexed: 06/08/2023]
Abstract
The sea cucumber Apostichopus japonicus is a valuable species in China. The extreme high temperature in the summer often results in high mortality. MicroRNAs (miRNAs) play important post-transcriptional regulatory roles in gene expression and can influence heat shock response (HSR) greatly. In this study, we determined the expression profiles of miRNAs under heat stress (HS) in A. japonicus by using high-throughput sequencing technique. Among the differential expression miRNAs, we highlighted 41 differentially expressed miRNAs, many of which were involved in immunity process and disease regulation. Gene ontology and pathway analyses of putative target genes were also carried out. Cell-substrate adherens junction and cell-substrate junction were significantly enriched in GO analysis. Moreover, we made a correlation analysis between remarkable miRNAs and the differentially expressed genes (DEGs) in sea cucumbers under HS. We identified 17 key miRNA-target pairs potentially regulated HSR of sea cucumbers. These results will provide new insights about miRNAs regulation and molecular adaptive mechanisms in sea cucumbers under HS.
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Affiliation(s)
- Chao Li
- College of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Dongxue Xu
- College of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China.
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37
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Moreira DC, Oliveira MF, Liz-Guimarães L, Diniz-Rojas N, Campos ÉG, Hermes-Lima M. Corrigendum: Current Trends and Research Challenges Regarding "Preparation for Oxidative Stress". Front Physiol 2018; 9:950. [PMID: 30042698 PMCID: PMC6053941 DOI: 10.3389/fphys.2018.00950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 06/28/2018] [Indexed: 11/25/2022] Open
Affiliation(s)
- Daniel C Moreira
- Departamento de Biologia Celular, Universidade de Brasília, Brasilia, Brazil.,Área de Morfologia, Faculdade de Medicina, Universidade de Brasília, Brasilia, Brazil
| | - Marcus F Oliveira
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Lara Liz-Guimarães
- Departamento de Biologia Celular, Universidade de Brasília, Brasilia, Brazil
| | - Nilda Diniz-Rojas
- Departamento de Genética e Morfologia, Universidade de Brasília, Brasilia, Brazil
| | - Élida G Campos
- Departamento de Biologia Celular, Universidade de Brasília, Brasilia, Brazil
| | - Marcelo Hermes-Lima
- Departamento de Biologia Celular, Universidade de Brasília, Brasilia, Brazil
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38
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Zeng X, Xu Y, Jiang J, Zhang F, Ma L, Wu D, Wang Y, Sun W. Identification of cold stress responsive microRNAs in two winter turnip rape (Brassica rapa L.) by high throughput sequencing. BMC PLANT BIOLOGY 2018; 18:52. [PMID: 29587648 PMCID: PMC5870505 DOI: 10.1186/s12870-018-1242-4] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Accepted: 01/17/2018] [Indexed: 05/21/2023]
Abstract
BACKGROUND Low temperature is a major abiotic stress affecting the production of rapeseed in China by impeding plant growth and development. A comprehensive knowledge of small-RNA expression pattern in Brassica rapa under cold stress could improve our knowledge of microRNA-mediated stress responses. RESULTS A total of 353 cold-responsive miRNAs, 84 putative novel and 269 conserved miRNAs, were identified from the leaves and roots of two winter turnip rape varieties 'Longyou 7' (cold-tolerant) and 'Tianyou 4' (cold-sensitive), which were stressed under - 4 °C for 8 h. Eight conserved (miR166h-3p-1, miR398b-3p, miR398b-3p-1, miR408d, miR156a-5p, miR396h, miR845a-1, miR166u) and two novel miRNAs (Bra-novel-miR3153-5p and Bra-novel-miR3172-5p) were differentially expressed in leaves of 'Longyou 7' under cold stress. Bra-novel-miR3936-5p was up-regulated in roots of 'Longyou 7' under cold stress. Four and five conserved miRNAs were differentially expressed in leaves and roots of 'Tianyou 4' after cold stress. Besides, we found two conserved miRNAs (miR319e and miR166m-2) were down-regulated in non-stressed roots of 'Longyou 7' compared with 'Tianyou 4'. After cold stress, we found two and eight miRNAs were differentially expressed in leaves and roots of 'Longyou 7' compared with 'Tianyou 4'. The differentially expressed miRNAs between two cultivars under cold stress include novel miRNAs and the members of the miR166 and miR319 families. A total of 211 target genes for 15 known miRNAs and two novel miRNAs were predicted by bioinformatic analysis, mainly involved in metabolic processes and stress responses. Five differentially expressed miRNAs and predicted target genes were confirmed by quantitative reverse transcription PCR, and the expressional changes of target genes were negatively correlated to differentially expressed miRNAs. Our data indicated that some candidate miRNAs (e.g., miR166e, miR319, and Bra-novel-miR3936-5p) may play important roles in plant response to cold stress. CONCLUSIONS Our work indicates that miRNA and putative target genes mediated metabolic processes and stress responses are significant to cold tolerance in B. rapa.
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Affiliation(s)
- Xiucun Zeng
- College of Agronomy and Biotechnology, Hexi University, Zhangye, 734000 China
| | - Yaozhao Xu
- College of Agronomy and Biotechnology, Hexi University, Zhangye, 734000 China
- College of Agronomy, Gansu Agricultural University, Lanzhou, 730070 China
| | - Jinjin Jiang
- Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou, 225009 China
| | - Fenqin Zhang
- College of Agronomy and Biotechnology, Hexi University, Zhangye, 734000 China
| | - Li Ma
- College of Agronomy and Biotechnology, Hexi University, Zhangye, 734000 China
| | - Dewei Wu
- Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou, 225009 China
| | - Youping Wang
- Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou, 225009 China
| | - Wancang Sun
- College of Agronomy, Gansu Agricultural University, Lanzhou, 730070 China
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Guo H, Lu ZC, Zhu XW, Zhu CH, Wang CG, Shen YC, Wang W. Differential expression of microRNAs in hemocytes from white shrimp Litopenaeus vannamei under copper stress. FISH & SHELLFISH IMMUNOLOGY 2018; 74:152-161. [PMID: 29305331 DOI: 10.1016/j.fsi.2017.12.053] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Revised: 12/19/2017] [Accepted: 12/28/2017] [Indexed: 06/07/2023]
Abstract
MicroRNAs (miRNAs) are small noncoding RNAs that regulate diverse cellular processes, including organismal stress response, through posttranscriptional repression of gene transcripts. They are known to have antiviral functions in aquatic crustacean species, but little is known about the role of miRNAs against environmental stress caused by Cu, a common chemical contaminant in aquatic environment. We performed small RNA sequencing to characterize the differentially expressed microRNAs in Cu exposed shrimp. A total of 4524 known miRNAs and 73 novel miRNAs were significantly (P < .05) differentially expressed after Cu exposure. The peak size of miRNAs was 22 nt. Among them, 218 miRNAs were conserved across 115 species. The validation of 12 miRNAs by stem-loop quantitative RT-PCR were found to be coherent with the expression profile of deep sequencing data as evaluated with Pearson's correlation coefficient (r = 0.707). Target genes of these differentially expressed miRNAs related to immune defense, apoptosis, and xenobiotics metabolism also showed significant changes in expression under Cu stress. The present study provides the first characterization of L. vannamei miRNAs and some target genes expression in response to Cu stress, and the findings support the hypothesis that certain miRNAs along with their target genes might be essential in the intricate adaptive response regulation networks. Our current study will provide valuable information to take an insight into molecular mechanism of L. vannamei against environmental stress.
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Affiliation(s)
- Hui Guo
- Key Laboratory of Marine Ecology and Aquaculture Environment of Zhanjiang, College of Fisheries, Guangdong Ocean University, Zhanjiang 524025, People's Republic of China
| | - Zhi-Cheng Lu
- Key Laboratory of Marine Ecology and Aquaculture Environment of Zhanjiang, College of Fisheries, Guangdong Ocean University, Zhanjiang 524025, People's Republic of China
| | - Xiao-Wen Zhu
- Key Laboratory of Marine Ecology and Aquaculture Environment of Zhanjiang, College of Fisheries, Guangdong Ocean University, Zhanjiang 524025, People's Republic of China
| | - Chun-Hua Zhu
- Key Laboratory of Marine Ecology and Aquaculture Environment of Zhanjiang, College of Fisheries, Guangdong Ocean University, Zhanjiang 524025, People's Republic of China
| | - Cheng-Gui Wang
- Key Laboratory of Marine Ecology and Aquaculture Environment of Zhanjiang, College of Fisheries, Guangdong Ocean University, Zhanjiang 524025, People's Republic of China
| | - Yu-Chun Shen
- Key Laboratory of Marine Ecology and Aquaculture Environment of Zhanjiang, College of Fisheries, Guangdong Ocean University, Zhanjiang 524025, People's Republic of China.
| | - Wei Wang
- College of Fisheries, Guangdong Ocean University, Zhanjiang 524025, People's Republic of China.
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40
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Dynamic regulation of six histone H3 lysine (K) methyltransferases in response to prolonged anoxia exposure in a freshwater turtle. Gene 2018; 649:50-57. [PMID: 29382574 DOI: 10.1016/j.gene.2018.01.086] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Revised: 01/03/2018] [Accepted: 01/26/2018] [Indexed: 12/26/2022]
Abstract
The importance of histone lysine methylation is well established in health, disease, early development, aging, and cancer. However, the potential role of histone H3 methylation in regulating gene expression in response to extended periods of oxygen deprivation (anoxia) in a natural, anoxia-tolerant model system is underexplored. Red-eared sliders (Trachemys scripta elegans) can tolerate and survive three months of absolute anoxia and recover without incurring detrimental cellular damage, mainly by reducing the overall metabolic rate by 90% when compared to normoxia. Stringent regulation of gene expression is a vital aspect of metabolic rate depression in red-eared sliders, and as such we examined the anoxia-responsive regulation of histone lysine methylation in the liver during 5 h and 20 h anoxia exposure. Interestingly, this is the first study to illustrate the existence of histone lysine methyltransferases (HKMTs) and corresponding histone H3 lysine methylation levels in the liver of anoxia-tolerant red-eared sliders. In brief, H3K4me1, a histone mark associated with active transcription, and two corresponding histone lysine methyltransferases that modify H3K4me1 site, significantly increased in response to anoxia. On the contrary, H3K27me1, another transcriptionally active histone mark, significantly decreased during 20 h anoxia, and a transcriptionally repressive histone mark, H3K9me3, and the corresponding KMTs, similarly increased during 20 h anoxia. Overall, the results suggest a dynamic regulation of histone H3 lysine methylation in the liver of red-eared sliders that could theoretically aid in the selective upregulation of genes that are necessary for anoxia survival, while globally suppressing others to conserve energy.
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41
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Batz ZA, Goff AC, Armbruster PA. MicroRNAs are differentially abundant during Aedes albopictus diapause maintenance but not diapause induction. INSECT MOLECULAR BIOLOGY 2017; 26:721-733. [PMID: 28776797 PMCID: PMC5673581 DOI: 10.1111/imb.12332] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Diapause is a programmed dormancy that allows organisms to tolerate predictable periods of unfavourable conditions by temporarily halting development and reducing metabolism. Diapause is widespread amongst insects and is crucial for allowing organisms to coordinate their growth and reproduction with favourable environmental conditions. Although the adaptive significance of diapause is well understood, the molecular mechanisms underpinning diapause remain unresolved. We performed high-throughput sequencing to investigate the role of microRNAs (miRNAs) in the diapause of the Asian tiger mosquito, Aedes albopictus. We first investigated miRNAs in diapause induction by characterizing maternally provisioned miRNAs in mature oocytes of Ae. albopictus under diapause-inducing and diapause-averting conditions. Second, we investigated miRNAs in diapause maintenance by characterizing miRNAs in diapause and nondiapause pharate larvae. We identified 162 miRNAs, 152 previously known and 10 putatively novel. We identified no differentially abundant miRNAs in mature oocytes and seven differentially abundant miRNAs in pharate larvae. The predicted targets of differentially abundant miRNAs include genes affecting several processes related to diapause maintenance including ecdysone regulation, immune response, lipid metabolism and regulation of development. Our results suggest that Ae. albopictus does not maternally provision a unique set of miRNAs during diapause induction but miRNAs are a component of diapause maintenance in this species.
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42
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Moreira DC, Oliveira MF, Liz-Guimarães L, Diniz-Rojas N, Campos ÉG, Hermes-Lima M. Current Trends and Research Challenges Regarding "Preparation for Oxidative Stress". Front Physiol 2017; 8:702. [PMID: 28993737 PMCID: PMC5622305 DOI: 10.3389/fphys.2017.00702] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 08/31/2017] [Indexed: 12/26/2022] Open
Abstract
Survival under stress, such as exposure to hypoxia, anoxia, freezing, dehydration, air exposure of water breathing organisms, and estivation, is commonly associated to enhanced endogenous antioxidants, a phenomenon coined "preparation for oxidative stress" (POS). The regulation of free radical metabolism seems to be crucial under these selective pressures, since this response is widespread among animals. A hypothesis of how POS works at the molecular level was recently proposed and relies on two main processes: increased reactive species production under hypoxia, and activation of redox-sensitive transcription factors and signaling pathways, increasing the expression of antioxidants. The present paper brings together the current knowledge on POS and considers its future directions. Data indicate the presence of POS in 83 animal species (71.6% among investigated species), distributed in eight animal phyla. Three main research challenges on POS are presented: (i) to identify the molecular mechanism(s) that mediate/induce POS, (ii) to identify the evolutionary origins of POS in animals, and (iii) to determine the presence of POS in natural environments. We firstly discuss the need of evidence for increased RS production in hypoxic conditions that underlie the POS response. Secondly, we discuss the phylogenetic origins of POS back 700 million years, by identifying POS-positive responses in cnidarians. Finally, we present the first reports of the POS adaptation strategy in the wild. The investigation of these research trends and challenges may prove useful to understand the evolution of animal redox adaptations and how they adapt to increasing stressful environments on Earth.
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Affiliation(s)
- Daniel C. Moreira
- Departamento de Biologia Celular, Universidade de BrasíliaBrasilia, Brazil
- Área de Morfologia, Faculdade de Medicina, Universidade de BrasíliaBrasilia, Brazil
| | - Marcus F. Oliveira
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de JaneiroRio de Janeiro, Brazil
| | - Lara Liz-Guimarães
- Departamento de Biologia Celular, Universidade de BrasíliaBrasilia, Brazil
| | - Nilda Diniz-Rojas
- Departamento de Genética e Morfologia, Universidade de BrasíliaBrasilia, Brazil
| | - Élida G. Campos
- Departamento de Biologia Celular, Universidade de BrasíliaBrasilia, Brazil
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43
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Exploration of low temperature microRNA function in an anoxia tolerant vertebrate ectotherm, the red eared slider turtle ( Trachemys scripta elegans ). J Therm Biol 2017; 68:139-146. [DOI: 10.1016/j.jtherbio.2016.09.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Revised: 09/07/2016] [Accepted: 09/12/2016] [Indexed: 12/14/2022]
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44
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Hu J, Barrett RDH. Epigenetics in natural animal populations. J Evol Biol 2017; 30:1612-1632. [PMID: 28597938 DOI: 10.1111/jeb.13130] [Citation(s) in RCA: 84] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Revised: 06/01/2017] [Accepted: 06/03/2017] [Indexed: 12/22/2022]
Abstract
Phenotypic plasticity is an important mechanism for populations to buffer themselves from environmental change. While it has long been appreciated that natural populations possess genetic variation in the extent of plasticity, a surge of recent evidence suggests that epigenetic variation could also play an important role in shaping phenotypic responses. Compared with genetic variation, epigenetic variation is more likely to have higher spontaneous rates of mutation and a more sensitive reaction to environmental inputs. In our review, we first provide an overview of recent studies on epigenetically encoded thermal plasticity in animals to illustrate environmentally-mediated epigenetic effects within and across generations. Second, we discuss the role of epigenetic effects during adaptation by exploring population epigenetics in natural animal populations. Finally, we evaluate the evolutionary potential of epigenetic variation depending on its autonomy from genetic variation and its transgenerational stability. Although many of the causal links between epigenetic variation and phenotypic plasticity remain elusive, new data has explored the role of epigenetic variation in facilitating evolution in natural populations. This recent progress in ecological epigenetics will be helpful for generating predictive models of the capacity of organisms to adapt to changing climates.
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Affiliation(s)
- J Hu
- Redpath Museum and Department of Biology, McGill University, Montreal, QC, Canada
| | - R D H Barrett
- Redpath Museum and Department of Biology, McGill University, Montreal, QC, Canada
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45
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Arfat Y, Chang H, Gao Y. Stress-responsive microRNAs are involved in re-programming of metabolic functions in hibernators. J Cell Physiol 2017; 233:2695-2704. [PMID: 28574587 DOI: 10.1002/jcp.26034] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Accepted: 06/01/2017] [Indexed: 12/21/2022]
Abstract
Mammalian hibernation includes re-programing of metabolic capacities, partially, encouraged by microRNAs (miRNAs). Albeit much is known about the functions of miRNAs, we need learning on low temperature miRNAs target determination. As hibernators can withstand low body temperatures (TB) for a long time without anguish tissue damage, understanding the means and mechanisms that empower them to do as such are of restorative intrigue. Nonetheless, these mechanisms by which miRNAs and the hibernators react to stressful conditions are not much clear. It is evident from recent data that the gene expression and the translation of mRNA to protein are controlled by miRNAs. The miRNAs also influence regulation of major cellular processes. As the significance of miRNAs in stress conditions adaptation are getting clearer, this audit article abridges the key alterations in miRNA expression and the mechanism that facilitates stress survival.
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Affiliation(s)
- Yasir Arfat
- Shaanxi Key Laboratory for Animal Conservation, Northwest University, Xi'an, China.,Key Laboratory of Resource Biology and Biotechnology in Western China (College of Life Sciences, Northwest University), Ministry of Education, Xi'an, China
| | - Hui Chang
- Shaanxi Key Laboratory for Animal Conservation, Northwest University, Xi'an, China.,Key Laboratory of Resource Biology and Biotechnology in Western China (College of Life Sciences, Northwest University), Ministry of Education, Xi'an, China
| | - Yunfang Gao
- Shaanxi Key Laboratory for Animal Conservation, Northwest University, Xi'an, China.,Key Laboratory of Resource Biology and Biotechnology in Western China (College of Life Sciences, Northwest University), Ministry of Education, Xi'an, China
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46
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Hypoxia and iron requirements are the main drivers in transcriptional adaptation of Kluyveromyces lactis during wine aerobic fermentation. Int J Food Microbiol 2017; 246:40-49. [DOI: 10.1016/j.ijfoodmicro.2017.01.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Revised: 01/17/2017] [Accepted: 01/24/2017] [Indexed: 01/06/2023]
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47
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Abstract
Freeze tolerance is an amazing winter survival strategy used by various amphibians and reptiles living in seasonally cold environments. These animals may spend weeks or months with up to ∼65% of their total body water frozen as extracellular ice and no physiological vital signs, and yet after thawing they return to normal life within a few hours. Two main principles of animal freeze tolerance have received much attention: the production of high concentrations of organic osmolytes (glucose, glycerol, urea among amphibians) that protect the intracellular environment, and the control of ice within the body (the first putative ice-binding protein in a frog was recently identified), but many other strategies of biochemical adaptation also contribute to freezing survival. Discussed herein are recent advances in our understanding of amphibian and reptile freeze tolerance with a focus on cell preservation strategies (chaperones, antioxidants, damage defense mechanisms), membrane transporters for water and cryoprotectants, energy metabolism, gene/protein adaptations, and the regulatory control of freeze-responsive hypometabolism at multiple levels (epigenetic regulation of DNA, microRNA action, cell signaling and transcription factor regulation, cell cycle control, and anti-apoptosis). All are providing a much more complete picture of life in the frozen state.
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Affiliation(s)
| | - Janet M. Storey
- Department of Biology, Carleton University, Ottawa, Ontario, Canada
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48
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Bogren LK, Grabek KR, Barsh GS, Martin SL. Comparative tissue transcriptomics highlights dynamic differences among tissues but conserved metabolic transcript prioritization in preparation for arousal from torpor. J Comp Physiol B 2017; 187:735-748. [PMID: 28332019 DOI: 10.1007/s00360-017-1073-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Revised: 11/02/2016] [Accepted: 02/26/2017] [Indexed: 12/01/2022]
Abstract
During the hibernation season, 13-lined ground squirrels spend days to weeks in torpor with body temperatures near freezing then spontaneously rewarm. The molecular drivers of the drastic physiological changes that orchestrate and permit torpor are not well understood. Although transcription effectively ceases at the low body temperatures of torpor, previous work has demonstrated that some transcripts are protected from bulk degradation in brown adipose tissue (BAT), consistent with the importance of their protein products for metabolic heat generation during arousal from torpor. We examined the transcriptome of skeletal muscle, heart, and liver to determine the patterns of differentially expressed genes in these tissues, and whether, like BAT, a subset of these were relatively increased during torpor. EDGE-tags were quantified from five distinct physiological states representing the seasonal and torpor-arousal cycles of 13-lined ground squirrels. Supervised clustering on relative transcript abundances with Random Forest separated the two states bracketing prolonged torpor, entrance into and aroused from torpor, in all three tissues. Independent analyses identified 3347, 6784, and 2433 differentially expressed transcripts among all sampling points in heart, skeletal muscle, and liver, respectively. There were few differentially expressed genes in common across all three tissues; these were enriched in mitochondrial and apoptotic pathway components. Divisive clustering of these data revealed unique cohorts of transcripts that increased across the torpor bout in each tissue with patterns reflecting various combinations of cycling within and between seasons as well as between torpor and arousal. Transcripts that increased across the torpor bout were likewise tissue specific. These data shed new light on the biochemical pathways that alter in concert with hibernation phenotype and provide a rich resource for further hypothesis-based studies.
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Affiliation(s)
- Lori K Bogren
- Cell and Developmental Biology, University of Colorado School of Medicine, Aurora, USA.
| | | | | | - Sandra L Martin
- Cell and Developmental Biology, University of Colorado School of Medicine, Aurora, USA
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49
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Villalobos-Escobedo JM, Herrera-Estrella A, Carreras-Villaseñor N. The interaction of fungi with the environment orchestrated by RNAi. Mycologia 2017; 108:556-71. [DOI: 10.3852/15-246] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Accepted: 01/07/2016] [Indexed: 11/10/2022]
Affiliation(s)
| | - Alfredo Herrera-Estrella
- Laboratorio Nacional de Genómica para la Biodiversidad. Cinvestav Campus Guanajuato. Km 9.6 Libramiento Norte, carretera Irapuato-León. 36821 Irapuato, Guanajuato, Mexico
| | - Nohemí Carreras-Villaseñor
- StelaGenomics México, S de RL de CV, Av. Camino Real de Guanajuato S/N, 36821 Irapuato, Guanajuato, Mexico
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50
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Frigault JJ, Morin MD, Morin PJ. Differential expression and emerging functions of non-coding RNAs in cold adaptation. J Comp Physiol B 2016; 187:19-28. [PMID: 27866230 DOI: 10.1007/s00360-016-1049-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Revised: 10/07/2016] [Accepted: 10/26/2016] [Indexed: 01/16/2023]
Abstract
Several species undergo substantial physiological and biochemical changes to confront the harsh conditions associated with winter. Small mammalian hibernators and cold-hardy insects are examples of natural models of cold adaptation that have been amply explored. While the molecular picture associated with cold adaptation has started to become clearer in recent years, notably through the use of high-throughput experimental approaches, the underlying cold-associated functions attributed to several non-coding RNAs, including microRNAs (miRNAs) and long non-coding RNAs (lncRNAs), remain to be better characterized. Nevertheless, key pioneering work has provided clues on the likely relevance of these molecules in cold adaptation. With an emphasis on mammalian hibernation and insect cold hardiness, this work first reviews various molecular changes documented so far in these processes. The cascades leading to miRNA and lncRNA production as well as the mechanisms of action of these non-coding RNAs are subsequently described. Finally, we present examples of differentially expressed non-coding RNAs in models of cold adaptation and elaborate on the potential significance of this modulation with respect to low-temperature adaptation.
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Affiliation(s)
- Jacques J Frigault
- Department of Chemistry and Biochemistry, Université de Moncton, 18 Antonine-Maillet Avenue, Moncton, NB, E1A 3E9, Canada
| | - Mathieu D Morin
- Department of Chemistry and Biochemistry, Université de Moncton, 18 Antonine-Maillet Avenue, Moncton, NB, E1A 3E9, Canada
| | - Pier Jr Morin
- Department of Chemistry and Biochemistry, Université de Moncton, 18 Antonine-Maillet Avenue, Moncton, NB, E1A 3E9, Canada.
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