51
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Cohen-Berkman M, Dudkevich R, Ben-Hamo S, Fishman A, Salzberg Y, Waldman Ben-Asher H, Lamm AT, Henis-Korenblit S. Endogenous siRNAs promote proteostasis and longevity in germline-less Caenorhabditis elegans. eLife 2020; 9:e50896. [PMID: 32213289 PMCID: PMC7136021 DOI: 10.7554/elife.50896] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 03/26/2020] [Indexed: 12/19/2022] Open
Abstract
How lifespan and the rate of aging are set is a key problem in biology. Small RNAs are conserved molecules that impact diverse biological processes through the control of gene expression. However, in contrast to miRNAs, the role of endo-siRNAs in aging remains unexplored. Here, by combining deep sequencing and genomic and genetic approaches in Caenorhabditis elegans, we reveal an unprecedented role for endo-siRNA molecules in the maintenance of proteostasis and lifespan extension in germline-less animals. Furthermore, we identify an endo-siRNA-regulated tyrosine phosphatase, which limits the longevity of germline-less animals by restricting the activity of the heat shock transcription factor HSF-1. Altogether, our findings point to endo-siRNAs as a link between germline removal and the HSF-1 proteostasis and longevity-promoting somatic pathway. This establishes a role for endo siRNAs in the aging process and identifies downstream genes and physiological processes that are regulated by the endo siRNAs to affect longevity.
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Affiliation(s)
- Moran Cohen-Berkman
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan UniversityRamat-GanIsrael
| | - Reut Dudkevich
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan UniversityRamat-GanIsrael
| | - Shani Ben-Hamo
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan UniversityRamat-GanIsrael
| | - Alla Fishman
- Faculty of Biology, Technion-Israel Institute of Technology, Technion CityHaifaIsrael
| | - Yehuda Salzberg
- Department of Neurobiology, Weizmann Institute of ScienceRehovotIsrael
| | | | - Ayelet T Lamm
- Faculty of Biology, Technion-Israel Institute of Technology, Technion CityHaifaIsrael
| | - Sivan Henis-Korenblit
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan UniversityRamat-GanIsrael
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52
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DAF-16/FoxO in Caenorhabditis elegans and Its Role in Metabolic Remodeling. Cells 2020; 9:cells9010109. [PMID: 31906434 PMCID: PMC7017163 DOI: 10.3390/cells9010109] [Citation(s) in RCA: 88] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 12/30/2019] [Accepted: 12/31/2019] [Indexed: 12/31/2022] Open
Abstract
DAF-16, the only forkhead box transcription factors class O (FoxO) homolog in Caenorhabditis elegans, integrates signals from upstream pathways to elicit transcriptional changes in many genes involved in aging, development, stress, metabolism, and immunity. The major regulator of DAF-16 activity is the insulin/insulin-like growth factor 1 (IGF-1) signaling (IIS) pathway, reduction of which leads to lifespan extension in worms, flies, mice, and humans. In C. elegans daf-2 mutants, reduced IIS leads to a heterochronic activation of a dauer survival program during adulthood. This program includes elevated antioxidant defense and a metabolic shift toward accumulation of carbohydrates (i.e., trehalose and glycogen) and triglycerides, and activation of the glyoxylate shunt, which could allow fat-to-carbohydrate conversion. The longevity of daf-2 mutants seems to be partially supported by endogenous trehalose, a nonreducing disaccharide that mammals cannot synthesize, which points toward considerable differences in downstream mechanisms by which IIS regulates aging in distinct groups.
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53
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Haque S, Ames RM, Moore K, Pilling LC, Peters LL, Bandinelli S, Ferrucci L, Harries LW. circRNAs expressed in human peripheral blood are associated with human aging phenotypes, cellular senescence and mouse lifespan. GeroScience 2019; 42:183-199. [PMID: 31811527 PMCID: PMC7031184 DOI: 10.1007/s11357-019-00120-z] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 10/04/2019] [Indexed: 10/25/2022] Open
Abstract
Circular RNAs (circRNAs) are an emerging class of non-coding RNA molecules that are thought to regulate gene expression and human disease. Despite the observation that circRNAs are known to accumulate in older organisms and have been reported in cellular senescence, their role in aging remains relatively unexplored. Here, we have assessed circRNA expression in aging human blood and followed up age-associated circRNA in relation to human aging phenotypes, mammalian longevity as measured by mouse median strain lifespan and cellular senescence in four different primary human cell types. We found that circRNAs circDEF6, circEP300, circFOXO3 and circFNDC3B demonstrate associations with parental longevity or hand grip strength in 306 subjects from the InCHIANTI study of aging, and furthermore, circFOXO3 and circEP300 also demonstrate differential expression in one or more human senescent cell types. Finally, four circRNAs tested showed evidence of conservation in mouse. Expression levels of one of these, circPlekhm1, was nominally associated with lifespan. These data suggest that circRNA may represent a novel class of regulatory RNA involved in the determination of aging phenotypes, which may show future promise as both biomarkers and future therapeutic targets for age-related disease.
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Affiliation(s)
- Shahnaz Haque
- RNA-Mediated Mechanisms of Disease Group, Institute of Biomedical and Clinical Sciences, University of Exeter Medical School, University of Exeter, RILD South, Barrack Road, Exeter, EX2 5DW, UK
| | - Ryan M Ames
- Biosciences, University of Exeter, Exeter, UK
| | - Karen Moore
- College of Life and Environmental Sciences, University of Exeter, Exeter, UK
| | - Luke C Pilling
- Epidemiology and Public Health, University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Luanne L Peters
- The Jackson Laboratory Nathan Shock Centre of Excellence in the Basic Biology of Aging, Bar Harbor, ME, USA
| | | | - Luigi Ferrucci
- National Institute on Aging, Clinical Research Branch, Harbor Hospital, Baltimore, MD, 21225, USA
| | - Lorna W Harries
- RNA-Mediated Mechanisms of Disease Group, Institute of Biomedical and Clinical Sciences, University of Exeter Medical School, University of Exeter, RILD South, Barrack Road, Exeter, EX2 5DW, UK.
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54
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Nehammer C, Ejlerskov P, Gopal S, Handley A, Ng L, Moreira P, Lee H, Issazadeh-Navikas S, Rubinsztein DC, Pocock R. Interferon-β-induced miR-1 alleviates toxic protein accumulation by controlling autophagy. eLife 2019; 8:49930. [PMID: 31799933 PMCID: PMC6914338 DOI: 10.7554/elife.49930] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 12/03/2019] [Indexed: 12/22/2022] Open
Abstract
Appropriate regulation of autophagy is crucial for clearing toxic proteins from cells. Defective autophagy results in accumulation of toxic protein aggregates that detrimentally affect cellular function and organismal survival. Here, we report that the microRNA miR-1 regulates the autophagy pathway through conserved targeting of the orthologous Tre-2/Bub2/CDC16 (TBC) Rab GTPase-activating proteins TBC-7 and TBC1D15 in Caenorhabditis elegans and mammalian cells, respectively. Loss of miR-1 causes TBC-7/TBC1D15 overexpression, leading to a block on autophagy. Further, we found that the cytokine interferon-β (IFN-β) can induce miR-1 expression in mammalian cells, reducing TBC1D15 levels, and safeguarding against proteotoxic challenges. Therefore, this work provides a potential therapeutic strategy for protein aggregation disorders.
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Affiliation(s)
- Camilla Nehammer
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute and Department of Anatomy and Developmental Biology, Monash University, Melbourne, Australia.,Biotech Research and Innovation Centre, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Patrick Ejlerskov
- Biotech Research and Innovation Centre, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,Cambridge Institute for Medical Research (CIMR), University of Cambridge, Cambridge, United Kingdom
| | - Sandeep Gopal
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute and Department of Anatomy and Developmental Biology, Monash University, Melbourne, Australia
| | - Ava Handley
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute and Department of Anatomy and Developmental Biology, Monash University, Melbourne, Australia
| | - Leelee Ng
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute and Department of Anatomy and Developmental Biology, Monash University, Melbourne, Australia
| | - Pedro Moreira
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute and Department of Anatomy and Developmental Biology, Monash University, Melbourne, Australia
| | - Huikyong Lee
- Cambridge Institute for Medical Research (CIMR), University of Cambridge, Cambridge, United Kingdom
| | - Shohreh Issazadeh-Navikas
- Biotech Research and Innovation Centre, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - David C Rubinsztein
- Cambridge Institute for Medical Research (CIMR), University of Cambridge, Cambridge, United Kingdom.,UK Dementia Research Institute, University of Cambridge, Cambridge, United Kingdom
| | - Roger Pocock
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute and Department of Anatomy and Developmental Biology, Monash University, Melbourne, Australia.,Biotech Research and Innovation Centre, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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55
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Kampinga HH, Mayer MP, Mogk A. Protein quality control: from mechanism to disease : EMBO Workshop, Costa de la Calma (Mallorca), Spain, April 28 - May 03, 2019. Cell Stress Chaperones 2019; 24:1013-1026. [PMID: 31713048 PMCID: PMC6882752 DOI: 10.1007/s12192-019-01040-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/26/2019] [Indexed: 12/11/2022] Open
Abstract
The cellular protein quality control machinery with its central constituents of chaperones and proteases is vital to maintain protein homeostasis under physiological conditions and to protect against acute stress conditions. Imbalances in protein homeostasis also are keys to a plethora of genetic and acquired, often age-related, diseases as well as aging in general. At the EMBO Workshop, speakers covered all major aspects of cellular protein quality control, from basic mechanisms at the molecular, cellular, and organismal level to medical translation. In this report, the highlights of the meeting will be summarized.
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Affiliation(s)
- Harm H Kampinga
- Department of Biomedical Science of Cells & Systems, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands.
| | - Matthias P Mayer
- Center for Molecular Biology (ZMBH), University of Heidelberg, Im Neuenheimer Feld 282, 69120, Heidelberg, Germany.
| | - Axel Mogk
- Center for Molecular Biology (ZMBH), University of Heidelberg, Im Neuenheimer Feld 282, 69120, Heidelberg, Germany.
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56
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Reynolds JA. Noncoding RNA Regulation of Dormant States in Evolutionarily Diverse Animals. THE BIOLOGICAL BULLETIN 2019; 237:192-209. [PMID: 31714856 DOI: 10.1086/705484] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Dormancy is evolutionarily widespread and can take many forms, including diapause, dauer formation, estivation, and hibernation. Each type of dormancy is characterized by distinct features; but accumulating evidence suggests that each is regulated by some common processes, often referred to as a common "toolkit" of regulatory mechanisms, that likely include noncoding RNAs that regulate gene expression. Noncoding RNAs, especially microRNAs, are well-known regulators of biological processes associated with numerous dormancy-related processes, including cell cycle progression, cell growth and proliferation, developmental timing, metabolism, and environmental stress tolerance. This review provides a summary of our current understanding of noncoding RNAs and their involvement in regulating dormancy.
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57
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Zhou J, Zhou LY, Tang X, Zhang J, Zhai LL, Yi YY, Yi J, Lin J, Qian J, Deng ZQ. Circ-Foxo3 is positively associated with the Foxo3 gene and leads to better prognosis of acute myeloid leukemia patients. BMC Cancer 2019; 19:930. [PMID: 31533653 PMCID: PMC6751826 DOI: 10.1186/s12885-019-5967-8] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 07/22/2019] [Indexed: 12/22/2022] Open
Abstract
Background The Foxo3 gene, belonging to the forkhead family, is one of the classes of transcription factors characterized by a forkhead DNA-binding domain, which usually considered being a cancer suppressor gene. Circ-Foxo3 is a circular structure which connects the 3’end to the 5’end. Scholars detected that circ-Foxo3 could compete with Foxo3 for binding to some miRNAs. Methods In this study, we will test the expression of Foxo3 and circ-Foxo3 in de novo acute myeloid leukemia (AML) patients to explore the relationship between Foxo3 gene and circ-Foxo3. All the de novo AML samples and normal control samples was measured by real-time quantitative PCR. A receiver operating characteristic curve was conducted to differentiate AML patients from control people. Association of Foxo3 expression and overall survival was conducted by Kaplan-Meier survival analysis. Results We found that the expression of Foxo3 gene in de novo patients was significantly lower than control samples (P = 0.009). Meanwhile, circ-Foxo3 also expressed lower in de novo AML patients than in control samples (P = 0.040). In different classifications, this trend could be observed more remarkably. In non-M3 patients, the Foxo3 high patients’ survival time was longer than Foxo3 low patients (P = 0.002). Besides, in non-favorable risk groups, patients with low expression of Foxo3 had longer survival time than Foxo3 high patients (P = 0.004). Furthermore, in normal Karyotypic patients, the overall survival time of patients with high-expressed Foxo3 was significantly longer than those with low expression (P = 0.034). Besides, Pearson analysis was also conducted between these two genes in AML patients. Results revealed that they were positively correlated (R = 0.63, P < 0.001). Conclusion In conclusion, we found that low expression of circ-Foxo3 and Foxo3 were frequent in AML patients, and patients with high expression of Foxo3 often had a trend of better prognosis.
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Affiliation(s)
- Jiao Zhou
- Department of Laboratory Center, The Affiliated People's Hospital of Jiangsu University, 8 Dianli Rd, Zhenjiang, 212002, Jiangsu, People's Republic of China.,The Key Lab of Precision Diagnosis and Treatment of Zhenjiang City, Zhenjiang, Jiangsu, People's Republic of China
| | - Ling-Yu Zhou
- Department of Laboratory Center, The Affiliated People's Hospital of Jiangsu University, 8 Dianli Rd, Zhenjiang, 212002, Jiangsu, People's Republic of China.,The Key Lab of Precision Diagnosis and Treatment of Zhenjiang City, Zhenjiang, Jiangsu, People's Republic of China
| | - Xi Tang
- Department of Laboratory Center, The Affiliated People's Hospital of Jiangsu University, 8 Dianli Rd, Zhenjiang, 212002, Jiangsu, People's Republic of China.,The Key Lab of Precision Diagnosis and Treatment of Zhenjiang City, Zhenjiang, Jiangsu, People's Republic of China
| | - Jing Zhang
- Department of Laboratory Center, The Affiliated People's Hospital of Jiangsu University, 8 Dianli Rd, Zhenjiang, 212002, Jiangsu, People's Republic of China.,The Key Lab of Precision Diagnosis and Treatment of Zhenjiang City, Zhenjiang, Jiangsu, People's Republic of China
| | - Ling-Ling Zhai
- Department of Laboratory Center, The Affiliated People's Hospital of Jiangsu University, 8 Dianli Rd, Zhenjiang, 212002, Jiangsu, People's Republic of China.,The Key Lab of Precision Diagnosis and Treatment of Zhenjiang City, Zhenjiang, Jiangsu, People's Republic of China
| | - Yun Yun Yi
- Department of Laboratory Center, The Affiliated People's Hospital of Jiangsu University, 8 Dianli Rd, Zhenjiang, 212002, Jiangsu, People's Republic of China.,The Key Lab of Precision Diagnosis and Treatment of Zhenjiang City, Zhenjiang, Jiangsu, People's Republic of China
| | - Jing Yi
- Department of Laboratory Center, The Affiliated People's Hospital of Jiangsu University, 8 Dianli Rd, Zhenjiang, 212002, Jiangsu, People's Republic of China.,The Key Lab of Precision Diagnosis and Treatment of Zhenjiang City, Zhenjiang, Jiangsu, People's Republic of China
| | - Jiang Lin
- Department of Laboratory Center, The Affiliated People's Hospital of Jiangsu University, 8 Dianli Rd, Zhenjiang, 212002, Jiangsu, People's Republic of China.,The Key Lab of Precision Diagnosis and Treatment of Zhenjiang City, Zhenjiang, Jiangsu, People's Republic of China
| | - Jun Qian
- Department of Hematology, The Affiliated People's Hospital of Jiangsu University, Zhenjiang, 212002, Jiangsu, People's Republic of China
| | - Zhao-Qun Deng
- Department of Laboratory Center, The Affiliated People's Hospital of Jiangsu University, 8 Dianli Rd, Zhenjiang, 212002, Jiangsu, People's Republic of China. .,The Key Lab of Precision Diagnosis and Treatment of Zhenjiang City, Zhenjiang, Jiangsu, People's Republic of China.
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58
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High-throughput identification of microRNAs in Taenia hydatigena, a cestode threatening livestock breeding industry. INFECTION GENETICS AND EVOLUTION 2019; 75:103985. [PMID: 31362070 DOI: 10.1016/j.meegid.2019.103985] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 07/23/2019] [Accepted: 07/26/2019] [Indexed: 12/11/2022]
Abstract
Infection of Cysticercus tenuicollis, the larval stage of Taenia hydatigena, is extensively found in sheep and pigs and jeopardizes the breeding and meat industry. miRNAs are a subclass of small noncoding regulatory RNAs and closely associated with the pathogenesis and biology of parasites. Here, using HiSeq sequencing we identified 49 known and 2 potential novel miRNAs in C. tenuicollis, of which both thy-miR-71 and -87 were predominant. Using RT-qPCR, 6 selected miRNAs were validated, and thy-miR-71 and -miR-87 were confirmed to be highly expressed, with the copy number of approximately 82,340 ± 2079 and 19,580 ± 609 per 1 ng total RNA, respectively. Similar to other cestodes, T. hydatigena was predicted to have two conserved miRNA clusters thy-miR-71/2c/2b and thy-miR-4989/277, and three members of the former were confirmed to reside sequentially within the genomic region of 253 bp by PCR. The current data provide us a valuable resource for further studies of a role of miRNAs in T. hydatigena biology and infection.
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59
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Cai H, Dhondt I, Vandemeulebroucke L, Vlaeminck C, Rasulova M, Braeckman BP. CBP-1 Acts in GABAergic Neurons to Double Life Span in Axenically Cultured Caenorhabditis elegans. J Gerontol A Biol Sci Med Sci 2019; 74:1198-1205. [PMID: 29099917 PMCID: PMC6625597 DOI: 10.1093/gerona/glx206] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 10/23/2017] [Indexed: 12/17/2022] Open
Abstract
When cultured in axenic medium, Caenorhabditis elegans shows the largest life-span extension compared with other dietary restriction regimens. However, the underlying molecular mechanism still remains elusive. The gene cbp-1, encoding the worm ortholog of p300/CBP (CREB-binding protein), is one of the very few key genes known to be essential for life span doubling under axenic dietary restriction (ADR). By using tissue-specific RNAi, we found that cbp-1 expression in the germline is essential for fertility, whereas this gene functions specifically in the GABAergic neurons to support the full life span-doubling effect of ADR. Surprisingly, GABA itself is not required for ADR-induced longevity, suggesting a role of neuropeptide signaling. In addition, chemotaxis assays illustrate that neuronal inactivation of CBP-1 affects the animals' food sensing behavior. Together, our results show that the strong life-span extension in axenic medium is under strict control of GABAergic neurons and may be linked to food sensing.
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Affiliation(s)
- Huaihan Cai
- Laboratory of Aging Physiology and Molecular Evolution, Biology Department, Ghent University, Belgium
| | - Ineke Dhondt
- Laboratory of Aging Physiology and Molecular Evolution, Biology Department, Ghent University, Belgium
| | | | - Caroline Vlaeminck
- Laboratory of Aging Physiology and Molecular Evolution, Biology Department, Ghent University, Belgium
| | - Madina Rasulova
- Laboratory of Aging Physiology and Molecular Evolution, Biology Department, Ghent University, Belgium
| | - Bart P Braeckman
- Laboratory of Aging Physiology and Molecular Evolution, Biology Department, Ghent University, Belgium
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60
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Kinser HE, Pincus Z. MicroRNAs as modulators of longevity and the aging process. Hum Genet 2019; 139:291-308. [PMID: 31297598 DOI: 10.1007/s00439-019-02046-0] [Citation(s) in RCA: 89] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 07/05/2019] [Indexed: 12/22/2022]
Abstract
MicroRNAs (miRNAs) are short, non-coding RNAs that post-transcriptionally repress translation or induce mRNA degradation of target transcripts through sequence-specific binding. miRNAs target hundreds of transcripts to regulate diverse biological pathways and processes, including aging. Many microRNAs are differentially expressed during aging, generating interest in their use as aging biomarkers and roles as regulators of the aging process. In the invertebrates Caenorhabditis elegans and Drosophila, a number of miRNAs have been found to both positive and negatively modulate longevity through canonical aging pathways. Recent studies have also shown that miRNAs regulate age-associated processes and pathologies in a diverse array of mammalian tissues, including brain, heart, bone, and muscle. The review will present an overview of these studies, highlighting the role of individual miRNAs as biomarkers of aging and regulators of longevity and tissue-specific aging processes.
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Affiliation(s)
- Holly E Kinser
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, USA
| | - Zachary Pincus
- Department of Developmental Biology and Department of Genetics, Washington University in St. Louis, St. Louis, USA.
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61
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Posner R, Toker IA, Antonova O, Star E, Anava S, Azmon E, Hendricks M, Bracha S, Gingold H, Rechavi O. Neuronal Small RNAs Control Behavior Transgenerationally. Cell 2019; 177:1814-1826.e15. [PMID: 31178120 PMCID: PMC6579485 DOI: 10.1016/j.cell.2019.04.029] [Citation(s) in RCA: 101] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 02/18/2019] [Accepted: 04/13/2019] [Indexed: 12/21/2022]
Abstract
It is unknown whether the activity of the nervous system can be inherited. In Caenorhabditis elegans nematodes, parental responses can transmit heritable small RNAs that regulate gene expression transgenerationally. In this study, we show that a neuronal process can impact the next generations. Neurons-specific synthesis of RDE-4-dependent small RNAs regulates germline amplified endogenous small interfering RNAs (siRNAs) and germline gene expression for multiple generations. Further, the production of small RNAs in neurons controls the chemotaxis behavior of the progeny for at least three generations via the germline Argonaute HRDE-1. Among the targets of these small RNAs, we identified the conserved gene saeg-2, which is transgenerationally downregulated in the germline. Silencing of saeg-2 following neuronal small RNA biogenesis is required for chemotaxis under stress. Thus, we propose a small-RNA-based mechanism for communication of neuronal processes transgenerationally. C. elegans neuronal small RNAs are characterized by RNA sequencing RDE-4-dependent neuronal endogenous small RNAs communicate with the germline Germline HRDE-1 mediates transgenerational regulation by neuronal small RNAs Neuronal small RNAs regulate germline genes to control behavior transgenerationally
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Affiliation(s)
- Rachel Posner
- Department of Neurobiology, Wise Faculty of Life Sciences and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Itai Antoine Toker
- Department of Neurobiology, Wise Faculty of Life Sciences and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Olga Antonova
- Department of Neurobiology, Wise Faculty of Life Sciences and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Ekaterina Star
- Department of Neurobiology, Wise Faculty of Life Sciences and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Sarit Anava
- Department of Neurobiology, Wise Faculty of Life Sciences and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Eran Azmon
- Department of Neurobiology, Wise Faculty of Life Sciences and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Michael Hendricks
- Department of Biology, McGill University, Montreal, QC H3A 1B1, Canada
| | - Shahar Bracha
- Department of Neurobiology, Wise Faculty of Life Sciences and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Hila Gingold
- Department of Neurobiology, Wise Faculty of Life Sciences and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Oded Rechavi
- Department of Neurobiology, Wise Faculty of Life Sciences and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 6997801, Israel.
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62
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Finger F, Ottens F, Springhorn A, Drexel T, Proksch L, Metz S, Cochella L, Hoppe T. Olfaction regulates organismal proteostasis and longevity via microRNA-dependent signaling. Nat Metab 2019; 1:350-359. [PMID: 31535080 PMCID: PMC6751085 DOI: 10.1038/s42255-019-0033-z] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The maintenance of proteostasis is crucial for any organism to survive and reproduce in an ever-changing environment, but its efficiency declines with age1. Posttranscriptional regulators such as microRNAs control protein translation of target mRNAs with major consequences for development, physiology, and longevity2,3. Here we show that food odor stimulates organismal proteostasis and promotes longevity in Caenorhabditis elegans through mir-71-mediated inhibition of tir-1 mRNA stability in olfactory AWC neurons. Screening a collection of microRNAs that control aging3 we find that miRNA mir-71 regulates lifespan and promotes ubiquitin-dependent protein turnover, particularly in the intestine. We show that mir-71 directly inhibits the toll receptor domain protein TIR-1 in AWC olfactory neurons and that disruption of mir-71/tir-1 or loss of AWC olfactory neurons eliminates the influence of food source on proteostasis. mir-71-mediated regulation of TIR-1 controls chemotactic behavior and is regulated by odor. Thus, odor perception influences cell-type specific miRNA-target interaction to regulate organismal proteostasis and longevity. We anticipate that the proposed mechanism of food perception will stimulate further research on neuroendocrine brain-to-gut communication and may open the possibility for therapeutic interventions to improve proteostasis and organismal health via the sense of smell, with potential implication for obesity, diabetes and aging.
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Affiliation(s)
- Fabian Finger
- Institute for Genetics and CECAD Research Center, University of Cologne, Cologne, Germany
| | - Franziska Ottens
- Institute for Genetics and CECAD Research Center, University of Cologne, Cologne, Germany
| | - Alexander Springhorn
- Institute for Genetics and CECAD Research Center, University of Cologne, Cologne, Germany
| | - Tanja Drexel
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | - Lucie Proksch
- Institute for Genetics and CECAD Research Center, University of Cologne, Cologne, Germany
| | - Sophia Metz
- Institute for Genetics and CECAD Research Center, University of Cologne, Cologne, Germany
| | - Luisa Cochella
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | - Thorsten Hoppe
- Institute for Genetics and CECAD Research Center, University of Cologne, Cologne, Germany.
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63
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Macchiaroli N, Cucher M, Kamenetzky L, Yones C, Bugnon L, Berriman M, Olson PD, Rosenzvit MC. Identification and expression profiling of microRNAs in Hymenolepis. Int J Parasitol 2019; 49:211-223. [PMID: 30677390 DOI: 10.1016/j.ijpara.2018.07.005] [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] [Received: 05/31/2018] [Revised: 07/20/2018] [Accepted: 07/23/2018] [Indexed: 02/08/2023]
Abstract
Tapeworms (cestodes) of the genus Hymenolepis are the causative agents of hymenolepiasis, a neglected zoonotic disease. Hymenolepis nana is the most prevalent human tapeworm, especially affecting children. The genomes of Hymenolepis microstoma and H. nana have been recently sequenced and assembled. MicroRNAs (miRNAs), a class of small non-coding RNAs, are principle regulators of gene expression at the post-transcriptional level and are involved in many different biological processes. In previous work, we experimentally identified miRNA genes in the cestodes Echinococcus, Taenia and Mesocestoides. However, current knowledge about miRNAs in Hymenolepis is limited. In this work we described for the first known time the expression profile of the miRNA complement in H. microstoma, and discovered miRNAs in H. nana. We found a reduced complement of 37 evolutionarily conserved miRNAs, putatively reflecting their low morphological complexity and parasitic lifestyle. We found high expression of a few miRNAs in the larval stage of H. microstoma that are conserved in other cestodes, suggesting that these miRNAs may have important roles in development, survival and for host-parasite interplay. We performed a comparative analysis of the identified miRNAs across the Cestoda and showed that most of the miRNAs in Hymenolepis are located in intergenic regions, implying that they are independently transcribed. We found a Hymenolepis-specific cluster composed of three members of the mir-36 family. Also, we found that one of the neighboring genes of mir-10 was a Hox gene as in most bilaterial species. This study provides a valuable resource for further experimental research in cestode biology that might lead to improved detection and control of these neglected parasites. The comprehensive identification and expression analysis of Hymenolepis miRNAs can help to identify novel biomarkers for diagnosis and/or novel therapeutic targets for the control of hymenolepiasis.
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Affiliation(s)
- Natalia Macchiaroli
- Instituto de Investigaciones en Microbiología y Parasitología Médicas (IMPaM), Facultad de Medicina, Universidad de Buenos Aires (UBA)-Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Buenos Aires, Argentina
| | - Marcela Cucher
- Instituto de Investigaciones en Microbiología y Parasitología Médicas (IMPaM), Facultad de Medicina, Universidad de Buenos Aires (UBA)-Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Buenos Aires, Argentina
| | - Laura Kamenetzky
- Instituto de Investigaciones en Microbiología y Parasitología Médicas (IMPaM), Facultad de Medicina, Universidad de Buenos Aires (UBA)-Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Buenos Aires, Argentina
| | - Cristian Yones
- Research Institute for Signals, Systems and Computational Intelligence, (sinc(i)), FICH-UNL-Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Santa Fe, Argentina
| | - Leandro Bugnon
- Research Institute for Signals, Systems and Computational Intelligence, (sinc(i)), FICH-UNL-Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Santa Fe, Argentina
| | - Matt Berriman
- Parasite Genomics Group, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Peter D Olson
- Department of Life Sciences, The Natural History Museum, London, UK
| | - Mara Cecilia Rosenzvit
- Instituto de Investigaciones en Microbiología y Parasitología Médicas (IMPaM), Facultad de Medicina, Universidad de Buenos Aires (UBA)-Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Buenos Aires, Argentina.
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64
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Dzakah EE, Waqas A, Wei S, Yu B, Wang X, Fu T, Liu L, Shan G. Loss of miR-83 extends lifespan and affects target gene expression in an age-dependent manner in Caenorhabditis elegans. J Genet Genomics 2018; 45:651-662. [PMID: 30595472 DOI: 10.1016/j.jgg.2018.11.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 10/11/2018] [Accepted: 11/06/2018] [Indexed: 02/06/2023]
Abstract
MicroRNAs (miRNAs) are short non-coding RNAs that are involved in the post-transcriptional regulation of protein-coding genes. miRNAs modulate lifespan and the aging process in a variety of organisms. In this study, we identified a role of miR-83 in regulating lifespan of Caenorhabditis elegans. mir-83 mutants exhibited extended lifespan, and the overexpression of miR-83 was sufficient to decrease the prolonged lifespan of the mutants. We observed upregulation of the expression levels of a set of miR-83 target genes in young mir-83 mutant adults; while different sets of genes were upregulated in older mir-83 mutant adults. In vivo assays showed that miR-83 regulated expression of target genes including din-1, spp-9 and col-178, and we demonstrated that daf-16 and din-1 were required for the extension of lifespan in the mir-83 mutants. The regulation of din-1 by miR-83 during aging resulted in the differential expression of din-1 targets such as gst-4 and gst-10. In daf-2 mutants, the expression level of miR-83 was significantly reduced compared to wild-type animals. We identified a role for miR-83 in modulating lifespan in C. elegans and provided molecular insights into its functional mechanism.
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Affiliation(s)
- Emmanuel Enoch Dzakah
- Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences, University of Science and Technology of China, Hefei 230027, China; Department of Molecular Biology and Biotechnology, School of Biological Sciences, College of Agriculture and Natural Sciences, University of Cape Coast, Cape Coast 03321, Ghana
| | - Ahmed Waqas
- Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences, University of Science and Technology of China, Hefei 230027, China
| | - Shuai Wei
- Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences, University of Science and Technology of China, Hefei 230027, China
| | - Bin Yu
- Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences, University of Science and Technology of China, Hefei 230027, China
| | - Xiaolin Wang
- Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences, University of Science and Technology of China, Hefei 230027, China
| | - Tao Fu
- Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences, University of Science and Technology of China, Hefei 230027, China
| | - Lei Liu
- Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences, University of Science and Technology of China, Hefei 230027, China
| | - Ge Shan
- Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences, University of Science and Technology of China, Hefei 230027, China; CAS Centre for Excellence in Molecular Cell Science, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China.
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65
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Dietrich C, Singh M, Kumar N, Singh SR. The Emerging Roles of microRNAs in Stem Cell Aging. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1056:11-26. [PMID: 29754172 DOI: 10.1007/978-3-319-74470-4_2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Aging is the continuous loss of tissue and organ function over time. MicroRNAs (miRNAs) are thought to play a vital role in this process. miRNAs are endogenous small noncoding RNAs that control the expression of target mRNA. They are involved in many biological processes such as developmental timing, differentiation, cell death, stem cell proliferation and differentiation, immune response, aging and cancer. Accumulating studies in recent years suggest that miRNAs play crucial roles in stem cell division and differentiation. In the present chapter, we present a brief overview of these studies and discuss their contributions toward our understanding of the importance of miRNAs in normal and aged stem cell function in various model systems.
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Affiliation(s)
- Catharine Dietrich
- Stem Cell Regulation and Animal Aging Section, Basic Research Laboratory, National Cancer Institute, Frederick, MD, USA
| | - Manish Singh
- Mouse Cancer Genetics Program, National Cancer Institute, Frederick, MD, USA
| | - Nishant Kumar
- Hospitalist Division, Department of Medicine, Inova Fairfax Medical Campus, Falls Church, VA, USA
| | - Shree Ram Singh
- Stem Cell Regulation and Animal Aging Section, Basic Research Laboratory, National Cancer Institute, Frederick, MD, USA.
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66
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Guo X, Zheng Y. Identification and characterization of microRNAs in a cestode Hydatigera taeniaeformis using deep sequencing approach. Exp Parasitol 2018; 194:32-37. [PMID: 30237048 DOI: 10.1016/j.exppara.2018.09.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 08/02/2018] [Accepted: 09/16/2018] [Indexed: 12/22/2022]
Abstract
Hydatigera taeniaeformis (formerly known as Taenia taeniaeformis) is a parasitic tapeworm that has a worldwide distribution. H. taeniaeformis is naturally transmitted between mice and cats and threatens to human health, especially those who are in close contact with pets. MicroRNAs (miRNAs) are a class of small regulatory non-coding RNAs involved in the regulation of parasite growth and development, parasite infection and immunology, and host-pathogen interactions. The miRNA profile of H. taeniaeformis remains to be elucidated. Herein, 47 conserved miRNAs (grouped into 34 miRNA families) and 4 novel miRNAs were identified in H. taeniaeformis metacestodes using deep sequencing approach. Among them, hta-miR-71, -let-7, and-miR-87 was absolutely predominant in H. taeniaeformis metacestodes. Moreover, comparative analysis revealed the presence of miR-71/2 and miR-4989/277 clusters in H. taeniaeformis. Nucleotide bias analysis of identified miRNAs showed that the adenine (A) was the dominant nucleotide at the beginning of the miRNAs, particularly at the positions of third and 7th nucleotides. The study provides rich data for further understandings of H. taeniaeformis biology.
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Affiliation(s)
- Xiaola Guo
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, CAAS, Lanzhou, 730046, Gansu, China.
| | - Yadong Zheng
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, CAAS, Lanzhou, 730046, Gansu, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University College of Veterinary Medicine, Yangzhou, 225009, China
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67
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Braman A, Weber PS, Tritten L, Geary T, Long M, Beachboard S, Mackenzie C. Further Characterization of Molecular Markers in Canine Dirofilaria immitis Infection. J Parasitol 2018; 104:697-701. [PMID: 30148419 DOI: 10.1645/18-12] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Dirofilaria immitis is a common filarial parasite found in dogs and cats in the Americas, with the pathophysiological consequences of the infection differing somewhat between these 2 host species. Recent research efforts have been focused on determining if the microRNAs (miRNAs) released from adult Dirofilariae have a role as markers for distinguishing the intensity of adult worm infection, as well as determining the presence of new infections. This study expands previous work on 2 nematode miRNAs, miR34 and miR-71, by addressing their ability to discriminate between low and high D. immitis adult worm intensities in dogs. Serum samples were collected from 13 dogs, 8 of which carried known numbers of adult D. immitis at autopsy in their hearts and pulmonary vessels. Three groups of canine sera were created based on D. immitis burden: "control" (0 worms; 5 animals), "low intensity" (10-18 worms; mean ± SD = 12.3 ± 4.4; 4 animals), and "high intensity" (41-72 worms; mean 62.5 ± 15.1; 4 animals) groups. A qPCR analysis was performed on each sample to measure plasma levels of miR-34 and miR-71; however, no significant differences were observed between these groups in terms of levels of miRNAs, so the low- and high-intensity samples were then combined into a single "infected" category and compared to the "non-infected" controls. Copy numbers of both miR-34 and miR-71 were significantly higher in infected compared to uninfected animals ( P = 0.015 and P = 0.027, respectively). The Ct values of expression compared with the adult worm intensity for each miRNA revealed that both miR-34 and miR-71 significantly discriminate between the infected and non-infected groups ( P value < 0.0001 for both). These findings support the contention that miRNA 34 and miRNA 71, which are filarial-specific miRNAs, can both serve as biomarkers for the presence of D. immitis infection in dogs, but at this point they do not appear to reflect the actual intensity of adult parasites present.
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Affiliation(s)
- Ashley Braman
- 1 Department of Pathobiology and Diagnostic Investigation, Michigan State University, East Lansing, Michigan 48824
| | - Patty Sue Weber
- 1 Department of Pathobiology and Diagnostic Investigation, Michigan State University, East Lansing, Michigan 48824
| | - Lucienne Tritten
- 2 The Institute of Parasitology, McGill University, Montreal, Quebec, Canada H3A 0G4
| | - Timothy Geary
- 2 The Institute of Parasitology, McGill University, Montreal, Quebec, Canada H3A 0G4
| | - Maureen Long
- 3 Department of Infectious Diseases and Pathology, University of Florida, Gainesville, Florida 32611
| | - Sarah Beachboard
- 3 Department of Infectious Diseases and Pathology, University of Florida, Gainesville, Florida 32611
| | - Charles Mackenzie
- 1 Department of Pathobiology and Diagnostic Investigation, Michigan State University, East Lansing, Michigan 48824
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Denzel MS, Lapierre LR, Mack HID. Emerging topics in C. elegans aging research: Transcriptional regulation, stress response and epigenetics. Mech Ageing Dev 2018; 177:4-21. [PMID: 30134144 PMCID: PMC6696993 DOI: 10.1016/j.mad.2018.08.001] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2018] [Revised: 08/09/2018] [Accepted: 08/10/2018] [Indexed: 12/13/2022]
Abstract
Key discoveries in aging research have been made possible with the use of model organisms. Caenorhabditis elegans is a short-lived nematode that has become a well-established system to study aging. The practicality and powerful genetic manipulations associated with this metazoan have revolutionized our ability to understand how organisms age. 25 years after the publication of the discovery of the daf-2 gene as a genetic modifier of lifespan, C. elegans remains as relevant as ever in the quest to understand the process of aging. Nematode aging research has proven useful in identifying transcriptional regulators, small molecule signals, cellular mechanisms, epigenetic modifications associated with stress resistance and longevity, and lifespan-extending compounds. Here, we review recent discoveries and selected topics that have emerged in aging research using this incredible little worm.
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Affiliation(s)
- Martin S Denzel
- Max Planck Institute for Biology of Ageing, Cologne, Germany.
| | - Louis R Lapierre
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI, USA.
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69
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Recent Molecular Genetic Explorations of Caenorhabditis elegans MicroRNAs. Genetics 2018; 209:651-673. [PMID: 29967059 PMCID: PMC6028246 DOI: 10.1534/genetics.118.300291] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 04/30/2018] [Indexed: 12/17/2022] Open
Abstract
MicroRNAs are small, noncoding RNAs that regulate gene expression at the post-transcriptional level in essentially all aspects of Caenorhabditis elegans biology. More than 140 genes that encode microRNAs in C. elegans regulate development, behavior, metabolism, and responses to physiological and environmental changes. Genetic analysis of C. elegans microRNA genes continues to enhance our fundamental understanding of how microRNAs are integrated into broader gene regulatory networks to control diverse biological processes, including growth, cell division, cell fate determination, behavior, longevity, and stress responses. As many of these microRNA sequences and the related processing machinery are conserved over nearly a billion years of animal phylogeny, the assignment of their functions via worm genetics may inform the functions of their orthologs in other animals, including humans. In vivo investigations are especially important for microRNAs because in silico extrapolation of their functions using mRNA target prediction programs can easily assign microRNAs to incorrect genetic pathways. At this mezzanine level of microRNA bioinformatic sophistication, genetic analysis continues to be the gold standard for pathway assignments.
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70
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Zhang Y, Zhang W, Dong M. The miR-58 microRNA family is regulated by insulin signaling and contributes to lifespan regulation in Caenorhabditis elegans. SCIENCE CHINA-LIFE SCIENCES 2018; 61:1060-1070. [PMID: 29948901 DOI: 10.1007/s11427-018-9308-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 03/29/2018] [Indexed: 01/21/2023]
Abstract
microRNAs regulate diverse biological processes such as development and aging by promoting degradation or inhibiting translation of their target mRNAs. In this study, we have found that the miR-58 family microRNAs regulate lifespan in C. elegans. Intriguingly, members of the miR-58 family affect lifespan differently, sometimes in opposite directions, and have complex genetic interactions. The abundances of the miR-58 family miRNAs are up-regulated in the long-lived daf-2 mutant in a daf-16-dependent manner, indicating that these miRNAs are effectors of insulin signaling in C. elegans. We also found that miR-58 is regulated by insulin signaling and partially required for the lifespan extension mediated by reduced insulin signaling, germline ablation, dietary restriction, and mild mitochondrial dysfunction. We further identified the daf-21, ins-1, and isw-1 mRNAs as endogenous targets of miR-58. Our study shows that miRNAs function in multiple lifespan extension mechanisms, and that the seed sequence is not the dominant factor defining the role of a miRNA in lifespan regulation.
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Affiliation(s)
- Yanping Zhang
- College of Life Science, Beijing Normal University, Beijing, 100875, China.,National Institute of Biological Sciences, Beijing, 102206, China.,Beijing Key Laboratory of the Cell Biology of Animal Aging, Beijing, 102206, China
| | - Wenhong Zhang
- National Institute of Biological Sciences, Beijing, 102206, China.,Beijing Key Laboratory of the Cell Biology of Animal Aging, Beijing, 102206, China
| | - Mengqiu Dong
- National Institute of Biological Sciences, Beijing, 102206, China. .,Beijing Key Laboratory of the Cell Biology of Animal Aging, Beijing, 102206, China.
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71
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Lardenoije R, Pishva E, Lunnon K, van den Hove DL. Neuroepigenetics of Aging and Age-Related Neurodegenerative Disorders. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2018; 158:49-82. [PMID: 30072060 DOI: 10.1016/bs.pmbts.2018.04.008] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Neurodegenerative diseases are complex, progressive disorders and affect millions of people worldwide, contributing significantly to the global burden of disease. In recent years, research has begun to investigate epigenetic mechanisms for a potential role in disease etiology. In this chapter, we describe the current state of play for epigenetic research into neurodegenerative disorders including Alzheimer's disease, Parkinson's disease and Huntington's disease. We focus on the recent evidence for a potential role of DNA modifications, histone modifications and non-coding RNA in the etiology of these disorders. Finally, we discuss how new technological and bioinformatics advances in the field of epigenetics could further progress our understanding about the underlying mechanisms of neurodegenerative diseases.
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Affiliation(s)
- Roy Lardenoije
- Department of Psychiatry and Neuropsychology, Maastricht University Medical Centre, Maastricht, The Netherlands
| | - Ehsan Pishva
- Department of Psychiatry and Neuropsychology, Maastricht University Medical Centre, Maastricht, The Netherlands; University of Exeter Medical School, University of Exeter, Exeter, United Kingdom
| | - Katie Lunnon
- University of Exeter Medical School, University of Exeter, Exeter, United Kingdom
| | - Daniel L van den Hove
- Department of Psychiatry and Neuropsychology, Maastricht University Medical Centre, Maastricht, The Netherlands.
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72
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Aalto AP, Nicastro IA, Broughton JP, Chipman LB, Schreiner WP, Chen JS, Pasquinelli AE. Opposing roles of microRNA Argonautes during Caenorhabditis elegans aging. PLoS Genet 2018; 14:e1007379. [PMID: 29927939 PMCID: PMC6013023 DOI: 10.1371/journal.pgen.1007379] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 04/25/2018] [Indexed: 01/08/2023] Open
Abstract
Argonaute (AGO) proteins partner with microRNAs (miRNAs) to target specific genes for post-transcriptional regulation. During larval development in Caenorhabditis elegans, Argonaute-Like Gene 1 (ALG-1) is the primary mediator of the miRNA pathway, while the related ALG-2 protein is largely dispensable. Here we show that in adult C. elegans these AGOs are differentially expressed and, surprisingly, work in opposition to each other; alg-1 promotes longevity, whereas alg-2 restricts lifespan. Transcriptional profiling of adult animals revealed that distinct miRNAs and largely non-overlapping sets of protein-coding genes are misregulated in alg-1 and alg-2 mutants. Interestingly, many of the differentially expressed genes are downstream targets of the Insulin/ IGF-1 Signaling (IIS) pathway, which controls lifespan by regulating the activity of the DAF-16/ FOXO transcription factor. Consistent with this observation, we show that daf-16 is required for the extended lifespan of alg-2 mutants. Furthermore, the long lifespan of daf-2 insulin receptor mutants, which depends on daf-16, is strongly reduced in animals lacking alg-1 activity. This work establishes an important role for AGO-mediated gene regulation in aging C. elegans and illustrates that the activity of homologous genes can switch from complementary to antagonistic, depending on the life stage.
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Affiliation(s)
- Antti P. Aalto
- Division of Biology, University of California, San Diego, La Jolla, CA, United States of America
| | - Ian A. Nicastro
- Division of Biology, University of California, San Diego, La Jolla, CA, United States of America
| | - James P. Broughton
- Division of Biology, University of California, San Diego, La Jolla, CA, United States of America
| | - Laura B. Chipman
- Division of Biology, University of California, San Diego, La Jolla, CA, United States of America
| | - William P. Schreiner
- Division of Biology, University of California, San Diego, La Jolla, CA, United States of America
| | - Jerry S. Chen
- Division of Biology, University of California, San Diego, La Jolla, CA, United States of America
| | - Amy E. Pasquinelli
- Division of Biology, University of California, San Diego, La Jolla, CA, United States of America
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73
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Abstract
MicroRNAs (miRNAs) are ∼22 nt RNAs that direct posttranscriptional repression of mRNA targets in diverse eukaryotic lineages. In humans and other mammals, these small RNAs help sculpt the expression of most mRNAs. This article reviews advances in our understanding of the defining features of metazoan miRNAs and their biogenesis, genomics, and evolution. It then reviews how metazoan miRNAs are regulated, how they recognize and cause repression of their targets, and the biological functions of this repression, with a compilation of knockout phenotypes that shows that important biological functions have been identified for most of the broadly conserved miRNAs of mammals.
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Affiliation(s)
- David P Bartel
- Howard Hughes Medical Institute and Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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74
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Inukai S, Pincus Z, de Lencastre A, Slack FJ. A microRNA feedback loop regulates global microRNA abundance during aging. RNA (NEW YORK, N.Y.) 2018; 24:159-172. [PMID: 29114017 PMCID: PMC5769744 DOI: 10.1261/rna.062190.117] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 10/29/2017] [Indexed: 06/07/2023]
Abstract
Expression levels of many microRNAs (miRNAs) change during aging, notably declining globally in a number of organisms and tissues across taxa. However, little is known about the mechanisms or the biological relevance for this change. We investigated the network of genes that controls miRNA transcription and processing during C. elegans aging. We found that miRNA biogenesis genes are highly networked with transcription factors and aging-associated miRNAs. In particular, miR-71, known to influence life span and itself up-regulated during aging, represses alg-1/Argonaute expression post-transcriptionally during aging. Increased ALG-1 abundance in mir-71 loss-of-function mutants led to globally increased miRNA expression. Interestingly, these mutants demonstrated widespread mRNA expression dysregulation and diminished levels of variability both in gene expression and in overall life span. Thus, the progressive molecular decline often thought to be the result of accumulated damage over an organism's life may be partially explained by a miRNA-directed mechanism of age-associated decline.
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Affiliation(s)
- Sachi Inukai
- Department of Molecular, Cellular and Developmental Biology, Yale University, P.O. Box 208103, New Haven, Connecticut 06520, USA
- Institute for RNA Medicine, Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02215, USA
| | - Zachary Pincus
- Department of Developmental Biology
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri 63110, USA
| | - Alexandre de Lencastre
- Department of Molecular, Cellular and Developmental Biology, Yale University, P.O. Box 208103, New Haven, Connecticut 06520, USA
| | - Frank J Slack
- Department of Molecular, Cellular and Developmental Biology, Yale University, P.O. Box 208103, New Haven, Connecticut 06520, USA
- Institute for RNA Medicine, Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02215, USA
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75
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FOXO1/3: Potential suppressors of fibrosis. Ageing Res Rev 2018; 41:42-52. [PMID: 29138094 DOI: 10.1016/j.arr.2017.11.002] [Citation(s) in RCA: 88] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Revised: 10/07/2017] [Accepted: 11/08/2017] [Indexed: 02/06/2023]
Abstract
Fibrosis is a universally age-related disease that involves nearly all organs. It is typically initiated by organic injury and eventually results in organ failure. There are still few effective therapeutic strategy targets for fibrogenesis. Forkhead box proteins O1 and O3 (FOXO1/3) have been shown to have favorable inhibitory effects on fibroblast activation and subsequent extracellular matrix production and can ameliorate fibrosis levels in numerous organs, including the heart, liver, lung, and kidney; they are therefore promising targets for anti-fibrosis therapy. Moreover, we can develop appropriate strategies to make the best use of FOXO1/3's anti-fibrosis properties. The information reviewed here should be significant for understanding the roles of FOXO1/3 in fibrosis and should contribute to the design of further studies related to FOXO1/3 and the fibrotic response and shed light on a potential treatment for fibrosis.
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76
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Gendron CM, Pletcher SD. MicroRNAs mir-184 and let-7 alter Drosophila metabolism and longevity. Aging Cell 2017; 16:1434-1438. [PMID: 28963741 PMCID: PMC5676060 DOI: 10.1111/acel.12673] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/11/2017] [Indexed: 11/29/2022] Open
Abstract
MicroRNAs (miRNAs) are small RNA molecules that regulate gene expression associated with many complex biological processes. By comparing miRNA expression between long‐lived cohorts of Drosophila melanogaster that were fed a low‐nutrient diet with normal‐lived control animals fed a high‐nutrient diet, we identified miR‐184, let‐7, miR‐125, and miR‐100 as candidate miRNAs involved in modulating aging. We found that ubiquitous, adult‐specific overexpression of these individual miRNAs led to significant changes in fat metabolism and/or lifespan. Most impressively, adult‐specific overexpression of let‐7 in female nervous tissue increased median fly lifespan by ~22%. We provide evidence that this lifespan extension is not due to alterations in nutrient intake or to decreased insulin signaling.
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Affiliation(s)
- Christi M. Gendron
- Department of Molecular and Integrative Physiology and the Geriatrics Center University of Michigan Ann Arbor Michigan 48109 USA
| | - Scott D. Pletcher
- Department of Molecular and Integrative Physiology and the Geriatrics Center University of Michigan Ann Arbor Michigan 48109 USA
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77
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Kato M, Kashem MA, Cheng C. An intestinal microRNA modulates the homeostatic adaptation to chronic oxidative stress in C. elegans. Aging (Albany NY) 2017; 8:1979-2005. [PMID: 27623524 PMCID: PMC5076448 DOI: 10.18632/aging.101029] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Accepted: 08/19/2016] [Indexed: 12/22/2022]
Abstract
Adaptation to an environmental or metabolic perturbation is a feature of the evolutionary process. Recent insights into microRNA function suggest that microRNAs serve as key players in a robust adaptive response against stress in animals through their capacity to fine-tune gene expression. However, it remains largely unclear how a microRNA-modulated downstream mechanism contributes to the process of homeostatic adaptation. Here we show that loss of an intestinally expressed microRNA gene, mir-60, in the nematode C. elegans promotes an adaptive response to chronic - a mild and long-term - oxidative stress exposure. The pathway involved appears to be unique since the canonical stress-responsive factors, such as DAF-16/FOXO, are dispensable for mir-60 loss to enhance oxidative stress resistance. Gene expression profiles revealed that genes encoding lysosomal proteases and those involved in xenobiotic metabolism and pathogen defense responses are up-regulated by the loss of mir-60. Detailed genetic studies and computational microRNA target prediction suggest that endocytosis components and a bZip transcription factor gene zip-10, which functions in innate immune response, are directly modulated by miR-60 in the intestine. Our findings suggest that the mir-60 loss facilitates adaptive response against chronic oxidative stress by ensuring the maintenance of cellular homeostasis.
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Affiliation(s)
- Masaomi Kato
- The Laboratory of Ageing, Centenary Institute, Camperdown, NSW 2050, Australia.,Sydney Medical School, The University of Sydney, Camperdown, NSW 2050, Australia
| | - Mohammed Abul Kashem
- The Laboratory of Ageing, Centenary Institute, Camperdown, NSW 2050, Australia.,Sydney Medical School, The University of Sydney, Camperdown, NSW 2050, Australia
| | - Chao Cheng
- Department of Biomedical Data Science, Geisel School of Medicine, Dartmouth College, Lebanon, NH 03756, USA.,Department of Molecular and Systems Biology, Geisel School of Medicine, Dartmouth College, Hanover, NH 03755, USA
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78
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Differential Expression of miRNAs in the Respiratory Tree of the Sea Cucumber Apostichopus japonicus Under Hypoxia Stress. G3-GENES GENOMES GENETICS 2017; 7:3681-3692. [PMID: 28916650 PMCID: PMC5677170 DOI: 10.1534/g3.117.1129] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The sea cucumber, an important economic species, has encountered high mortality since 2013 in northern China because of seasonal environmental stress such as hypoxia, high temperature, and low salinity. MicroRNAs (miRNAs) are important in regulating gene expression in marine organisms in response to environmental change. In this study, high-throughput sequencing was used to investigate alterations in miRNA expression in the sea cucumber under different levels of dissolved oxygen (DO). Nine small RNA libraries were constructed from the sea cucumber respiratory trees. A total of 26 differentially expressed miRNAs, including 12 upregulated and 14 downregulated miRNAs, were observed in severe hypoxia (DO 2 mg/L) compared with mild hypoxia (DO 4 mg/L) and normoxic conditions (DO 8 mg/L). Twelve differentially expressed miRNAs were clustered in severe hypoxia. In addition, real-time PCR revealed that 14 randomly selected differentially expressed miRNAs showed significantly increased expressions in severe hypoxia and the expressions of nine miRNAs, including key miRNAs such as Aja-miR-1, Aja-miR-2008, and Aja-miR-184, were consistent with the sequencing results. Moreover, gene ontology and pathway analyses of putative target genes suggest that these miRNAs are important in redox, transport, transcription, and hydrolysis under hypoxia stress. Notably, novel-miR-1, novel-miR-2, and novel-miR-3 were specifically clustered and upregulated in severe hypoxia, which may provide new insights into novel “hypoxamiR” identification. These results will provide a basis for future studies of miRNA regulation and molecular adaptive mechanisms in sea cucumbers under hypoxia stress.
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79
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Weaver BP, Han M. Tag team: Roles of miRNAs and Proteolytic Regulators in Ensuring Robust Gene Expression Dynamics. Trends Genet 2017; 34:21-29. [PMID: 29037438 DOI: 10.1016/j.tig.2017.09.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Revised: 08/17/2017] [Accepted: 09/25/2017] [Indexed: 01/18/2023]
Abstract
Lack of prominent developmental defects arising from loss of many individual miRNAs is consistent with the observations of collaborative networks between miRNAs and roles for miRNAs in regulating stress responses. However, these characteristics may only partially explain the seemingly nonessential nature of many miRNAs. Non-miRNA gene expression regulatory mechanisms also collaborate with miRNA-induced silencing complex (miRISC) to support robust gene expression dynamics. Genetic enhancer screens have revealed roles of miRNAs and other gene repressive mechanisms in development or other cellular processes that were masked by genetic redundancy. Besides discussing the breadth of the non-miRNA genes, we use LIN-28 as an example to illustrate how distinct regulatory systems, including miRNAs and multiple protein stability mechanisms, work at different levels to target expression of a given gene and provide tissue-specific and stage-specific regulation of gene expression.
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Affiliation(s)
- Benjamin P Weaver
- The Howard Hughes Medical Institute and Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO 80309, USA.
| | - Min Han
- The Howard Hughes Medical Institute and Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO 80309, USA
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80
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Guo X, Zhang X, Yang J, Jin X, Ding J, Xiang H, Ayaz M, Luo X, Zheng Y. Suppression of nemo-like kinase by miR-71 in Echinococcus multilocularis. Exp Parasitol 2017; 183:1-5. [PMID: 29037783 DOI: 10.1016/j.exppara.2017.10.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Revised: 09/20/2017] [Accepted: 10/12/2017] [Indexed: 11/24/2022]
Abstract
Echinococcus multilocularis metacestodes are a causative pathogen for alveolar echinococcosis in human beings, and have been found to express miRNAs including emu-miR-71. miR-71 is evolutionarily conserved and highly expressed across platyhelminths, but little is known about its role. Here it was shown that emu-miR-71 was differentially expressed in protoscoleces and was unlikely to be expressed in neoblasts. The results of the luciferase assay indicated that emu-miR-71 was able to bind in vitro to the 3'-UTR of emu-nlk, encoding a key regulator of cell division, causing significant downregulation of luciferase activity (p < 0.01) compared to the negative control and the construct with mutations in the binding site. Consistent with the decreased luciferase activity, transfection of emu-miR-71 mimics into protoscoleces notably repressed emu-NLK (p < 0.05). These results demonstrate the suppression of emu-nlk by emu-miR-71, potentially involved in the protoscolex development.
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Affiliation(s)
- Xiaola Guo
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, CAAS, Lanzhou 730046, China
| | - Xueyong Zhang
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, CAAS, Lanzhou 730046, China; The Academy of Animal and Veterinary Sciences, Qinghai University, Xining 810016, China
| | - Jing Yang
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, CAAS, Lanzhou 730046, China
| | - Xiaoliang Jin
- Department of Ophthalmology, Shanghai Ninth People's Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Juntao Ding
- College of Life Science and Technology, Xinjiang University, Urumqi 830046, China
| | - Haitao Xiang
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, CAAS, Lanzhou 730046, China; College of Veterinary Medicine, Gansu Agricultural University, Lanzhou 730070, China
| | - Mazhar Ayaz
- Department of Pathobiology, Faculty of Veterinary Sciences, Bahauddin Zakariya University, Multan 60800, Pakistan
| | - Xuenong Luo
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, CAAS, Lanzhou 730046, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou 225009, China.
| | - Yadong Zheng
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, CAAS, Lanzhou 730046, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou 225009, China.
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81
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Quintana JF, Babayan SA, Buck AH. Small RNAs and extracellular vesicles in filarial nematodes: From nematode development to diagnostics. Parasite Immunol 2017; 39. [PMID: 27748953 DOI: 10.1111/pim.12395] [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: 08/23/2016] [Revised: 10/08/2016] [Accepted: 10/12/2016] [Indexed: 02/06/2023]
Abstract
Parasitic nematodes have evolved sophisticated mechanisms to communicate with their hosts in order to survive and successfully establish an infection. The transfer of RNA within extracellular vesicles (EVs) has recently been described as a mechanism that could contribute to this communication in filarial nematodes. It has been shown that these EVs are loaded with several types of RNAs, including microRNAs, leading to the hypothesis that parasites could actively use these molecules to manipulate host gene expression and to the exciting prospect that these pathways could result in new diagnostic and therapeutic strategies. Here, we review the literature on the diverse RNAi pathways that operate in nematodes and more specifically our current knowledge of extracellular RNA (exRNA) and EVs derived from filarial nematodes in vitro and within their hosts. We further detail some of the issues and questions related to the capacity of RNA-mediated communication to function in parasite-host interactions and the ability of exRNA to enable us to distinguish and detect different nematode parasites in their hosts.
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Affiliation(s)
- J F Quintana
- Institute of Immunology and Infection Research and Centre for Immunity, Infection & Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - S A Babayan
- Institute of Biodiversity Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK
| | - A H Buck
- Institute of Immunology and Infection Research and Centre for Immunity, Infection & Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
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82
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Baxi K, Ghavidel A, Waddell B, Harkness TA, de Carvalho CE. Regulation of Lysosomal Function by the DAF-16 Forkhead Transcription Factor Couples Reproduction to Aging in Caenorhabditis elegans. Genetics 2017; 207:83-101. [PMID: 28696216 PMCID: PMC5586388 DOI: 10.1534/genetics.117.204222] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Accepted: 07/03/2017] [Indexed: 02/06/2023] Open
Abstract
Aging in eukaryotes is accompanied by widespread deterioration of the somatic tissue. Yet, abolishing germ cells delays the age-dependent somatic decline in Caenorhabditis elegans In adult worms lacking germ cells, the activation of the DAF-9/DAF-12 steroid signaling pathway in the gonad recruits DAF-16 activity in the intestine to promote longevity-associated phenotypes. However, the impact of this pathway on the fitness of normally reproducing animals is less clear. Here, we explore the link between progeny production and somatic aging and identify the loss of lysosomal acidity-a critical regulator of the proteolytic output of these organelles-as a novel biomarker of aging in C. elegans The increase in lysosomal pH in older worms is not a passive consequence of aging, but instead is timed with the cessation of reproduction, and correlates with the reduction in proteostasis in early adult life. Our results further implicate the steroid signaling pathway and DAF-16 in dynamically regulating lysosomal pH in the intestine of wild-type worms in response to the reproductive cycle. In the intestine of reproducing worms, DAF-16 promotes acidic lysosomes by upregulating the expression of v-ATPase genes. These findings support a model in which protein clearance in the soma is linked to reproduction in the gonad via the active regulation of lysosomal acidification.
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Affiliation(s)
- Kunal Baxi
- Department of Biology, University of Saskatchewan, Saskatoon, Saskatchewan S7N5E2, Canada
| | - Ata Ghavidel
- Department of Anatomy and Cell Biology, University of Saskatchewan, Saskatoon, Saskatchewan S7N5E2, Canada
| | - Brandon Waddell
- Department of Biology, University of Saskatchewan, Saskatoon, Saskatchewan S7N5E2, Canada
| | - Troy A Harkness
- Department of Anatomy and Cell Biology, University of Saskatchewan, Saskatoon, Saskatchewan S7N5E2, Canada
| | - Carlos E de Carvalho
- Department of Biology, University of Saskatchewan, Saskatoon, Saskatchewan S7N5E2, Canada
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83
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Sun X, Chen WD, Wang YD. DAF-16/FOXO Transcription Factor in Aging and Longevity. Front Pharmacol 2017; 8:548. [PMID: 28878670 PMCID: PMC5572328 DOI: 10.3389/fphar.2017.00548] [Citation(s) in RCA: 145] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Accepted: 08/04/2017] [Indexed: 02/01/2023] Open
Abstract
Aging is associated with age-related diseases and an increase susceptibility of cancer. Dissecting the molecular mechanisms that underlie aging and longevity would contribute to implications for preventing and treating the age-dependent diseases or cancers. Multiple signaling pathways such as the insulin/IGF-1 signaling pathway, TOR signaling, AMPK pathway, JNK pathway and germline signaling have been found to be involved in aging and longevity. And DAF-16/FOXO, as a key transcription factor, could integrate different signals from these pathways to modulate aging, and longevity via shuttling from cytoplasm to nucleus. Hence, understanding how DAF-16/FOXO functions will be pivotal to illustrate the processes of aging and longevity. Here, we summarized how DAF-16/FOXO receives signals from these pathways to affect aging and longevity. We also briefly discussed the transcriptional regulation and posttranslational modifications of DAF-16/FOXO, its co-factors as well as its potential downstream targets participating in lifespan according to the published data in C. elegans and in mammals, and in most cases, we may focus on the studies in C. elegans which has been considered to be a very good animal model for longevity research.
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Affiliation(s)
- Xiaojuan Sun
- Key Laboratory of Receptor-Mediated Gene Regulation and Drug Discovery, School of Medicine, Henan UniversityKaifeng, China
| | - Wei-Dong Chen
- Key Laboratory of Receptor-Mediated Gene Regulation and Drug Discovery, School of Medicine, Henan UniversityKaifeng, China
| | - Yan-Dong Wang
- State Key Laboratory of Chemical Resource Engineering, College of Life Science and Technology, Beijing University of Chemical TechnologyBeijing, China
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84
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Ashapkin VV, Kutueva LI, Vanyushin BF. Aging as an Epigenetic Phenomenon. Curr Genomics 2017; 18:385-407. [PMID: 29081695 PMCID: PMC5635645 DOI: 10.2174/1389202918666170412112130] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2015] [Revised: 01/17/2016] [Accepted: 02/09/2016] [Indexed: 12/22/2022] Open
Abstract
INTRODUCTION Hypermethylation of genes associated with promoter CpG islands, and hypomethylation of CpG poor genes, repeat sequences, transposable elements and intergenic genome sections occur during aging in mammals. Methylation levels of certain CpG sites display strict correlation to age and could be used as "epigenetic clock" to predict biological age. Multi-substrate deacetylases SIRT1 and SIRT6 affect aging via locus-specific modulations of chromatin structure and activity of multiple regulatory proteins involved in aging. Random errors in DNA methylation and other epigenetic marks during aging increase the transcriptional noise, and thus lead to enhanced phenotypic variation between cells of the same tissue. Such variation could cause progressive organ dysfunction observed in aged individuals. Multiple experimental data show that induction of NF-κB regulated gene sets occurs in various tissues of aged mammals. Upregulation of multiple miRNAs occurs at mid age leading to downregulation of enzymes and regulatory proteins involved in basic cellular functions, such as DNA repair, oxidative phosphorylation, intermediate metabolism, and others. CONCLUSION Strong evidence shows that all epigenetic systems contribute to the lifespan control in various organisms. Similar to other cell systems, epigenome is prone to gradual degradation due to the genome damage, stressful agents, and other aging factors. But unlike mutations and other kinds of the genome damage, age-related epigenetic changes could be fully or partially reversed to a "young" state.
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Affiliation(s)
- Vasily V Ashapkin
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Lyudmila I Kutueva
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Boris F Vanyushin
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
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85
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Arora N, Tripathi S, Singh AK, Mondal P, Mishra A, Prasad A. Micromanagement of Immune System: Role of miRNAs in Helminthic Infections. Front Microbiol 2017; 8:586. [PMID: 28450853 PMCID: PMC5390025 DOI: 10.3389/fmicb.2017.00586] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Accepted: 03/21/2017] [Indexed: 01/09/2023] Open
Abstract
Helminthic infections fall under neglected tropical diseases, although they inflict severe morbidity to human and causes major economic burden on health care system in many developing countries. There is increased effort to understand their immunopathology in recent days due to their immuno-modulatory capabilities. Immune response is primarily controlled at the transcriptional level, however, microRNA-mediated RNA interference is emerging as important regulatory machinery that works at the translation level. In the past decade, microRNA (miRNA/miR) research has advanced with significant momentum. The result is ever increasing list of curated sequences from a broad panel of organisms including helminths. Several miRNAs had been discovered from trematodes, nematodes and cestodes like let-7, miR155, miR-199, miR-134, miR-223, miR-146, and fhe-mir-125a etc., with potential role in immune modulation. These miRs had been associated with TGF-β, MAPK, Toll-like receptor, PI3K/AKT signaling pathways and insulin growth factor regulation. Thus, controlling the immune cells development, survival, proliferation and death. Apart from micromanagement of immune system, they also express certain unique miRNA also like cis-miR-001, cis-miR-2, cis-miR-6, cis-miR-10, cis-miR-18, cis-miR-19, trs-mir-0001, fhe-miR-01, fhe-miR-07, fhe-miR-08, egr-miR-4988, egr-miR-4989 etc. The specific role played by most of these species specific unique miRs are yet to be discovered. However, these newly discovered miRNAs might serve as novel targets for therapeutic intervention or biomarkers for parasitic infections.
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Affiliation(s)
- Naina Arora
- School of Basic Sciences, Indian Institute of Technology MandiMandi, India
| | - Shweta Tripathi
- School of Basic Sciences, Indian Institute of Technology MandiMandi, India
| | - Aloukick K Singh
- Department of Immunology, Weizmann Institute of ScienceRehovot, Israel
| | - Prosenjit Mondal
- School of Basic Sciences, Indian Institute of Technology MandiMandi, India
| | - Amit Mishra
- Cellular and Molecular Neurobiology Unit, Indian Institute of Technology JodhpurJodhpur, India
| | - Amit Prasad
- School of Basic Sciences, Indian Institute of Technology MandiMandi, India
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86
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Macchiaroli N, Maldonado LL, Zarowiecki M, Cucher M, Gismondi MI, Kamenetzky L, Rosenzvit MC. Genome-wide identification of microRNA targets in the neglected disease pathogens of the genus Echinococcus. Mol Biochem Parasitol 2017; 214:91-100. [PMID: 28385564 DOI: 10.1016/j.molbiopara.2017.04.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Revised: 03/30/2017] [Accepted: 04/01/2017] [Indexed: 01/01/2023]
Abstract
MicroRNAs (miRNAs), a class of small non-coding RNAs, are key regulators of gene expression at post-transcriptional level and play essential roles in biological processes such as development. MiRNAs silence target mRNAs by binding to complementary sequences in the 3'untranslated regions (3'UTRs). The parasitic helminths of the genus Echinococcus are the causative agents of echinococcosis, a zoonotic neglected disease. In previous work, we performed a comprehensive identification and characterization of Echinococcus miRNAs. However, current knowledge about their targets is limited. Since target prediction algorithms rely on complementarity between 3'UTRs and miRNA sequences, a major limitation is the lack of accurate sequence information of 3'UTR for most species including parasitic helminths. We performed RNA-seq and developed a pipeline that integrates the transcriptomic data with available genomic data of this parasite in order to identify 3'UTRs of Echinococcus canadensis. The high confidence set of 3'UTRs obtained allowed the prediction of miRNA targets in Echinococcus through a bioinformatic approach. We performed for the first time a comparative analysis of miRNA targets in Echinococcus and Taenia. We found that many evolutionarily conserved target sites in Echinococcus and Taenia may be functional and under selective pressure. Signaling pathways such as MAPK and Wnt were among the most represented pathways indicating miRNA roles in parasite growth and development. Genome-wide identification and characterization of miRNA target genes in Echinococcus provide valuable information to guide experimental studies in order to understand miRNA functions in the parasites biology. miRNAs involved in essential functions, especially those being absent in the host or showing sequence divergence with respect to host orthologs, might be considered as novel therapeutic targets for echinococcosis control.
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Affiliation(s)
- Natalia Macchiaroli
- Instituto de Investigaciones en Microbiología y Parasitología Médicas (IMPaM), Facultad de Medicina, Universidad de Buenos Aires (UBA)-Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Buenos Aires, Argentina
| | - Lucas L Maldonado
- Instituto de Investigaciones en Microbiología y Parasitología Médicas (IMPaM), Facultad de Medicina, Universidad de Buenos Aires (UBA)-Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Buenos Aires, Argentina
| | - Magdalena Zarowiecki
- Parasite Genomics Group, Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - Marcela Cucher
- Instituto de Investigaciones en Microbiología y Parasitología Médicas (IMPaM), Facultad de Medicina, Universidad de Buenos Aires (UBA)-Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Buenos Aires, Argentina
| | | | - Laura Kamenetzky
- Instituto de Investigaciones en Microbiología y Parasitología Médicas (IMPaM), Facultad de Medicina, Universidad de Buenos Aires (UBA)-Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Buenos Aires, Argentina
| | - Mara Cecilia Rosenzvit
- Instituto de Investigaciones en Microbiología y Parasitología Médicas (IMPaM), Facultad de Medicina, Universidad de Buenos Aires (UBA)-Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Buenos Aires, Argentina.
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87
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Zheng Y. High-throughput identification of miRNAs of Taenia ovis, a cestode threatening sheep industry. INFECTION GENETICS AND EVOLUTION 2017; 51:98-100. [PMID: 28342885 DOI: 10.1016/j.meegid.2017.03.023] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Revised: 03/18/2017] [Accepted: 03/21/2017] [Indexed: 01/15/2023]
Abstract
Taenia ovis is a tapeworm that is mainly transmitted between dogs and sheep or goats and has an adverse effect on sheep industry. miRNAs are short regulatory non-coding RNAs, involved in parasite development and growth as well as parasite infection. The miRNA profile of T. ovis remains to be established. Herein, 33 known miRNAs belonging to 23 different families were identified in T. ovis metacestodes using deep sequencing approach. Of them, expression of some miRNAs such as tov-miR-10 and -let-7 was absolutely predominant. Moreover, comparative analysis revealed the presence of a miR-71/2b/2c cluster in T. ovis, which was also completely conserved in other 6 cestodes. The study provides rich data for further understandings of T. ovis biology.
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Affiliation(s)
- Yadong Zheng
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, CAAS, Lanzhou 730046, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou 225009, China.
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88
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MicroRNAs miR-203-3p, miR-664-3p and miR-708-5p are associated with median strain lifespan in mice. Sci Rep 2017; 7:44620. [PMID: 28304372 PMCID: PMC5356331 DOI: 10.1038/srep44620] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Accepted: 02/10/2017] [Indexed: 02/07/2023] Open
Abstract
MicroRNAs (miRNAs) are small non-coding RNA species that have been shown to have roles in multiple processes that occur in higher eukaryotes. They act by binding to specific sequences in the 3’ untranslated region of their target genes and causing the transcripts to be degraded by the RNA-induced silencing complex (RISC). MicroRNAs have previously been reported to demonstrate altered expression in several aging phenotypes such as cellular senescence and age itself. Here, we have measured the expression levels of 521 small regulatory microRNAs (miRNAs) in spleen tissue from young and old animals of 6 mouse strains with different median strain lifespans by quantitative real-time PCR. Expression levels of 3 microRNAs were robustly associated with strain lifespan, after correction for multiple statistical testing (miR-203-3p [β-coefficient = −0.6447, p = 4.8 × 10−11], miR-664-3p [β-coefficient = 0.5552, p = 5.1 × 10−8] and miR-708-5p [β-coefficient = 0.4986, p = 1.6 × 10−6]). Pathway analysis of binding sites for these three microRNAs revealed enrichment of target genes involved in key aging and longevity pathways including mTOR, FOXO and MAPK, most of which also demonstrated associations with longevity. Our results suggests that miR-203-3p, miR-664-3p and miR-708-5p may be implicated in pathways determining lifespan in mammals.
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89
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Gillet FX, Bournaud C, Antonino de Souza Júnior JD, Grossi-de-Sa MF. Plant-parasitic nematodes: towards understanding molecular players in stress responses. ANNALS OF BOTANY 2017; 119:775-789. [PMID: 28087659 PMCID: PMC5378187 DOI: 10.1093/aob/mcw260] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Revised: 10/24/2016] [Indexed: 05/05/2023]
Abstract
BACKGROUND Plant-parasitic nematode interactions occur within a vast molecular plant immunity network. Following initial contact with the host plant roots, plant-parasitic nematodes (PPNs) activate basal immune responses. Defence priming involves the release in the apoplast of toxic molecules derived from reactive species or secondary metabolism. In turn, PPNs must overcome the poisonous and stressful environment at the plant-nematode interface. The ability of PPNs to escape this first line of plant immunity is crucial and will determine its virulence. SCOPE Nematodes trigger crucial regulatory cytoprotective mechanisms, including antioxidant and detoxification pathways. Knowledge of the upstream regulatory components that contribute to both of these pathways in PPNs remains elusive. In this review, we discuss how PPNs probably orchestrate cytoprotection to resist plant immune responses, postulating that it may be derived from ancient molecular mechanisms. The review focuses on two transcription factors, DAF-16 and SKN-1 , which are conserved in the animal kingdom and are central regulators of cell homeostasis and immune function. Both regulate the unfolding protein response and the antioxidant and detoxification pathways. DAF-16 and SKN-1 target a broad spectrum of Caenorhabditis elegans genes coding for numerous protein families present in the secretome of PPNs. Moreover, some regulatory elements of DAF-16 and SKN-1 from C. elegans have already been identified as important genes for PPN infection. CONCLUSION DAF-16 and SKN-1 genes may play a pivotal role in PPNs during parasitism. In the context of their hub status and mode of regulation, we suggest alternative strategies for control of PPNs through RNAi approaches.
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Affiliation(s)
- François-Xavier Gillet
- Embrapa Genetic Resources and Biotechnology, PqEB Final Av. W/5 Norte, CEP 70·770-900, Brasília, DF, Brazil
| | - Caroline Bournaud
- Embrapa Genetic Resources and Biotechnology, PqEB Final Av. W/5 Norte, CEP 70·770-900, Brasília, DF, Brazil
| | | | - Maria Fatima Grossi-de-Sa
- Embrapa Genetic Resources and Biotechnology, PqEB Final Av. W/5 Norte, CEP 70·770-900, Brasília, DF, Brazil
- Catholic University of Brasilia, Brasília-DF, Brazil
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90
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Pu YZ, Wan QL, Ding AJ, Luo HR, Wu GS. Quantitative proteomics analysis of Caenorhabditis elegans upon germ cell loss. J Proteomics 2017; 156:85-93. [DOI: 10.1016/j.jprot.2017.01.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Revised: 01/14/2017] [Accepted: 01/19/2017] [Indexed: 10/20/2022]
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91
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Starvation-Induced Stress Response Is Critically Impacted by Ceramide Levels in Caenorhabditis elegans. Genetics 2016; 205:775-785. [PMID: 27974500 DOI: 10.1534/genetics.116.194282] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Accepted: 12/07/2016] [Indexed: 12/24/2022] Open
Abstract
Our understanding of the cellular mechanisms by which animals regulate their response to starvation is limited, despite the strong relevance of the problem to major human health issues. The L1 diapause of Caenorhabditis elegans, where first-stage larvae arrest in response to a food-less environment, is an excellent system to study this mechanism. We found, through genetic manipulation and lipid analysis, that biosynthesis of ceramide, particularly those with longer fatty acid side chains, critically impacts animal survival during L1 diapause. Genetic interaction analysis suggests that ceramide may act in both insulin-IGF-1 signaling (IIS)-dependent and IIS-independent pathways to affect starvation survival. Genetic and expression analyses indicate that ceramide is required for maintaining the proper expression of previously characterized starvation-responsive genes, genes that are regulated by the IIS pathway and tumor suppressor Rb, and genes responsive to pathogen. These findings provide an important insight into the roles of sphingolipid metabolism, not only in starvation response, but also in aging and food-response-related human health problems.
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92
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Basika T, Macchiaroli N, Cucher M, Espínola S, Kamenetzky L, Zaha A, Rosenzvit M, Ferreira HB. Identification and profiling of microRNAs in two developmental stages of the model cestode parasite Mesocestoides corti. Mol Biochem Parasitol 2016; 210:37-49. [DOI: 10.1016/j.molbiopara.2016.08.004] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Revised: 08/15/2016] [Accepted: 08/16/2016] [Indexed: 12/21/2022]
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93
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Stage-Wise Identification and Analysis of miRNA from Root-Knot Nematode Meloidogyne incognita. Int J Mol Sci 2016; 17:ijms17101758. [PMID: 27775666 PMCID: PMC5085782 DOI: 10.3390/ijms17101758] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Revised: 10/10/2016] [Accepted: 10/13/2016] [Indexed: 12/25/2022] Open
Abstract
In this study, we investigated global changes in miRNAs of Meloidogyne incognita throughout its life cycle. Small RNA sequencing resulted in approximately 62, 38, 38, 35, and 39 Mb reads in the egg, J2, J3, J4, and female stages, respectively. Overall, we identified 2724 known and 383 novel miRNAs (read count > 10) from all stages, of which 169 known and 13 novel miRNA were common to all the five stages. Among the stage-specific miRNAs, miR-286 was highly expressed in eggs, miR-2401 in J2, miR-8 and miR-187 in J3, miR-6736 in J4, and miR-17 in the female stages. These miRNAs are reported to be involved in embryo and neural development, muscular function, and control of apoptosis. Cluster analysis indicated the presence of 91 miRNA clusters, of which 36 clusters were novel and identified in this study. Comparison of miRNA families with other nematodes showed 17 families to be commonly absent in animal parasitic nematodes and M. incognita. Validation of 43 predicted common and stage-specific miRNA by quantitative PCR (qPCR) indicated their expression in the nematode. Stage-wise exploration of M. incognita miRNAs has not been carried out before and this work presents information on common and stage-specific miRNAs of the root-knot nematode.
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94
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Williams AB, Schumacher B. DNA damage responses and stress resistance: Concepts from bacterial SOS to metazoan immunity. Mech Ageing Dev 2016; 165:27-32. [PMID: 27687175 DOI: 10.1016/j.mad.2016.09.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Revised: 09/20/2016] [Accepted: 09/25/2016] [Indexed: 11/26/2022]
Abstract
The critical need for species preservation has driven the evolution of mechanisms that integrate stress signals from both exogenous and endogenous sources. Past research has been largely focused on cell-autonomous stress responses; however, recently their systemic outcomes within an organism and their implications at the ecological and species levels have emerged. Maintenance of species depends on the high fidelity transmission of the genome over infinite generations; thus, many pathways exist to monitor and restore the integrity of the genome and to coordinate DNA repair with other cellular processes, such as cell division and growth. The specifics of these DNA damage responses (DDRs) vary vastly but some general themes are conserved from ancient organisms, such as bacteria and archaea, to humans. Despite decades of research, however, DDRs still have many layers of complexity and some surprises left to be discovered. One of the most interesting current research topics is the link between DNA damage and stress resistance: the outcomes of DDRs can protect the organism from other secondary challenges. At this time, these types of responses are best characterized in bacteria and the simple metazoan model, Caenorhabditis elegans, but it is becoming clear that similar processes also exist in higher organisms.
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Affiliation(s)
- Ashley B Williams
- Institute for Genome Stability in Ageing and Disease, Medical Faculty, University of Cologne, Joseph-Stelzmann-Str. 26, 50931 Cologne, Germany; Cologne Excellence Cluster for Cellular Stress Responses in Ageing-Associated Diseases (CECAD), Center for Molecular Medicine Cologne (CMMC) and Systems Biology of Ageing Cologne, University of Cologne, Joseph-Stelzmann-Str. 26, 50931 Cologne, Germany.
| | - Björn Schumacher
- Institute for Genome Stability in Ageing and Disease, Medical Faculty, University of Cologne, Joseph-Stelzmann-Str. 26, 50931 Cologne, Germany; Cologne Excellence Cluster for Cellular Stress Responses in Ageing-Associated Diseases (CECAD), Center for Molecular Medicine Cologne (CMMC) and Systems Biology of Ageing Cologne, University of Cologne, Joseph-Stelzmann-Str. 26, 50931 Cologne, Germany.
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95
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Zhu Z, Zhang D, Lee H, Jin Y. Caenorhabditis elegans: An important tool for dissecting microRNA functions. ACTA ACUST UNITED AC 2016; 1:34-36. [PMID: 28529981 DOI: 10.15761/bgg.1000106] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Caenorhabditis elegans (C. elegans), a member of the phylum Nematoda, carries the evolutionarily conserved genes comparing to mammals. Due to its short lifespan and completely sequenced genome, C. elegans becomes a potentially powerful model for mechanistic studies in human diseases. In this mini review, we will outline the current understandings on C. elegans as a model organism for microRNA (miRNA)-related research in the pathogenesis of human diseases.
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Affiliation(s)
- Ziwen Zhu
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Boston University, Boston, USA
| | - Duo Zhang
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Boston University, Boston, USA
| | - Heedoo Lee
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Boston University, Boston, USA
| | - Yang Jin
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Boston University, Boston, USA
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96
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Roles for ROS and hydrogen sulfide in the longevity response to germline loss in Caenorhabditis elegans. Proc Natl Acad Sci U S A 2016; 113:E2832-41. [PMID: 27140632 DOI: 10.1073/pnas.1524727113] [Citation(s) in RCA: 90] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In Caenorhabditis elegans, removing germ cells slows aging and extends life. Here we show that transcription factors that extend life and confer protection to age-related protein-aggregation toxicity are activated early in adulthood in response to a burst of reactive oxygen species (ROS) and a shift in sulfur metabolism. Germline loss triggers H2S production, mitochondrial biogenesis, and a dynamic pattern of ROS in specific somatic tissues. A cytoskeletal protein, KRI-1, plays a key role in the generation of H2S and ROS. These kri-1-dependent redox species, in turn, promote life extension by activating SKN-1/Nrf2 and the mitochondrial unfolded-protein response, respectively. Both H2S and, remarkably, kri-1-dependent ROS are required for the life extension produced by low levels of the superoxide-generator paraquat and by a mutation that inhibits respiration. Together our findings link reproductive signaling to mitochondria and define an inducible, kri-1-dependent redox-signaling module that can be invoked in different contexts to extend life and counteract proteotoxicity.
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97
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Gao X, Tyagi R, Magrini V, Ly A, Jasmer DP, Mitreva M. Compartmentalization of functions and predicted miRNA regulation among contiguous regions of the nematode intestine. RNA Biol 2016; 14:1335-1352. [PMID: 27002534 DOI: 10.1080/15476286.2016.1166333] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The intestine of parasitic nematodes has proven an important target for therapies aimed at prevention and treatment of diseases caused by these pathogens in humans, animals and plants. We have developed a unique research model with the intestine of Ascaris suum, the large round worm of swine and humans, that will enhance biological research on this tissue. To expand utility of this model, we quantitatively compared expression of 15,382 coding RNAs and 277 noncoding, micro RNAs (miRNAs) among 3 contiguous regions of the adult A. suum intestine. Differentially expressed transcripts were identified among regions, with the largest number expressed at significantly higher levels in the anterior region, identifying this region as the most functionally unique compared to middle and posterior regions. We further identified 64 exon splice variants (from 47 genes) that are differentially expressed among these regions. A total of 2,063 intestinal mRNA transcripts were predicted to be targeted by intestinal miRNA, and negative correlation coefficients for miRNA:mRNA abundances predicted 22 likely influential miRNAs and 503 likely associated miRNA:mRNA pairs. A. suum intestinal miRNAs were identified that are conserved with intestinal miRNAs from C. elegans (10 mature sequences and 13 seed sequences conserved), and prospective intestinal miRNAs from the murine gastrointestinal nematode, Heligmosomoides polygyrus (5 mature and 11 seeds). Most of the conserved intestinal miRNAs were also high abundance miRNAs. The data provide the most comprehensive compilation of constitutively and differentially expressed genes along the length of the intestine for any nematode species. The information will guide prospective development of many hypotheses on nematode intestinal functions encoded by mRNAs, miRNAs and interactions between these RNA populations.
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Affiliation(s)
- Xin Gao
- a McDonnell Genome Institute, Washington University in St. Louis , St. Louis , MO , USA
| | - Rahul Tyagi
- a McDonnell Genome Institute, Washington University in St. Louis , St. Louis , MO , USA
| | - Vincent Magrini
- a McDonnell Genome Institute, Washington University in St. Louis , St. Louis , MO , USA
| | - Amy Ly
- a McDonnell Genome Institute, Washington University in St. Louis , St. Louis , MO , USA
| | - Douglas P Jasmer
- b Department of Veterinary Microbiology and Pathology , Washington State University , Pullman , WA , USA
| | - Makedonka Mitreva
- a McDonnell Genome Institute, Washington University in St. Louis , St. Louis , MO , USA.,c Department of Internal Medicine , Washington University School of Medicine , St. Louis , MO , USA
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98
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Effects of Echinococcus multilocularis miR-71 mimics on murine macrophage RAW264.7 cells. Int Immunopharmacol 2016; 34:259-262. [PMID: 26995025 DOI: 10.1016/j.intimp.2016.03.015] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2015] [Revised: 02/02/2016] [Accepted: 03/12/2016] [Indexed: 11/21/2022]
Abstract
The microRNAs (miRNAs) are a class of small regulatory non-coding RNA that contributes to the activation of host-pathogen cross-talk during infection. In helminthes, miR-71 is highly conserved and it has recently been detected in nematode exosomes, as well as in the sera and/or fluids of infected humans and mice. However, the role of miR-71 during infection remains poorly characterized. Herein, we show that Ago1 and Ago4, which encode key components of the small RNA-induced silencing complex (RISC), were up-regulated in murine macrophage RAW264.7 cells transfected by Echinococcus multilocularis miR-71 (emu-miR-71) mimics. Using a miRNA PCR array, none of the 84 miRNAs involved in inflammation or autoimmunity were significantly up- or down-regulated in the transfected cells (p>0.05). Although it did not influence IL-10 production by the treated cells (p>0.05), the mimics significantly repressed the production of NO 12 h after treatment with LPS and IFN-γ (p<0.01), identifying another potential mechanism whereby parasites can carefully regulate host levels of NO. These findings indicate that the release of parasite-derived miR-71 into hosts can affect the functions of macrophages, and possibly represents an exciting direction for studies of the interplay between parasites and hosts.
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99
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Takeda T, Tanabe H. Lifespan and reproduction in brain-specific miR-29-knockdown mouse. Biochem Biophys Res Commun 2016; 471:454-8. [PMID: 26902119 DOI: 10.1016/j.bbrc.2016.02.055] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 02/15/2016] [Indexed: 11/18/2022]
Abstract
The microRNA miR-29 is widely distributed and highly expressed in adult mouse brain during the mouse's lifetime. We recently created conditional mutant mice whose miR-29 was brain-specifically knocked down through overexpression of an antisense RNA transgene against miR-29. To explore a role for brain miR-29 in maximizing organismal fitness, we assessed somatic growth, reproduction, and lifespan in the miR-29-knockdown (KD) mice and their wild-type (WT) littermates. The KD mice were developmentally indistinguishable from WT mice with respect to gross morphology and physical activity. Fertility testing revealed that KD males were subfertile, whereas KD females were hyperfertile, only in terms of reproductive success, when compared to their gender-matched WT correspondents. Another phenotypic difference between KD and WT animals appeared in their lifespan data; KD males displayed an overall increasing tendency in post-reproductive survival relative to WT males. In contrast, KD females were prone to shorter lifespans than WT females. These results clarify that brain-targeted miR-29 knockdown affects both lifespan and reproduction in a gender-dependent manner, and moreover that the reciprocal responsiveness to the miR-29 knockdown between these two phenotypes in both genders closely follow life-course models based on the classical trade-off prediction wherein elaborate early-life energetic investment in reproduction entails accelerated late-life declines in survival, and vice versa. Thus, this study identified miR-29 as the first mammalian miRNA that is directly implicated in the lifetime trade-off between the two major fitness components, lifespan and reproduction.
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Affiliation(s)
- Toru Takeda
- Department of Bioscience, Faculty of Agriculture, Kinki University, 3327-204 Nakamachi, Nara 631-8505, Japan
| | - Hiroyuki Tanabe
- Department of Bioscience, Faculty of Agriculture, Kinki University, 3327-204 Nakamachi, Nara 631-8505, Japan.
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100
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GÜÇLÜ DURGUN S, ÖZTÜRK AR, ATALAY A. Analysis of global microRNAome profiles of Caenorhabditis elegans oocytes and early embryos. Turk J Biol 2016. [DOI: 10.3906/biy-1602-62] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
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