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Dong Z, Wang F, Liu Y, Li Y, Yu H, Peng S, Sun T, Qu M, Sun K, Wang L, Ma Y, Chen K, Zhao J, Lin Q. Genomic and single-cell analyses reveal genetic signatures of swimming pattern and diapause strategy in jellyfish. Nat Commun 2024; 15:5936. [PMID: 39009560 PMCID: PMC11250803 DOI: 10.1038/s41467-024-49848-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 06/21/2024] [Indexed: 07/17/2024] Open
Abstract
Jellyfish exhibit innovative swimming patterns that contribute to exploring the origins of animal locomotion. However, the genetic and cellular basis of these patterns remains unclear. Herein, we generated chromosome-level genome assemblies of two jellyfish species, Turritopsis rubra and Aurelia coerulea, which exhibit straight and free-swimming patterns, respectively. We observe positive selection of numerous genes involved in statolith formation, hair cell ciliogenesis, ciliary motility, and motor neuron function. The lineage-specific absence of otolith morphogenesis- and ciliary movement-related genes in T. rubra may be associated with homeostatic structural statocyst loss and straight swimming pattern. Notably, single-cell transcriptomic analyses covering key developmental stages reveal the enrichment of diapause-related genes in the cyst during reverse development, suggesting that the sustained diapause state favours the development of new polyps under favourable conditions. This study highlights the complex relationship between genetics, locomotion patterns and survival strategies in jellyfish, thereby providing valuable insights into the evolutionary lineages of movement and adaptation in the animal kingdom.
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Affiliation(s)
- Zhijun Dong
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, Shandong, 264003, China.
- University of Chinese Academy of Sciences, Beijing, 100101, China.
| | - Fanghan Wang
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, Shandong, 264003, China
- University of Chinese Academy of Sciences, Beijing, 100101, China
| | - Yali Liu
- University of Chinese Academy of Sciences, Beijing, 100101, China
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
- Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
| | - Yongxue Li
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, Shandong, 264003, China
- University of Chinese Academy of Sciences, Beijing, 100101, China
| | - Haiyan Yu
- College of the Environment and Ecology, Xiamen University, Xiamen, 361102, China
| | - Saijun Peng
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, Shandong, 264003, China
- University of Chinese Academy of Sciences, Beijing, 100101, China
| | - Tingting Sun
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, Shandong, 264003, China
- University of Chinese Academy of Sciences, Beijing, 100101, China
| | - Meng Qu
- University of Chinese Academy of Sciences, Beijing, 100101, China
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
- Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
| | - Ke Sun
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan, 650500, China
| | - Lei Wang
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, Shandong, 264003, China
- University of Chinese Academy of Sciences, Beijing, 100101, China
| | - Yuanqing Ma
- Shandong Key Laboratory of Marine Ecological Restoration, Shandong Marine Resource and Environment Research Institute, Yantai, Shandong, 264006, China
| | - Kai Chen
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan, 650500, China
| | - Jianmin Zhao
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, Shandong, 264003, China.
- University of Chinese Academy of Sciences, Beijing, 100101, China.
| | - Qiang Lin
- University of Chinese Academy of Sciences, Beijing, 100101, China.
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China.
- Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China.
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2
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Frydrychová RČ, Konopová B, Peska V, Brejcha M, Sábová M. Telomeres and telomerase: active but complex players in life-history decisions. Biogerontology 2024; 25:205-226. [PMID: 37610666 DOI: 10.1007/s10522-023-10060-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 08/01/2023] [Indexed: 08/24/2023]
Abstract
Studies on human telomeres have established that telomeres exert a significant influence on lifespan and health of organisms. However, recent research has indicated that the original idea that telomeres affect lifespan in a universal and central manner across all eukaryotic species is an oversimplification. Indeed, findings from a variety of animal species revealed that the role of telomere biology in aging is more subtle and intricate than previously recognized. Here, we show how telomere biology varies depending on the taxon. We also show how telomere biology corresponds to basic life history traits and affects the life table of a species and investments in growth, body size, reproduction, and lifespan; telomeres are hypothesized to shape evolutionary perspectives for species in an active but complex manner. Our evaluation is based on telomere biology data from many examples from throughout the animal kingdom that vary according to the degree of organismal complexity and life history strategies.
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Affiliation(s)
- Radmila Čapková Frydrychová
- Institute of Entomology, Biology Centre of the Czech Academy of Sciences, Branišovská 31, 370 05, Ceske Budejovice, Czech Republic.
- Faculty of Science, University of South Bohemia, Branišovská 1760, 370 05, Ceske Budejovice, Czech Republic.
| | - Barbora Konopová
- Institute of Entomology, Biology Centre of the Czech Academy of Sciences, Branišovská 31, 370 05, Ceske Budejovice, Czech Republic
| | - Vratislav Peska
- Department of Cell Biology and Radiobiology, Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 00, Brno, Czech Republic
| | - Miloslav Brejcha
- Institute of Entomology, Biology Centre of the Czech Academy of Sciences, Branišovská 31, 370 05, Ceske Budejovice, Czech Republic
- Faculty of Science, University of South Bohemia, Branišovská 1760, 370 05, Ceske Budejovice, Czech Republic
| | - Michala Sábová
- Institute of Entomology, Biology Centre of the Czech Academy of Sciences, Branišovská 31, 370 05, Ceske Budejovice, Czech Republic
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3
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Rahman SU, Qadeer A, Wu Z. Role and Potential Mechanisms of Nicotinamide Mononucleotide in Aging. Aging Dis 2024; 15:565-583. [PMID: 37548938 PMCID: PMC10917541 DOI: 10.14336/ad.2023.0519-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 05/19/2023] [Indexed: 08/08/2023] Open
Abstract
Nicotinamide adenine dinucleotide (NAD+) has recently attracted much attention due to its role in aging and lifespan extension. NAD+ directly and indirectly affects many cellular processes, including metabolic pathways, DNA repair, and immune cell activities. These mechanisms are critical for maintaining cellular homeostasis. However, the decline in NAD+ levels with aging impairs tissue function, which has been associated with several age-related diseases. In fact, the aging population has been steadily increasing worldwide, and it is important to restore NAD+ levels and reverse or delay these age-related disorders. Therefore, there is an increasing demand for healthy products that can mitigate aging, extend lifespan, and halt age-related consequences. In this case, several studies in humans and animals have targeted NAD+ metabolism with NAD+ intermediates. Among them, nicotinamide mononucleotide (NMN), a precursor in the biosynthesis of NAD+, has recently received much attention from the scientific community for its anti-aging properties. In model organisms, ingestion of NMN has been shown to improve age-related diseases and probably delay death. Here, we review aspects of NMN biosynthesis and the mechanism of its absorption, as well as potential anti-aging mechanisms of NMN, including recent preclinical and clinical tests, adverse effects, limitations, and perceived challenges.
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Affiliation(s)
- Sajid Ur Rahman
- Department of Food Science and Engineering, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Abdul Qadeer
- Institute for Infectious Diseases and Vaccine Development, Tongji University School of Medicine, Shanghai, 200072, China.
| | - Ziyun Wu
- Department of Food Science and Engineering, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China.
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Shilovsky GA, Putyatina TS, Markov AV. Evolution of Longevity in Tetrapods: Safety Is More Important than Metabolism Level. BIOCHEMISTRY. BIOKHIMIIA 2024; 89:322-340. [PMID: 38622099 DOI: 10.1134/s0006297924020111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Revised: 12/04/2023] [Accepted: 12/29/2023] [Indexed: 04/17/2024]
Abstract
Various environmental morphological and behavioral factors can determine the longevity of representatives of various taxa. Long-lived species develop systems aimed at increasing organism stability, defense, and, ultimately, lifespan. Long-lived species to a different extent manifest the factors favoring longevity (gerontological success), such as body size, slow metabolism, activity of body's repair and antioxidant defense systems, resistance to toxic substances and tumorigenesis, and presence of neotenic features. In continuation of our studies of mammals, we investigated the characteristics that distinguish long-lived ectotherms (crocodiles and turtles) and compared them with those of other ectotherms (squamates and amphibians) and endotherms (birds and mammals). We also discussed mathematical indicators used to assess the predisposition to longevity in different species, including standard indicators (mortality rate, maximum lifespan, coefficient of variation of lifespan) and their derivatives. Evolutionary patterns of aging are further explained by the protective phenotypes and life history strategies. We assessed the relationship between the lifespan and various studied factors, such as body size and temperature, encephalization, protection of occupied ecological niches, presence of protective structures (for example, shells and osteoderms), and environmental temperature, and the influence of these factors on the variation of the lifespan as a statistical parameter. Our studies did not confirm the hypothesis on the metabolism level and temperature as the most decisive factors of longevity. It was found that animals protected by shells (e.g., turtles with their exceptional longevity) live longer than species that have poison or lack such protective adaptations. The improvement of defense against external threats in long-lived ectotherms is consistent with the characteristics of long-lived endotherms (for example, naked mole-rats that live in underground tunnels, or bats and birds, whose ability to fly is one of the best defense mechanisms).
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Affiliation(s)
- Gregory A Shilovsky
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia.
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
- Institute for Information Transmission Problems (Kharkevich Institute), Russian Academy of Sciences, Moscow, 127051, Russia
| | - Tatyana S Putyatina
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
| | - Alexander V Markov
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
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5
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Tartiere AG, Freije JMP, López-Otín C. The hallmarks of aging as a conceptual framework for health and longevity research. FRONTIERS IN AGING 2024; 5:1334261. [PMID: 38292053 PMCID: PMC10824251 DOI: 10.3389/fragi.2024.1334261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 01/03/2024] [Indexed: 02/01/2024]
Abstract
The inexorability of the aging process has sparked the curiosity of human beings since ancient times. However, despite this interest and the extraordinary scientific advances in the field, the complexity of the process has hampered its comprehension. In this context, The Hallmarks of Aging were defined in 2013 with the aim of establishing an organized, systematic and integrative view of this topic, which would serve as a conceptual framework for aging research. Ten years later and promoted by the progress in the area, an updated version included three new hallmarks while maintaining the original scope. The aim of this review is to determine to what extent The Hallmarks of Aging achieved the purpose that gave rise to them. For this aim, we have reviewed the literature citing any of the two versions of The Hallmarks of Aging and conclude that they have served as a conceptual framework not only for aging research but also for related areas of knowledge. Finally, this review discusses the new candidates to become part of the Hallmarks list, analyzing the evidence that supports whether they should or should not be incorporated.
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Affiliation(s)
- Antonio G. Tartiere
- Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Oncología (IUOPA), Universidad de Oviedo, Oviedo, Spain
| | - José M. P. Freije
- Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Oncología (IUOPA), Universidad de Oviedo, Oviedo, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - Carlos López-Otín
- Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Oncología (IUOPA), Universidad de Oviedo, Oviedo, Spain
- Facultad de Ciencias de la Vida y la Naturaleza, Universidad Nebrija, Madrid, Spain
- Centre de Recherche des Cordeliers, Universite de Paris Cite, Sorbonne Universite, INSERM, Paris, France
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Bonuccelli G, Brooks DR, Shepherd S, Sotgia F, Lisanti MP. Antibiotics that target mitochondria extend lifespan in C. elegans. Aging (Albany NY) 2023; 15:11764-11781. [PMID: 37950722 PMCID: PMC10683609 DOI: 10.18632/aging.205229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 09/25/2023] [Indexed: 11/13/2023]
Abstract
Aging is a continuous degenerative process caused by a progressive decline of cell and tissue functions in an organism. It is induced by the accumulation of damage that affects normal cellular processes, ultimately leading to cell death. It has been speculated for many years that mitochondria play a key role in the aging process. In the aim of characterizing the implications of mitochondria in aging, here we used Caenorhabditis elegans (C. elegans) as an organismal model treated a panel of mitochondrial inhibitors and assessed for survival. In our study, we assessed survival by evaluating worm lifespan, and we assessed aging markers by evaluating the pharyngeal muscle contraction, the accumulation of lipofuscin pigment and ATP levels. Our results show that treatment of worms with either doxycycline, azithromycin (inhibitors of the small and the large mitochondrial ribosomes, respectively), or a combination of both, significantly extended median lifespan of C. elegans, enhanced their pharyngeal pumping rate, reduced their lipofuscin content and their energy consumption (ATP levels), as compared to control untreated worms, suggesting an aging-abrogating effect for these drugs. Similarly, DPI, an inhibitor of mitochondrial complex I and II, was capable of prolonging the median lifespan of treated worms. On the other hand, subjecting worms to vitamin C, a pro-oxidant, failed to extend C. elegans lifespan and upregulated its energy consumption, revealing an increase in ATP level. Therefore, our longevity study reveals that mitochondrial inhibitors (i.e., mitochondria-targeting antibiotics) could abrogate aging and extend lifespan in C. elegans.
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Affiliation(s)
- Gloria Bonuccelli
- Translational Medicine, School of Science, Engineering and Environment (SEE), University of Salford, Greater Manchester M5 4BR, UK
| | - Darren R. Brooks
- Translational Medicine, School of Science, Engineering and Environment (SEE), University of Salford, Greater Manchester M5 4BR, UK
| | - Sally Shepherd
- Translational Medicine, School of Science, Engineering and Environment (SEE), University of Salford, Greater Manchester M5 4BR, UK
| | - Federica Sotgia
- Translational Medicine, School of Science, Engineering and Environment (SEE), University of Salford, Greater Manchester M5 4BR, UK
| | - Michael P. Lisanti
- Translational Medicine, School of Science, Engineering and Environment (SEE), University of Salford, Greater Manchester M5 4BR, UK
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7
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Li S, Vazquez JM, Sudmant PH. The evolution of aging and lifespan. Trends Genet 2023; 39:830-843. [PMID: 37714733 PMCID: PMC11147682 DOI: 10.1016/j.tig.2023.08.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 08/18/2023] [Accepted: 08/21/2023] [Indexed: 09/17/2023]
Abstract
Aging is a nearly inescapable trait among organisms yet lifespan varies tremendously across different species and spans several orders of magnitude in vertebrates alone. This vast phenotypic diversity is driven by distinct evolutionary trajectories and tradeoffs that are reflected in patterns of diversification and constraint in organismal genomes. Age-specific impacts of selection also shape allele frequencies in populations, thus impacting disease susceptibility and environment-specific mortality risk. Further, the mutational processes that spawn this genetic diversity in both germline and somatic cells are strongly influenced by age and life history. We discuss recent advances in our understanding of the evolution of aging and lifespan at organismal, population, and cellular scales, and highlight outstanding questions that remain unanswered.
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Affiliation(s)
- Stacy Li
- Department of Integrative Biology, University of California, Berkeley, CA, USA; Center for Computational Biology, University of California, Berkeley, CA. USA
| | - Juan Manuel Vazquez
- Department of Integrative Biology, University of California, Berkeley, CA, USA
| | - Peter H Sudmant
- Department of Integrative Biology, University of California, Berkeley, CA, USA; Center for Computational Biology, University of California, Berkeley, CA. USA.
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8
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López-Gil L, Pascual-Ahuir A, Proft M. Genomic Instability and Epigenetic Changes during Aging. Int J Mol Sci 2023; 24:14279. [PMID: 37762580 PMCID: PMC10531692 DOI: 10.3390/ijms241814279] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 09/15/2023] [Accepted: 09/18/2023] [Indexed: 09/29/2023] Open
Abstract
Aging is considered the deterioration of physiological functions along with an increased mortality rate. This scientific review focuses on the central importance of genomic instability during the aging process, encompassing a range of cellular and molecular changes that occur with advancing age. In particular, this revision addresses the genetic and epigenetic alterations that contribute to genomic instability, such as telomere shortening, DNA damage accumulation, and decreased DNA repair capacity. Furthermore, the review explores the epigenetic changes that occur with aging, including modifications to histones, DNA methylation patterns, and the role of non-coding RNAs. Finally, the review discusses the organization of chromatin and its contribution to genomic instability, including heterochromatin loss, chromatin remodeling, and changes in nucleosome and histone abundance. In conclusion, this review highlights the fundamental role that genomic instability plays in the aging process and underscores the need for continued research into these complex biological mechanisms.
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Affiliation(s)
- Lucía López-Gil
- Department of Biotechnology, Instituto de Biología Molecular y Celular de Plantas, Universitat Politècnica de València, Ingeniero Fausto Elio s/n, 46022 Valencia, Spain;
- Department of Molecular and Cellular Pathology and Therapy, Instituto de Biomedicina de Valencia IBV-CSIC, Consejo Superior de Investigaciones Científicas CSIC, Jaime Roig 11, 46010 Valencia, Spain
| | - Amparo Pascual-Ahuir
- Department of Biotechnology, Instituto de Biología Molecular y Celular de Plantas, Universitat Politècnica de València, Ingeniero Fausto Elio s/n, 46022 Valencia, Spain;
| | - Markus Proft
- Department of Molecular and Cellular Pathology and Therapy, Instituto de Biomedicina de Valencia IBV-CSIC, Consejo Superior de Investigaciones Científicas CSIC, Jaime Roig 11, 46010 Valencia, Spain
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Martinez-Banaclocha MA. Targeting the Cysteine Redox Proteome in Parkinson's Disease: The Role of Glutathione Precursors and Beyond. Antioxidants (Basel) 2023; 12:1373. [PMID: 37507913 PMCID: PMC10376658 DOI: 10.3390/antiox12071373] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Revised: 06/22/2023] [Accepted: 06/28/2023] [Indexed: 07/30/2023] Open
Abstract
Encouraging recent data on the molecular pathways underlying aging have identified variants and expansions of genes associated with DNA replication and repair, telomere and stem cell maintenance, regulation of the redox microenvironment, and intercellular communication. In addition, cell rejuvenation requires silencing some transcription factors and the activation of pluripotency, indicating that hidden molecular networks must integrate and synchronize all these cellular mechanisms. Therefore, in addition to gene sequence expansions and variations associated with senescence, the optimization of transcriptional regulation and protein crosstalk is essential. The protein cysteinome is crucial in cellular regulation and plays unexpected roles in the aging of complex organisms, which show cumulative somatic mutations, telomere attrition, epigenetic modifications, and oxidative dysregulation, culminating in cellular senescence. The cysteine thiol groups are highly redox-active, allowing high functional versatility as structural disulfides, redox-active disulfides, active-site nucleophiles, proton donors, and metal ligands to participate in multiple regulatory sites in proteins. Also, antioxidant systems control diverse cellular functions, including the transcription machinery, which partially depends on the catalytically active cysteines that can reduce disulfide bonds in numerous target proteins, driving their biological integration. Since we have previously proposed a fundamental role of cysteine-mediated redox deregulation in neurodegeneration, we suggest that cellular rejuvenation of the cysteine redox proteome using GSH precursors, like N-acetyl-cysteine, is an underestimated multitarget therapeutic approach that would be particularly beneficial in Parkinson's disease.
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10
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López-Martínez J, Álvarez-Tello FJ, Porchas-Cornejo MA, Nevárez-López CA, Muhlia-Almazán A, Urías-Padilla KV. Multiple reproduction forms in the polyps of the cannonball jellyfish Stomolophus sp. 2: Probable life-cycle reversal. JOURNAL OF EXPERIMENTAL ZOOLOGY. PART A, ECOLOGICAL AND INTEGRATIVE PHYSIOLOGY 2023; 339:239-252. [PMID: 36470843 DOI: 10.1002/jez.2673] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 10/17/2022] [Accepted: 10/27/2022] [Indexed: 12/12/2022]
Abstract
The jellyfish genera Stomolophus spp. is one of the most abundant in the Pacific Ocean, yet it has not been thoroughly studied. Until recently, research has been developed and directed to its knowledge because of the economic interest in its exploitation. The genus Stomolophus in the Pacific Ocean is composed of five species (S. agaricus, S. chunii, S. collaris, S. fritillaria, and S. meleagris), and Stomolophus sp. 2 has been recently reported in the central part of the Gulf of California. Therefore, this study aimed to describe in vivo the different developmental stages of Stomolophus sp. 2 life cycle. As a result, multiple polyp reproduction forms were described, such as polyp-stolon formation, polydisc strobilation with more than 20 ephyrae formed by each strobila, and polyp formation directly from juvenile ephyra. In the degenerating phase, the polyps turned into cysts induced by stress conditions, such as changes in temperature, oxygen, and food availability. The life cycle of Stomolophus sp. 2 can be distinguished from that of S. meleagris by showing various asexual reproduction mechanisms and polydisc-like strobilation. The formation of polyps directly from the ectoderm of degenerating juvenile medusae suggests the possibility of a reversion cycle. Because of the different life cycles between S. meleagris and S. sp. 2, in addition to their morphological and genetic differences, this study proposes that Stomolophus sp. 2 should be considered a new species and suggests the name Stomolophus yaquilli, in reference to the indigenous community that lives in the species distribution area.
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Affiliation(s)
| | | | | | | | - Adriana Muhlia-Almazán
- Centro de Investigación en Alimentos y Desarrollo, A. C. (CIAD) Unidad Hermosillo, Carretera Gustavo Enrique Astiazarán Rosas, Sonora, Mexico
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11
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Jones RG, Dimet-Wiley A, Haghani A, da Silva FM, Brightwell CR, Lim S, Khadgi S, Wen Y, Dungan CM, Brooke RT, Greene NP, Peterson CA, McCarthy JJ, Horvath S, Watowich SJ, Fry CS, Murach KA. A molecular signature defining exercise adaptation with ageing and in vivo partial reprogramming in skeletal muscle. J Physiol 2023; 601:763-782. [PMID: 36533424 PMCID: PMC9987218 DOI: 10.1113/jp283836] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022] Open
Abstract
Exercise promotes functional improvements in aged tissues, but the extent to which it simulates partial molecular reprogramming is unknown. Using transcriptome profiling from (1) a skeletal muscle-specific in vivo Oct3/4, Klf4, Sox2 and Myc (OKSM) reprogramming-factor expression murine model; (2) an in vivo inducible muscle-specific Myc induction murine model; (3) a translatable high-volume hypertrophic exercise training approach in aged mice; and (4) human exercise muscle biopsies, we collectively defined exercise-induced genes that are common to partial reprogramming. Late-life exercise training lowered murine DNA methylation age according to several contemporary muscle-specific clocks. A comparison of the murine soleus transcriptome after late-life exercise training to the soleus transcriptome after OKSM induction revealed an overlapping signature that included higher JunB and Sun1. Also, within this signature, downregulation of specific mitochondrial and muscle-enriched genes was conserved in skeletal muscle of long-term exercise-trained humans; among these was muscle-specific Abra/Stars. Myc is the OKSM factor most induced by exercise in muscle and was elevated following exercise training in aged mice. A pulse of MYC rewired the global soleus muscle methylome, and the transcriptome after a MYC pulse partially recapitulated OKSM induction. A common signature also emerged in the murine MYC-controlled and exercise adaptation transcriptomes, including lower muscle-specific Melusin and reactive oxygen species-associated Romo1. With Myc, OKSM and exercise training in mice, as well habitual exercise in humans, the complex I accessory subunit Ndufb11 was lower; low Ndufb11 is linked to longevity in rodents. Collectively, exercise shares similarities with genetic in vivo partial reprogramming. KEY POINTS: Advances in the last decade related to cellular epigenetic reprogramming (e.g. DNA methylome remodelling) toward a pluripotent state via the Yamanaka transcription factors Oct3/4, Klf4, Sox2 and Myc (OKSM) provide a window into potential mechanisms for combatting the deleterious effects of cellular ageing. Using global gene expression analysis, we compared the effects of in vivo OKSM-mediated partial reprogramming in skeletal muscle fibres of mice to the effects of late-life murine exercise training in muscle. Myc is the Yamanaka factor most induced by exercise in skeletal muscle, and so we compared the MYC-controlled transcriptome in muscle to Yamanaka factor-mediated and exercise adaptation mRNA landscapes in mice and humans. A single pulse of MYC is sufficient to remodel the muscle methylome. We identify partial reprogramming-associated genes that are innately altered by exercise training and conserved in humans, and propose that MYC contributes to some of these responses.
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Affiliation(s)
- Ronald G. Jones
- University of Arkansas, Exercise Science Research Center, Department of Health, Human Performance, and Recreation, Fayetteville, AR, USA
| | | | - Amin Haghani
- University of California Los Angeles, Department of Human Genetics, Los Angeles, CA, USA
- Altos Labs, San Diego, CA, USA
| | - Francielly Morena da Silva
- University of Arkansas, Exercise Science Research Center, Department of Health, Human Performance, and Recreation, Fayetteville, AR, USA
- University of Arkansas, Cachexia Research Laboratory, Department of Health, Human Performance, and Recreation, Fayetteville, AR, USA
| | - Camille R. Brightwell
- University of Kentucky Center for Muscle Biology, Lexington, KY, USA
- University of Kentucky, Department of Athletic Training and Clinical Nutrition, Lexington, KY, USA
| | - Seongkyun Lim
- University of Arkansas, Exercise Science Research Center, Department of Health, Human Performance, and Recreation, Fayetteville, AR, USA
- University of Arkansas, Cachexia Research Laboratory, Department of Health, Human Performance, and Recreation, Fayetteville, AR, USA
| | - Sabin Khadgi
- University of Arkansas, Exercise Science Research Center, Department of Health, Human Performance, and Recreation, Fayetteville, AR, USA
| | - Yuan Wen
- University of Kentucky Center for Muscle Biology, Lexington, KY, USA
- University of Kentucky, Department of Physical Therapy, Lexington, KY, USA
| | - Cory M. Dungan
- University of Kentucky Center for Muscle Biology, Lexington, KY, USA
- University of Kentucky, Department of Physical Therapy, Lexington, KY, USA
| | | | - Nicholas P. Greene
- University of Arkansas, Exercise Science Research Center, Department of Health, Human Performance, and Recreation, Fayetteville, AR, USA
- University of Arkansas, Cachexia Research Laboratory, Department of Health, Human Performance, and Recreation, Fayetteville, AR, USA
- University of Arkansas, Cell and Molecular Biology Graduate Program, Fayetteville, AR, USA
| | - Charlotte A. Peterson
- University of Kentucky Center for Muscle Biology, Lexington, KY, USA
- University of Kentucky, Department of Physical Therapy, Lexington, KY, USA
- University of Kentucky, Department of Physiology, Lexington, KY, USA
| | - John J. McCarthy
- Altos Labs, San Diego, CA, USA
- University of Kentucky, Department of Physiology, Lexington, KY, USA
| | - Steve Horvath
- University of California Los Angeles, Department of Human Genetics, Los Angeles, CA, USA
- Altos Labs, San Diego, CA, USA
| | - Stanley J. Watowich
- Ridgeline Therapeutics, Houston, TX, USA
- University of Texas Medical Branch, Department of Biochemistry and Molecular Biology, Galveston, TX, USA
| | - Christopher S. Fry
- University of Kentucky Center for Muscle Biology, Lexington, KY, USA
- University of Kentucky, Department of Athletic Training and Clinical Nutrition, Lexington, KY, USA
| | - Kevin A. Murach
- University of Arkansas, Exercise Science Research Center, Department of Health, Human Performance, and Recreation, Fayetteville, AR, USA
- University of Arkansas, Cell and Molecular Biology Graduate Program, Fayetteville, AR, USA
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12
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Hasegawa Y, Watanabe T, Otsuka R, Toné S, Kubota S, Hirakawa H. Genome assembly and transcriptomic analyses of the repeatedly rejuvenating jellyfish Turritopsis dohrnii. DNA Res 2022; 30:6909006. [PMID: 36519838 PMCID: PMC9835754 DOI: 10.1093/dnares/dsac047] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Revised: 11/16/2022] [Accepted: 11/24/2022] [Indexed: 12/23/2022] Open
Abstract
Only two hydromedusan species, Turritopsis dohrnii and T. sp., have exhibited experimental multiple-repeat life cycle reversion in the laboratory, which can be artificially induced by various means such as incubation with CsCl, heat shock, and mechanical damage with needles. In the present study, we constructed a genome assembly of T. dohrnii using Pacific Biosciences long-reads and Illumina short-reads, for which the genome DNA was extracted from 1,500 young medusae originated from a single clone. The total length of the draft genome sequence of T. dohrnii was 435.9 Mb (N50 length 747.2 kb). We identified 23,314 high-confidence genes and found the characteristics of RNA expression amongst developmental stages. Our genome assembly and transcriptome data provide a key model system resource that will be useful for understanding cyclical rejuvenation.
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Affiliation(s)
- Yoshinori Hasegawa
- To whom correspondence should be addressed. Tel: +81 438 52 3944. Fax: +81 438 52 3921. (Y.H); Tel: +81 438 52 3906. Fax: +81 438 52 3924. (H.H)
| | - Takashi Watanabe
- Department of Applied Genomics, Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan
| | - Reo Otsuka
- Graduate School of Science and Engineering, Tokyo Denki University, Hatoyama, Saitama 350-0394, Japan
| | - Shigenobu Toné
- Graduate School of Science and Engineering, Tokyo Denki University, Hatoyama, Saitama 350-0394, Japan
| | - Shin Kubota
- Turritopsis Immortal Jellyfish Regenerative Biological Research/Experience Laboratory, Arita, Wakayama 643-0002, Japan
| | - Hideki Hirakawa
- To whom correspondence should be addressed. Tel: +81 438 52 3944. Fax: +81 438 52 3921. (Y.H); Tel: +81 438 52 3906. Fax: +81 438 52 3924. (H.H)
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13
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Abstract
'Age reprogramming' refers to the process by which the molecular and cellular pathways of a cell that are subject to age-related decline are rejuvenated without passage through an embryonic stage. This process differs from the rejuvenation observed in differentiated derivatives of induced pluripotent stem cells, which involves passage through an embryonic stage and loss of cellular identity. Accordingly, the study of age reprogramming can provide an understanding of how ageing can be reversed while retaining cellular identity and the specialised function(s) of a cell, which will be of benefit to regenerative medicine. Here, we highlight recent work that has provided a more nuanced understanding of age reprogramming and point to some open questions in the field that might be explored in the future.
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Affiliation(s)
- Prim B. Singh
- Department of Medicine, Nazarbayev University School of Medicine, 5/1 Kerei Zhanibek Khandar Street, Astana 010000, Republic of Kazakhstan,Author for correspondence ()
| | - Assem Zhakupova
- Department of Medicine, Nazarbayev University School of Medicine, 5/1 Kerei Zhanibek Khandar Street, Astana 010000, Republic of Kazakhstan
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14
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A set of common buccal CpGs that predict epigenetic age and associate with lifespan-regulating genes. iScience 2022; 25:105304. [PMID: 36304118 PMCID: PMC9593711 DOI: 10.1016/j.isci.2022.105304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 08/11/2022] [Accepted: 10/02/2022] [Indexed: 11/23/2022] Open
Abstract
Epigenetic aging clocks are computational models that use DNA methylation sites to predict age. Since cheek swabs are non-invasive and painless, collecting DNA from buccal tissue is highly desirable. Here, we review 11 existing clocks that have been applied to buccal tissue. Two of these were exclusively trained on adults and, while moderately accurate, have not been used to capture health-relevant differences in epigenetic age. Using 130 common CpGs utilized by two or more existing buccal clocks, we generate a proof-of-concept predictor in an adult methylomic dataset. In addition to accurately estimating age (r = 0.95 and mean absolute error = 3.88 years), this clock predicted that Down syndrome subjects were significantly older relative to controls. A literature and database review of CpG-associated genes identified numerous genes (e.g., CLOCK, ELOVL2, and VGF) and molecules (e.g., alpha-linolenic acid, glycine, and spermidine) reported to influence lifespan and/or age-related disease in model organisms. 130 CpGs have been used by two or more aging clocks applied to human buccal tissue Common CpG genes are linked to the adaptive immune system and telomere maintenance Common CpGs can be used to build a novel, proof-of-concept epigenetic aging clock Several compounds associated with common CpG genes regulate lifespan in animals
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