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Saha P, Ajgaonkar S, Maniar D, Sahare S, Mehta D, Nair S. Current insights into transcriptional role(s) for the nutraceutical Withania somnifera in inflammation and aging. Front Nutr 2024; 11:1370951. [PMID: 38765810 PMCID: PMC11099240 DOI: 10.3389/fnut.2024.1370951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Accepted: 04/15/2024] [Indexed: 05/22/2024] Open
Abstract
The health-beneficial effects of nutraceuticals in various diseases have received enhanced attention in recent years. Aging is a continuous process wherein physiological activity of an individual declines over time and is characterized by various indefinite hallmarks which contribute toward aging-related comorbidities in an individual which include many neurodegenerative diseases, cardiac problems, diabetes, bone-degeneration, and cancer. Cellular senescence is a homeostatic biological process that has an important function in driving aging. Currently, a growing body of evidence substantiates the connection between epigenetic modifications and the aging process, along with aging-related diseases. These modifications are now being recognized as promising targets for emerging therapeutic interventions. Considering that almost all the biological processes are modulated by RNAs, numerous RNA-binding proteins have been found to be linked to aging and age-related complexities. Currently, studies have shed light on the ability of the nutraceutical Withania somnifera (Ashwagandha) to influence RNA expression, stability, and processing, offering insights into its mechanisms of action. By targeting RNA-related pathways, Withania somnifera may exhibit promising effects in ameliorating age-associated molecular changes, which include modifications in gene expression and signaling networks. This review summarizes the potential role of Withania somnifera as a nutraceutical in modulating RNA-level changes associated with aging, encompassing both in vitro and in vivo studies. Taken together, the putative role(s) of Withania in modulation of key RNAs will provide insights into understanding the aging process and facilitate the development of various preventive and therapeutic strategies employing nutraceuticals for healthy aging.
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Affiliation(s)
- Praful Saha
- PhytoVeda Pvt. Ltd., Mumbai, India
- Viridis Biopharma Pvt. Ltd., Mumbai, India
| | - Saiprasad Ajgaonkar
- PhytoVeda Pvt. Ltd., Mumbai, India
- Viridis Biopharma Pvt. Ltd., Mumbai, India
| | - Dishant Maniar
- PhytoVeda Pvt. Ltd., Mumbai, India
- Viridis Biopharma Pvt. Ltd., Mumbai, India
| | - Simran Sahare
- PhytoVeda Pvt. Ltd., Mumbai, India
- Viridis Biopharma Pvt. Ltd., Mumbai, India
| | - Dilip Mehta
- PhytoVeda Pvt. Ltd., Mumbai, India
- Viridis Biopharma Pvt. Ltd., Mumbai, India
| | - Sujit Nair
- PhytoVeda Pvt. Ltd., Mumbai, India
- Viridis Biopharma Pvt. Ltd., Mumbai, India
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Enkhbaatar T, Skoneczny M, Stępień K, Mołoń M, Skoneczna A. Live while the DNA lasts. The role of autophagy in DNA loss and survival of diploid yeast cells during chronological aging. Aging (Albany NY) 2023; 15:9965-9983. [PMID: 37815879 PMCID: PMC10599738 DOI: 10.18632/aging.205102] [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: 06/13/2023] [Accepted: 09/06/2023] [Indexed: 10/12/2023]
Abstract
Aging is inevitable and affects all cell types, thus yeast cells are often used as a model in aging studies. There are two approaches to studying aging in yeast: replicative aging, which describes the proliferative potential of cells, and chronological aging, which is used for studying post-mitotic cells. While analyzing the chronological lifespan (CLS) of diploid Saccharomyces cerevisiae cells, we discovered a remarkable phenomenon: ploidy reduction during aging progression. To uncover the mechanism behind this unusual process we used yeast strains undergoing a CLS assay, looking for various aging parameters. Cell mortality, regrowth ability, autophagy induction and cellular DNA content measurements indicated that during the CLS assay, dying cells lost their DNA, and only diploids survived. We demonstrated that autophagy was responsible for the gradual loss of DNA. The nucleophagy marker activation at the start of the CLS experiment correlated with the significant drop in cell viability. The activation of piecemeal microautophagy of nucleus (PMN) markers appeared to accompany the chronological aging process until the end. Our findings emphasize the significance of maintaining at least one intact copy of the genome for the survival of post-mitotic diploid cells. During chronological aging, cellular components, including DNA, are exposed to increasing stress, leading to DNA damage and fragmentation in aging cells. We propose that PMN-dependent clearance of damaged DNA from the nucleus helps prevent genome rearrangements. However, as long as one copy of the genome can be rebuilt, cells can still survive.
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Affiliation(s)
- Tuguldur Enkhbaatar
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw 02-106, Poland
| | - Marek Skoneczny
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw 02-106, Poland
| | - Karolina Stępień
- Institute of Medical Sciences, Rzeszów University, Rzeszów 35-959, Poland
| | - Mateusz Mołoń
- Institute of Biology, Rzeszów University, Rzeszów 35-601, Poland
| | - Adrianna Skoneczna
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw 02-106, Poland
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3
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Emerson FJ, Lee SS. Chromatin: the old and young of it. Front Mol Biosci 2023; 10:1270285. [PMID: 37877123 PMCID: PMC10591336 DOI: 10.3389/fmolb.2023.1270285] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 09/20/2023] [Indexed: 10/26/2023] Open
Abstract
Aging affects nearly all aspects of our cells, from our DNA to our proteins to how our cells handle stress and communicate with each other. Age-related chromatin changes are of particular interest because chromatin can dynamically respond to the cellular and organismal environment, and many modifications at chromatin are reversible. Changes at chromatin occur during aging, and evidence from model organisms suggests that chromatin factors could play a role in modulating the aging process itself, as altering proteins that work at chromatin often affect the lifespan of yeast, worms, flies, and mice. The field of chromatin and aging is rapidly expanding, and high-resolution genomics tools make it possible to survey the chromatin environment or track chromatin factors implicated in longevity with precision that was not previously possible. In this review, we discuss the state of chromatin and aging research. We include examples from yeast, Drosophila, mice, and humans, but we particularly focus on the commonly used aging model, the worm Caenorhabditis elegans, in which there are many examples of chromatin factors that modulate longevity. We include evidence of both age-related changes to chromatin and evidence of specific chromatin factors linked to longevity in core histones, nuclear architecture, chromatin remodeling, and histone modifications.
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Affiliation(s)
| | - Siu Sylvia Lee
- Lee Lab, Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, United States
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Regulation of ribosomal RNA gene copy number, transcription and nucleolus organization in eukaryotes. Nat Rev Mol Cell Biol 2023; 24:414-429. [PMID: 36732602 DOI: 10.1038/s41580-022-00573-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/14/2022] [Indexed: 02/04/2023]
Abstract
One of the first biological machineries to be created seems to have been the ribosome. Since then, organisms have dedicated great efforts to optimize this apparatus. The ribosomal RNA (rRNA) contained within ribosomes is crucial for protein synthesis and maintenance of cellular function in all known organisms. In eukaryotic cells, rRNA is produced from ribosomal DNA clusters of tandem rRNA genes, whose organization in the nucleolus, maintenance and transcription are strictly regulated to satisfy the substantial demand for rRNA required for ribosome biogenesis. Recent studies have elucidated mechanisms underlying the integrity of ribosomal DNA and regulation of its transcription, including epigenetic mechanisms and a unique recombination and copy-number control system to stably maintain high rRNA gene copy number. In this Review, we disucss how the crucial maintenance of rRNA gene copy number through control of gene amplification and of rRNA production by RNA polymerase I are orchestrated. We also discuss how liquid-liquid phase separation controls the architecture and function of the nucleolus and the relationship between rRNA production, cell senescence and disease.
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Paxman J, Zhou Z, O'Laughlin R, Liu Y, Li Y, Tian W, Su H, Jiang Y, Holness SE, Stasiowski E, Tsimring LS, Pillus L, Hasty J, Hao N. Age-dependent aggregation of ribosomal RNA-binding proteins links deterioration in chromatin stability with challenges to proteostasis. eLife 2022; 11:e75978. [PMID: 36194205 PMCID: PMC9578700 DOI: 10.7554/elife.75978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 10/03/2022] [Indexed: 11/13/2022] Open
Abstract
Chromatin instability and protein homeostasis (proteostasis) stress are two well-established hallmarks of aging, which have been considered largely independent of each other. Using microfluidics and single-cell imaging approaches, we observed that, during the replicative aging of Saccharomyces cerevisiae, a challenge to proteostasis occurs specifically in the fraction of cells with decreased stability within the ribosomal DNA (rDNA). A screen of 170 yeast RNA-binding proteins identified ribosomal RNA (rRNA)-binding proteins as the most enriched group that aggregate upon a decrease in rDNA stability induced by inhibition of a conserved lysine deacetylase Sir2. Further, loss of rDNA stability induces age-dependent aggregation of rRNA-binding proteins through aberrant overproduction of rRNAs. These aggregates contribute to age-induced proteostasis decline and limit cellular lifespan. Our findings reveal a mechanism underlying the interconnection between chromatin instability and proteostasis stress and highlight the importance of cell-to-cell variability in aging processes.
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Affiliation(s)
- Julie Paxman
- Department of Molecular Biology, Division of Biological Sciences, University of California, San DiegoLa JollaUnited States
| | - Zhen Zhou
- Department of Molecular Biology, Division of Biological Sciences, University of California, San DiegoLa JollaUnited States
| | - Richard O'Laughlin
- Department of Bioengineering, University of California, San DiegoLa JollaUnited States
| | - Yuting Liu
- Department of Molecular Biology, Division of Biological Sciences, University of California, San DiegoLa JollaUnited States
| | - Yang Li
- Department of Molecular Biology, Division of Biological Sciences, University of California, San DiegoLa JollaUnited States
| | - Wanying Tian
- Department of Molecular Biology, Division of Biological Sciences, University of California, San DiegoLa JollaUnited States
| | - Hetian Su
- Department of Molecular Biology, Division of Biological Sciences, University of California, San DiegoLa JollaUnited States
| | - Yanfei Jiang
- Department of Molecular Biology, Division of Biological Sciences, University of California, San DiegoLa JollaUnited States
| | - Shayna E Holness
- Department of Chemistry and Biochemistry, University of California, San DiegoLa JollaUnited States
| | - Elizabeth Stasiowski
- Department of Bioengineering, University of California, San DiegoLa JollaUnited States
| | - Lev S Tsimring
- Synthetic Biology Institute, University of California, San DiegoLa JollaUnited States
| | - Lorraine Pillus
- Department of Molecular Biology, Division of Biological Sciences, University of California, San DiegoLa JollaUnited States
- UCSD Moores Cancer Center, University of California San, DiegoLa JollaUnited States
| | - Jeff Hasty
- Department of Molecular Biology, Division of Biological Sciences, University of California, San DiegoLa JollaUnited States
- Department of Bioengineering, University of California, San DiegoLa JollaUnited States
- Synthetic Biology Institute, University of California, San DiegoLa JollaUnited States
| | - Nan Hao
- Department of Molecular Biology, Division of Biological Sciences, University of California, San DiegoLa JollaUnited States
- Department of Bioengineering, University of California, San DiegoLa JollaUnited States
- Synthetic Biology Institute, University of California, San DiegoLa JollaUnited States
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6
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Abstract
Genome instability causes cellular senescence in many organisms. The rRNA gene cluster (rDNA) is one of the most unstable regions in the genome and this instability might convey a signal that induces senescence in the budding yeast. The instability of rDNA mostly depends on replication fork blocking (RFB) activity which induces recombination and gene amplification. By overexpression of Fob1, responsible for the RFB activity, we found that unstable rDNA induces cell cycle arrest and restricts replicative life span. We isolated yeast mutants that grew normally while Fob1 was overexpressed, expecting that some of the mutated genes would be related to the production of a “senescence signal” that elongates cell cycle, stops cell division and finally restricts replicative life span. Our screen identified three suppressor genes, RPS12, UBC4, and CCR4. Replicative life spans of the rps12 and ubc4 mutants were longer than that of wild-type cells. An increase in the levels of extrachromosomal rDNA circles and noncoding transcripts, known to shorten replicative life span, was observed in ubc4 and rps12 respectively, while DNA double strand-breaks at the RFB that are triggers of rDNA instability were reduced in the rps12 mutant. Overall, our observations indicate that Rps12 and Ubc4 contribute to the connection between rDNA instability and replicative life span.
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Grosfeld EV, Bidiuk VA, Mitkevich OV, Ghazy ESMO, Kushnirov VV, Alexandrov AI. A Systematic Survey of Characteristic Features of Yeast Cell Death Triggered by External Factors. J Fungi (Basel) 2021; 7:886. [PMID: 34829175 PMCID: PMC8626022 DOI: 10.3390/jof7110886] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 10/15/2021] [Accepted: 10/17/2021] [Indexed: 12/20/2022] Open
Abstract
Cell death in response to distinct stimuli can manifest different morphological traits. It also depends on various cell death signaling pathways, extensively characterized in higher eukaryotes but less so in microorganisms. The study of cell death in yeast, and specifically Saccharomyces cerevisiae, can potentially be productive for understanding cell death, since numerous killing stimuli have been characterized for this organism. Here, we systematized the literature on external treatments that kill yeast, and which contains at least minimal data on cell death mechanisms. Data from 707 papers from the 7000 obtained using keyword searches were used to create a reference table for filtering types of cell death according to commonly assayed parameters. This table provides a resource for orientation within the literature; however, it also highlights that the common view of similarity between non-necrotic death in yeast and apoptosis in mammals has not provided sufficient progress to create a clear classification of cell death types. Differences in experimental setups also prevent direct comparison between different stimuli. Thus, side-by-side comparisons of various cell death-inducing stimuli under comparable conditions using existing and novel markers that can differentiate between types of cell death seem like a promising direction for future studies.
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Affiliation(s)
- Erika V. Grosfeld
- Moscow Institute of Physics and Technology, 9 Institutskiy per, Dolgoprudny, 141700 Moscow, Russia;
- Federal Research Center of Biotechnology of the RAS, Bach Institute of Biochemistry, 119071 Moscow, Russia; (V.A.B.); (O.V.M.); (E.S.M.O.G.); (V.V.K.)
| | - Victoria A. Bidiuk
- Federal Research Center of Biotechnology of the RAS, Bach Institute of Biochemistry, 119071 Moscow, Russia; (V.A.B.); (O.V.M.); (E.S.M.O.G.); (V.V.K.)
| | - Olga V. Mitkevich
- Federal Research Center of Biotechnology of the RAS, Bach Institute of Biochemistry, 119071 Moscow, Russia; (V.A.B.); (O.V.M.); (E.S.M.O.G.); (V.V.K.)
| | - Eslam S. M. O. Ghazy
- Federal Research Center of Biotechnology of the RAS, Bach Institute of Biochemistry, 119071 Moscow, Russia; (V.A.B.); (O.V.M.); (E.S.M.O.G.); (V.V.K.)
- Institute of Biochemical Technology and Nanotechnology, Peoples’ Friendship University of Russia (RUDN), 6 Miklukho-Maklaya Street, 117198 Moscow, Russia
- Department of Microbiology, Faculty of Pharmacy, Tanta University, Tanta 31111, Egypt
| | - Vitaliy V. Kushnirov
- Federal Research Center of Biotechnology of the RAS, Bach Institute of Biochemistry, 119071 Moscow, Russia; (V.A.B.); (O.V.M.); (E.S.M.O.G.); (V.V.K.)
| | - Alexander I. Alexandrov
- Federal Research Center of Biotechnology of the RAS, Bach Institute of Biochemistry, 119071 Moscow, Russia; (V.A.B.); (O.V.M.); (E.S.M.O.G.); (V.V.K.)
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8
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Lee MB, Kiflezghi MG, Tsuchiya M, Wasko B, Carr DT, Uppal PA, Grayden KA, Elala YC, Nguyen TA, Wang J, Ragosti P, Nguyen S, Zhao YT, Kim D, Thon S, Sinha I, Tang TT, Tran NHB, Tran THB, Moore MD, Li MAK, Rodriguez K, Promislow DEL, Kaeberlein M. Pterocarpus marsupium extract extends replicative lifespan in budding yeast. GeroScience 2021; 43:2595-2609. [PMID: 34297314 PMCID: PMC8599564 DOI: 10.1007/s11357-021-00418-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 07/05/2021] [Indexed: 02/02/2023] Open
Abstract
As the molecular mechanisms of biological aging become better understood, there is growing interest in identifying interventions that target those mechanisms to promote extended health and longevity. The budding yeast Saccharomyces cerevisiae has served as a premier model organism for identifying genetic and molecular factors that modulate cellular aging and is a powerful system in which to evaluate candidate longevity interventions. Here we screened a collection of natural products and natural product mixtures for effects on the growth rate, mTOR-mediated growth inhibition, and replicative lifespan. No mTOR inhibitory activity was detected, but several of the treatments affected growth rate and lifespan. The strongest lifespan shortening effects were observed for green tea extract and berberine. The most robust lifespan extension was detected from an extract of Pterocarpus marsupium and another mixture containing Pterocarpus marsupium extract. These findings illustrate the utility of the yeast system for longevity intervention discovery and identify Pterocarpus marsupium extract as a potentially fruitful longevity intervention for testing in higher eukaryotes.
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Affiliation(s)
- Mitchell B. Lee
- Department of Laboratory Medicine and Pathology, School of Medicine, University of Washington, Box 357470, Seattle, WA 98195-7470 USA
| | - Michael G. Kiflezghi
- Department of Laboratory Medicine and Pathology, School of Medicine, University of Washington, Box 357470, Seattle, WA 98195-7470 USA
| | - Mitsuhiro Tsuchiya
- Department of Laboratory Medicine and Pathology, School of Medicine, University of Washington, Box 357470, Seattle, WA 98195-7470 USA
| | - Brian Wasko
- Department of Laboratory Medicine and Pathology, School of Medicine, University of Washington, Box 357470, Seattle, WA 98195-7470 USA ,Department of Biology and Biotechnology, University of Houston-Clear Lake, Houston, TX USA
| | - Daniel T. Carr
- Department of Laboratory Medicine and Pathology, School of Medicine, University of Washington, Box 357470, Seattle, WA 98195-7470 USA
| | - Priya A. Uppal
- Department of Laboratory Medicine and Pathology, School of Medicine, University of Washington, Box 357470, Seattle, WA 98195-7470 USA
| | - Katherine A. Grayden
- Department of Laboratory Medicine and Pathology, School of Medicine, University of Washington, Box 357470, Seattle, WA 98195-7470 USA
| | - Yordanos C. Elala
- Department of Laboratory Medicine and Pathology, School of Medicine, University of Washington, Box 357470, Seattle, WA 98195-7470 USA
| | - Tu Anh Nguyen
- Department of Laboratory Medicine and Pathology, School of Medicine, University of Washington, Box 357470, Seattle, WA 98195-7470 USA
| | - Jesse Wang
- Department of Laboratory Medicine and Pathology, School of Medicine, University of Washington, Box 357470, Seattle, WA 98195-7470 USA
| | - Priya Ragosti
- Department of Laboratory Medicine and Pathology, School of Medicine, University of Washington, Box 357470, Seattle, WA 98195-7470 USA
| | - Sunny Nguyen
- Department of Laboratory Medicine and Pathology, School of Medicine, University of Washington, Box 357470, Seattle, WA 98195-7470 USA
| | - Yan Ting Zhao
- Department of Laboratory Medicine and Pathology, School of Medicine, University of Washington, Box 357470, Seattle, WA 98195-7470 USA ,Department of Oral Health Sciences, School of Dentistry, University of Washington, Seattle, WA USA
| | - Deborah Kim
- Department of Laboratory Medicine and Pathology, School of Medicine, University of Washington, Box 357470, Seattle, WA 98195-7470 USA
| | - Socheata Thon
- Department of Laboratory Medicine and Pathology, School of Medicine, University of Washington, Box 357470, Seattle, WA 98195-7470 USA
| | - Irika Sinha
- Department of Laboratory Medicine and Pathology, School of Medicine, University of Washington, Box 357470, Seattle, WA 98195-7470 USA
| | - Thao T. Tang
- Department of Laboratory Medicine and Pathology, School of Medicine, University of Washington, Box 357470, Seattle, WA 98195-7470 USA
| | - Ngoc H. B. Tran
- Department of Laboratory Medicine and Pathology, School of Medicine, University of Washington, Box 357470, Seattle, WA 98195-7470 USA
| | - Thu H. B. Tran
- Department of Laboratory Medicine and Pathology, School of Medicine, University of Washington, Box 357470, Seattle, WA 98195-7470 USA
| | - Margarete D. Moore
- Department of Laboratory Medicine and Pathology, School of Medicine, University of Washington, Box 357470, Seattle, WA 98195-7470 USA
| | - Mary Ann K. Li
- Department of Laboratory Medicine and Pathology, School of Medicine, University of Washington, Box 357470, Seattle, WA 98195-7470 USA
| | - Karl Rodriguez
- Department of Cell Systems and Anatomy, University of Texas Health Sciences Center, San Antonio, TX USA ,Sam and Ann Barshop Center for Longevity and Aging Studies, University of Texas Health Science Center, San Antonio, TX USA
| | - Daniel E. L. Promislow
- Department of Laboratory Medicine and Pathology, School of Medicine, University of Washington, Box 357470, Seattle, WA 98195-7470 USA ,Department of Biology, University of Washington, Seattle, WA USA
| | - Matt Kaeberlein
- Department of Laboratory Medicine and Pathology, School of Medicine, University of Washington, Box 357470, Seattle, WA 98195-7470 USA
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Feng MW, Adams PD. A new mechanistic insight into fate decisions during yeast cell aging process. Mech Ageing Dev 2021; 198:111542. [PMID: 34273382 DOI: 10.1016/j.mad.2021.111542] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 07/08/2021] [Indexed: 10/20/2022]
Abstract
Despite massive technological advances in mammalian models in recent years, studies in yeast still have the power to inform on the basic mechanisms of aging. Illustrating this, in Nan Hao's recent article published in the journal Science, he and his lab use microfluidics and fluorescent imaging technology to analyze the dynamics and interactions of aging mechanisms within yeast cells. They focused in on the Sir2 gene and the heme activator protein and, through the manipulation of these two molecular aging pathways, were able to determine that yeast cells can undergo one of three modes of aging, with one of them having a significantly longer lifespan than the others. These findings provide unexpected insights into mechanisms of aging, apparently as regulated fate-decision process, and open up avenues for future research.
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Affiliation(s)
- Morgan W Feng
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, 92037, United States
| | - Peter D Adams
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, 92037, United States.
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10
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Yu R, Cao X, Sun L, Zhu JY, Wasko BM, Liu W, Crutcher E, Liu H, Jo MC, Qin L, Kaeberlein M, Han Z, Dang W. Inactivating histone deacetylase HDA promotes longevity by mobilizing trehalose metabolism. Nat Commun 2021; 12:1981. [PMID: 33790287 PMCID: PMC8012573 DOI: 10.1038/s41467-021-22257-2] [Citation(s) in RCA: 21] [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: 08/26/2020] [Accepted: 03/02/2021] [Indexed: 02/01/2023] Open
Abstract
Histone acetylations are important epigenetic markers for transcriptional activation in response to metabolic changes and various stresses. Using the high-throughput SEquencing-Based Yeast replicative Lifespan screen method and the yeast knockout collection, we demonstrate that the HDA complex, a class-II histone deacetylase (HDAC), regulates aging through its target of acetylated H3K18 at storage carbohydrate genes. We find that, in addition to longer lifespan, disruption of HDA results in resistance to DNA damage and osmotic stresses. We show that these effects are due to increased promoter H3K18 acetylation and transcriptional activation in the trehalose metabolic pathway in the absence of HDA. Furthermore, we determine that the longevity effect of HDA is independent of the Cyc8-Tup1 repressor complex known to interact with HDA and coordinate transcriptional repression. Silencing the HDA homologs in C. elegans and Drosophila increases their lifespan and delays aging-associated physical declines in adult flies. Hence, we demonstrate that this HDAC controls an evolutionarily conserved longevity pathway.
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Affiliation(s)
- Ruofan Yu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX, USA
| | - Xiaohua Cao
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX, USA
| | - Luyang Sun
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX, USA
| | - Jun-Yi Zhu
- Center for Precision Disease Modeling, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Brian M Wasko
- Department of Pathology, University of Washington, Seattle, WA, USA
- University of Houston, Clear Lake, TX, USA
| | - Wei Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX, USA
| | - Emeline Crutcher
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX, USA
| | - Haiying Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX, USA
| | | | - Lidong Qin
- Department of Nanomedicine, Houston Methodist Research Institute, Houston, TX, USA
| | - Matt Kaeberlein
- Department of Pathology, University of Washington, Seattle, WA, USA
| | - Zhe Han
- Center for Precision Disease Modeling, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Weiwei Dang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX, USA.
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11
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Amani J, Gorjizadeh N, Younesi S, Najafi M, Ashrafi AM, Irian S, Gorjizadeh N, Azizian K. Cyclin-dependent kinase inhibitors (CDKIs) and the DNA damage response: The link between signaling pathways and cancer. DNA Repair (Amst) 2021; 102:103103. [PMID: 33812232 DOI: 10.1016/j.dnarep.2021.103103] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Accepted: 03/16/2021] [Indexed: 02/08/2023]
Abstract
At the cellular level, DNA repair mechanisms are crucial in maintaining both genomic integrity and stability. DNA damage appears to be a central culprit in tumor onset and progression. Cyclin-dependent kinases (CDKs) and their regulatory partners coordinate the cell cycle progression. Aberrant CDK activity has been linked to a variety of cancers through deregulation of cell-cycle control. Besides DNA damaging agents and chromosome instability (CIN), disruptions in the levels of cell cycle regulators including cyclin-dependent kinase inhibitors (CDKIs) would result in unscheduled proliferation and cell division. The INK4 and Cip/Kip (CDK interacting protein/kinase inhibitor protein) family of CDKI proteins are involved in cell cycle regulation, transcription regulation, apoptosis, and cell migration. A thorough understanding of how these CDKIs regulate the DNA damage response through multiple signaling pathways may provide an opportunity to design efficient treatment strategies to inhibit carcinogenesis.
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Affiliation(s)
- Jafar Amani
- Applied Microbiology Research Center, System Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Nassim Gorjizadeh
- Cellular and Molecular Biology Research Center, Health Research Institute, Babol University of Medical Sciences, Babol, Iran
| | - Simin Younesi
- School of Health and Biomedical Sciences, RMIT University, Melbourne, Vic., Australia
| | - Mojtaba Najafi
- Department of Genetics, Faculty of Animal Sciences, Gorgan University of Agricultural Sciences and Natural Resources, Golestan, Iran
| | - Arash M Ashrafi
- Cellular and Molecular Biology Research Center, Health Research Institute, Babol University of Medical Sciences, Babol, Iran
| | - Saeed Irian
- Department of Cell and Molecular Biology, Faculty of Biological Sciences, Kharazmi University, Tehran, Iran
| | - Negar Gorjizadeh
- Cellular and Molecular Biology Research Center, Health Research Institute, Babol University of Medical Sciences, Babol, Iran; Department of Cell and Molecular Biology, Faculty of Biological Sciences, Kharazmi University, Tehran, Iran.
| | - Khalil Azizian
- Department of Clinical Microbiology, Sirjan School of Medical Sciences, Sirjan, Iran.
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12
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Li J, Rinnerthaler M, Hartl J, Weber M, Karl T, Breitenbach-Koller H, Mülleder M, Vowinckel J, Marx H, Sauer M, Mattanovich D, Ata Ö, De S, Greslehner GP, Geltinger F, Burhans B, Grant C, Doronina V, Ralser M, Streubel MK, Grabner C, Jarolim S, Moßhammer C, Gourlay CW, Hasek J, Cullen PJ, Liti G, Ralser M, Breitenbach M. Slow Growth and Increased Spontaneous Mutation Frequency in Respiratory Deficient afo1- Yeast Suppressed by a Dominant Mutation in ATP3. G3 (BETHESDA, MD.) 2020; 10:4637-4648. [PMID: 33093184 PMCID: PMC7718765 DOI: 10.1534/g3.120.401537] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 10/19/2020] [Indexed: 12/26/2022]
Abstract
A yeast deletion mutation in the nuclear-encoded gene, AFO1, which codes for a mitochondrial ribosomal protein, led to slow growth on glucose, the inability to grow on glycerol or ethanol, and loss of mitochondrial DNA and respiration. We noticed that afo1- yeast readily obtains secondary mutations that suppress aspects of this phenotype, including its growth defect. We characterized and identified a dominant missense suppressor mutation in the ATP3 gene. Comparing isogenic slowly growing rho-zero and rapidly growing suppressed afo1- strains under carefully controlled fermentation conditions showed that energy charge was not significantly different between strains and was not causal for the observed growth properties. Surprisingly, in a wild-type background, the dominant suppressor allele of ATP3 still allowed respiratory growth but increased the petite frequency. Similarly, a slow-growing respiratory deficient afo1- strain displayed an about twofold increase in spontaneous frequency of point mutations (comparable to the rho-zero strain) while the suppressed strain showed mutation frequency comparable to the respiratory-competent WT strain. We conclude, that phenotypes that result from afo1- are mostly explained by rapidly emerging mutations that compensate for the slow growth that typically follows respiratory deficiency.
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Affiliation(s)
- Jing Li
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
- Universite Cote d'Azur, CNRS, Inserm, IRCAN, Nice, France
| | | | - Johannes Hartl
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, 80 Tennis Court Rd, Cambridge CB2 1GA, UK
- Department of Biochemistry, Charité University Medicine, Berlin Germany
| | - Manuela Weber
- Department of Biosciences, University of Salzburg, Austria
| | - Thomas Karl
- Department of Biosciences, University of Salzburg, Austria
| | | | - Michael Mülleder
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, 80 Tennis Court Rd, Cambridge CB2 1GA, UK
- Department of Biochemistry, Charité University Medicine, Berlin Germany
- The Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, 1Midland Rd, London NW1 1AT, UK
| | - Jakob Vowinckel
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, 80 Tennis Court Rd, Cambridge CB2 1GA, UK
- Biognosys AG, Wagistrasse 21, 8952 Schlieren, Switzerland
| | - Hans Marx
- Institute of Microbiology and Microbial Biotechnology, Department of Biotechnology, University of Natural Resources and Life Sciences, Muthgasse 18, A-1190 Vienna, Austria
| | - Michael Sauer
- Institute of Microbiology and Microbial Biotechnology, Department of Biotechnology, University of Natural Resources and Life Sciences, Muthgasse 18, A-1190 Vienna, Austria
| | - Diethard Mattanovich
- Institute of Microbiology and Microbial Biotechnology, Department of Biotechnology, University of Natural Resources and Life Sciences, Muthgasse 18, A-1190 Vienna, Austria
- ACIB GmbH, Austrian Centre of Industrial Biotechnology, Muthgasse 11, A-1190 Vienna, Austria
| | - Özge Ata
- Institute of Microbiology and Microbial Biotechnology, Department of Biotechnology, University of Natural Resources and Life Sciences, Muthgasse 18, A-1190 Vienna, Austria
- ACIB GmbH, Austrian Centre of Industrial Biotechnology, Muthgasse 11, A-1190 Vienna, Austria
| | - Sonakshi De
- Institute of Microbiology and Microbial Biotechnology, Department of Biotechnology, University of Natural Resources and Life Sciences, Muthgasse 18, A-1190 Vienna, Austria
- ACIB GmbH, Austrian Centre of Industrial Biotechnology, Muthgasse 11, A-1190 Vienna, Austria
| | | | | | - Bill Burhans
- Department of Molecular and Cellular Biology, Roswell Park Cancer Institute, Buffalo, New York
| | - Chris Grant
- Faculty of Biology, Medicine, and Health, University of Manchester, Manchester M13 9PT, UK
| | | | - Meryem Ralser
- The Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, 1Midland Rd, London NW1 1AT, UK
| | | | | | | | | | - Campbell W Gourlay
- Department of Biosciences, University of Kent, Canterbury Kent CT2 7NJ, United Kingdom
| | - Jiri Hasek
- Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, Prague 4 142 20, Czech Republic
| | - Paul J Cullen
- Department of Biological Sciences, University at Buffalo, NY 14260
| | - Gianni Liti
- Institute for Research on Cancer and Ageing of Nice (IRCAN), CNRS, INSERM, Université Côte d'Azur, 06107 NICE, France
| | - Markus Ralser
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, 80 Tennis Court Rd, Cambridge CB2 1GA, UK
- Department of Biochemistry, Charité University Medicine, Berlin Germany
- The Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, 1Midland Rd, London NW1 1AT, UK
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13
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Mouton SN, Thaller DJ, Crane MM, Rempel IL, Terpstra OT, Steen A, Kaeberlein M, Lusk CP, Boersma AJ, Veenhoff LM. A physicochemical perspective of aging from single-cell analysis of pH, macromolecular and organellar crowding in yeast. eLife 2020; 9:e54707. [PMID: 32990592 PMCID: PMC7556870 DOI: 10.7554/elife.54707] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 09/28/2020] [Indexed: 01/03/2023] Open
Abstract
Cellular aging is a multifactorial process that is characterized by a decline in homeostatic capacity, best described at the molecular level. Physicochemical properties such as pH and macromolecular crowding are essential to all molecular processes in cells and require maintenance. Whether a drift in physicochemical properties contributes to the overall decline of homeostasis in aging is not known. Here, we show that the cytosol of yeast cells acidifies modestly in early aging and sharply after senescence. Using a macromolecular crowding sensor optimized for long-term FRET measurements, we show that crowding is rather stable and that the stability of crowding is a stronger predictor for lifespan than the absolute crowding levels. Additionally, in aged cells, we observe drastic changes in organellar volume, leading to crowding on the micrometer scale, which we term organellar crowding. Our measurements provide an initial framework of physicochemical parameters of replicatively aged yeast cells.
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Affiliation(s)
- Sara N Mouton
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center GroningenGroningenNetherlands
| | - David J Thaller
- Department of Cell Biology, Yale School of MedicineNew HavenUnited States
| | - Matthew M Crane
- Department of Pathology, School of Medicine, University of WashingtonSeattleUnited States
| | - Irina L Rempel
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center GroningenGroningenNetherlands
| | - Owen T Terpstra
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center GroningenGroningenNetherlands
| | - Anton Steen
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center GroningenGroningenNetherlands
| | - Matt Kaeberlein
- Department of Pathology, School of Medicine, University of WashingtonSeattleUnited States
| | - C Patrick Lusk
- Department of Cell Biology, Yale School of MedicineNew HavenUnited States
| | | | - Liesbeth M Veenhoff
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center GroningenGroningenNetherlands
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14
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Yan Y, Guo G, Huang J, Gao M, Zhu Q, Zeng S, Gong Z, Xu Z. Current understanding of extrachromosomal circular DNA in cancer pathogenesis and therapeutic resistance. J Hematol Oncol 2020; 13:124. [PMID: 32928268 PMCID: PMC7491193 DOI: 10.1186/s13045-020-00960-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 09/03/2020] [Indexed: 02/08/2023] Open
Abstract
Extrachromosomal circular DNA was recently found to be particularly abundant in multiple human cancer cells, although its frequency varies among different tumor types. Elevated levels of extrachromosomal circular DNA have been considered an effective biomarker of cancer pathogenesis. Multiple reports have demonstrated that the amplification of oncogenes and therapeutic resistance genes located on extrachromosomal DNA is a frequent event that drives intratumoral genetic heterogeneity and provides a potential evolutionary advantage. This review highlights the current understanding of the extrachromosomal circular DNA present in the tissues and circulation of patients with advanced cancers and provides a detailed discussion of their substantial roles in tumor regulation. Confirming the presence of cancer-related extrachromosomal circular DNA would provide a putative testing strategy for the precision diagnosis and treatment of human malignancies in clinical practice.
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Affiliation(s)
- Yuanliang Yan
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China.,Department of Oncology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Guijie Guo
- Department of Oncology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Jinzhou Huang
- Department of Oncology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Ming Gao
- Department of Oncology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Qian Zhu
- Department of Oncology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Shuangshuang Zeng
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Zhicheng Gong
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Zhijie Xu
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China. .,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China.
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15
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Li Y, Jiang Y, Paxman J, O'Laughlin R, Klepin S, Zhu Y, Pillus L, Tsimring LS, Hasty J, Hao N. A programmable fate decision landscape underlies single-cell aging in yeast. Science 2020; 369:325-329. [PMID: 32675375 DOI: 10.1126/science.aax9552] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 01/24/2020] [Accepted: 05/13/2020] [Indexed: 12/12/2022]
Abstract
Chromatin instability and mitochondrial decline are conserved processes that contribute to cellular aging. Although both processes have been explored individually in the context of their distinct signaling pathways, the mechanism that determines which process dominates during aging of individual cells is unknown. We show that interactions between the chromatin silencing and mitochondrial pathways lead to an epigenetic landscape of yeast replicative aging with multiple equilibrium states that represent different types of terminal states of aging. The structure of the landscape drives single-cell differentiation toward one of these states during aging, whereby the fate is determined quite early and is insensitive to intracellular noise. Guided by a quantitative model of the aging landscape, we genetically engineered a long-lived equilibrium state characterized by an extended life span.
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Affiliation(s)
- Yang Li
- Section of Molecular Biology, Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Yanfei Jiang
- Section of Molecular Biology, Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Julie Paxman
- Section of Molecular Biology, Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Richard O'Laughlin
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA
| | - Stephen Klepin
- Section of Molecular Biology, Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Yuelian Zhu
- Section of Molecular Biology, Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Lorraine Pillus
- Section of Molecular Biology, Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA.,UCSD Moores Cancer Center, University of California San Diego, La Jolla, CA 92093, USA
| | - Lev S Tsimring
- BioCircuits Institute, University of California San Diego, La Jolla, CA 92093, USA
| | - Jeff Hasty
- Section of Molecular Biology, Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA.,Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA.,BioCircuits Institute, University of California San Diego, La Jolla, CA 92093, USA
| | - Nan Hao
- Section of Molecular Biology, Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA. .,BioCircuits Institute, University of California San Diego, La Jolla, CA 92093, USA
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16
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Moreno DF, Aldea M. Proteostatic stress as a nodal hallmark of replicative aging. Exp Cell Res 2020; 394:112163. [PMID: 32640194 DOI: 10.1016/j.yexcr.2020.112163] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 07/01/2020] [Accepted: 07/03/2020] [Indexed: 11/30/2022]
Abstract
Aging is characterized by the progressive decline of physiology at the cell, tissue and organism level, leading to an increased risk of mortality. Proteotoxic stress, mitochondrial dysfunction and genomic instability are considered major universal drivers of cell aging, and accumulating evidence establishes clear biunivocal relationships among these key hallmarks. In this regard, the finite lifespan of the budding yeast, together with the extensive armamentarium of available analytical tools, has made this single cell eukaryote a key model to study aging at molecular and cellular levels. Here we review the current data that link proteostasis to cell cycle progression in the budding yeast, focusing on senescence as an inherent phenotype displayed by aged cells. Recent advances in high-throughput systems to study yeast mother cells while they replicate are providing crucial information on aging-related processes and their temporal interdependencies at a systems level. In our view, the available data point to the existence of multiple feedback mechanisms among the major causal factors of aging, which would converge into the loss of proteostasis as a nodal driver of cell senescence and death.
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Affiliation(s)
- David F Moreno
- Molecular Biology Institute of Barcelona (IBMB), CSIC, 08028, Barcelona, Catalonia, Spain
| | - Martí Aldea
- Molecular Biology Institute of Barcelona (IBMB), CSIC, 08028, Barcelona, Catalonia, Spain.
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