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Alfatah M, Lim JJJ, Zhang Y, Naaz A, Cheng TYN, Yogasundaram S, Faidzinn NA, Lin JJ, Eisenhaber B, Eisenhaber F. Uncharacterized yeast gene YBR238C, an effector of TORC1 signaling in a mitochondrial feedback loop, accelerates cellular aging via HAP4- and RMD9-dependent mechanisms. eLife 2024; 12:RP92178. [PMID: 38713053 PMCID: PMC11076046 DOI: 10.7554/elife.92178] [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] [Indexed: 05/08/2024] Open
Abstract
Uncovering the regulators of cellular aging will unravel the complexity of aging biology and identify potential therapeutic interventions to delay the onset and progress of chronic, aging-related diseases. In this work, we systematically compared genesets involved in regulating the lifespan of Saccharomyces cerevisiae (a powerful model organism to study the cellular aging of humans) and those with expression changes under rapamycin treatment. Among the functionally uncharacterized genes in the overlap set, YBR238C stood out as the only one downregulated by rapamycin and with an increased chronological and replicative lifespan upon deletion. We show that YBR238C and its paralog RMD9 oppositely affect mitochondria and aging. YBR238C deletion increases the cellular lifespan by enhancing mitochondrial function. Its overexpression accelerates cellular aging via mitochondrial dysfunction. We find that the phenotypic effect of YBR238C is largely explained by HAP4- and RMD9-dependent mechanisms. Furthermore, we find that genetic- or chemical-based induction of mitochondrial dysfunction increases TORC1 (Target of Rapamycin Complex 1) activity that, subsequently, accelerates cellular aging. Notably, TORC1 inhibition by rapamycin (or deletion of YBR238C) improves the shortened lifespan under these mitochondrial dysfunction conditions in yeast and human cells. The growth of mutant cells (a proxy of TORC1 activity) with enhanced mitochondrial function is sensitive to rapamycin whereas the growth of defective mitochondrial mutants is largely resistant to rapamycin compared to wild type. Our findings demonstrate a feedback loop between TORC1 and mitochondria (the TORC1-MItochondria-TORC1 (TOMITO) signaling process) that regulates cellular aging processes. Hereby, YBR238C is an effector of TORC1 modulating mitochondrial function.
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Affiliation(s)
- Mohammad Alfatah
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
| | - Jolyn Jia Jia Lim
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
| | - Yizhong Zhang
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
| | - Arshia Naaz
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
| | - Trishia Yi Ning Cheng
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
| | - Sonia Yogasundaram
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
| | - Nashrul Afiq Faidzinn
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
| | - Jovian Jing Lin
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
| | - Birgit Eisenhaber
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
- LASA – Lausitz Advanced Scientific Applications gGmbHWeißwasserGermany
| | - Frank Eisenhaber
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
- LASA – Lausitz Advanced Scientific Applications gGmbHWeißwasserGermany
- School of Biological Sciences (SBS), Nanyang Technological University (NTU)SingaporeSingapore
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Ohtsuka H, Shimasaki T, Aiba H. Low-Molecular Weight Compounds that Extend the Chronological Lifespan of Yeasts, Saccharomyces cerevisiae, and Schizosaccharomyces pombe. Adv Biol (Weinh) 2024; 8:e2400138. [PMID: 38616173 DOI: 10.1002/adbi.202400138] [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: 03/11/2024] [Revised: 04/04/2024] [Indexed: 04/16/2024]
Abstract
Yeast is an excellent model organism for research for regulating aging and lifespan, and the studies have made many contributions to date, including identifying various factors and signaling pathways related to aging and lifespan. More than 20 years have passed since molecular biological perspectives are adopted in this research field, and intracellular factors and signal pathways that control aging and lifespan have evolutionarily conserved from yeast to mammals. Furthermore, these findings have been applied to control the aging and lifespan of various model organisms by adjustment of the nutritional environment, genetic manipulation, and drug treatment using low-molecular weight compounds. Among these, drug treatment is easier than the other methods, and research into drugs that regulate aging and lifespan is consequently expected to become more active. Chronological lifespan, a definition of yeast lifespan, refers to the survival period of a cell population under nondividing conditions. Herein, low-molecular weight compounds are summarized that extend the chronological lifespan of Saccharomyces cerevisiae and Schizosaccharomyces pombe, along with their intracellular functions. The low-molecular weight compounds are also discussed that extend the lifespan of other model organisms. Compounds that have so far only been studied in yeast may soon extend lifespan in other organisms.
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Affiliation(s)
- Hokuto Ohtsuka
- Laboratory of Molecular Microbiology, Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, Aichi, Japan
| | - Takafumi Shimasaki
- Laboratory of Molecular Microbiology, Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, Aichi, Japan
| | - Hirofumi Aiba
- Laboratory of Molecular Microbiology, Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, Aichi, Japan
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R K, Kumar A, Vinod Kumar K, Sengupta A, Kundal K, Sharma S, Pawar A, Krishna PS, Alfatah M, Ray S, Tiwari B, Kumar R. AagingBase: a comprehensive database of anti-aging peptides. Database (Oxford) 2024; 2024:baae016. [PMID: 38470883 PMCID: PMC10930205 DOI: 10.1093/database/baae016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 01/07/2024] [Accepted: 03/05/2024] [Indexed: 03/14/2024]
Abstract
The process of aging is an intrinsic and inevitable aspect of life that impacts every living organism. As biotechnological advancements continue to shape our understanding of medicine, peptide therapeutics have emerged as a promising strategy for anti-aging interventions. This is primarily due to their favorable attributes, such as low immunogenicity and cost-effective production. Peptide-based treatments have garnered widespread acceptance and interest in aging research, particularly in the context of age-related therapies. To effectively develop anti-aging treatments, a comprehensive understanding of the physicochemical characteristics of anti-aging peptides is essential. Factors such as amino acid composition, instability index, hydrophobic areas and other relevant properties significantly determine their efficacy as potential therapeutic agents. Consequently, the creation of 'AagingBase', a comprehensive database for anti-aging peptides, aims to facilitate research on aging by leveraging the potential of peptide therapies. AagingBase houses experimentally validated 282 anti-aging peptides collected from 54 research articles and 236 patents. Employing state-of-the-art computational techniques, the acquired sequences have undergone rigorous physicochemical calculations. Furthermore, AagingBase presents users with various informative analyses highlighting atomic compositions, secondary structure fractions, tertiary structure, amino acid compositions and frequencies. The database also offers advanced search and filtering options and similarity search, thereby aiding researchers in understanding their biological functions. Hence, the database enables efficient identification and prioritization of potential peptide candidates in geriatric medicine and holds immense potential for advancing geriatric medicine research and innovations. AagingBase can be accessed without any restriction. Database URL: https://project.iith.ac.in/cgntlab/aagingbase/.
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Affiliation(s)
- Kunjulakshmi R
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Telangana 502284, India
- Department of Biological Sciences, Indian Institute of Science Education and Research, Berhampur, Odisha 760010, India
| | - Ambuj Kumar
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Telangana 502284, India
| | - Keerthana Vinod Kumar
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Telangana 502284, India
| | - Avik Sengupta
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Telangana 502284, India
| | - Kavita Kundal
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Telangana 502284, India
| | - Simran Sharma
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Telangana 502284, India
| | - Ankita Pawar
- School of Biotechnology, Amrita Vishwa Vidyapeetham, Amritapuri, Clappana P.O., Kollam, Kerala 690525, India
| | - Pithani Sai Krishna
- School of Biotechnology, Amrita Vishwa Vidyapeetham, Amritapuri, Clappana P.O., Kollam, Kerala 690525, India
| | - Mohammad Alfatah
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, Matrix #07-01, Singapore 138671, Republic of Singapore
| | - Sandipan Ray
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Telangana 502284, India
| | - Bhavana Tiwari
- Department of Biological Sciences, Indian Institute of Science Education and Research, Berhampur, Odisha 760010, India
| | - Rahul Kumar
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Telangana 502284, India
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Alfatah M, Zhang Y, Naaz A, Cheng TYN, Eisenhaber F. PICLS with human cells is the first high throughput screening method for identifying novel compounds that extend lifespan. Biol Direct 2024; 19:8. [PMID: 38254217 PMCID: PMC10804585 DOI: 10.1186/s13062-024-00455-4] [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: 11/30/2023] [Accepted: 01/18/2024] [Indexed: 01/24/2024] Open
Abstract
Gerontology research on anti-aging interventions with drugs could be an answer to age-related diseases, aiming at closing the gap between lifespan and healthspan. Here, we present two methods for assaying chronological lifespan in human cells: (1) a version of the classical outgrowth assay with quantitative assessment of surviving cells and (2) a version of the PICLS method (propidium iodide fluorescent-based measurement of cell death). Both methods are fast, simple to conduct, cost-effective, produce quantitative data for further analysis and can be used with diverse human cell lines. Whereas the first method is ideal for validation and testing the post-intervention reproductive potential of surviving cells, the second method has true high-throughput screening potential. The new technologies were validated with known anti-aging compounds (2,5-anhydro-D-mannitol and rapamycin). Using the high-throughput screening method, we screened a library of 162 chemical entities and identified three compounds that extend the longevity of human cells.
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Affiliation(s)
- Mohammad Alfatah
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, Matrix #07-01, Singapore, 138671, Republic of Singapore.
| | - Yizhong Zhang
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, Matrix #07-01, Singapore, 138671, Republic of Singapore
| | - Arshia Naaz
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Genome #02-01, Singapore, 138672, Republic of Singapore
| | - Trishia Yi Ning Cheng
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, Matrix #07-01, Singapore, 138671, Republic of Singapore
| | - Frank Eisenhaber
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, Matrix #07-01, Singapore, 138671, Republic of Singapore
- LASA - Lausitz Advanced Scientific Applications gGmbH, Straße der Einheit 2-24, 02943, Weißwasser, Federal Republic of Germany
- School of Biological Sciences (SBS), Nanyang Technological University (NTU), Singapore, 637551, Republic of Singapore
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Tantoso E, Eisenhaber B, Sinha S, Jensen LJ, Eisenhaber F. Did the early full genome sequencing of yeast boost gene function discovery? Biol Direct 2023; 18:46. [PMID: 37574542 PMCID: PMC10424406 DOI: 10.1186/s13062-023-00403-8] [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: 07/15/2023] [Accepted: 08/01/2023] [Indexed: 08/15/2023] Open
Abstract
BACKGROUND Although the genome of Saccharomyces cerevisiae (S. cerevisiae) was the first one of a eukaryote organism that was fully sequenced (in 1996), a complete understanding of the potential of encoded biomolecular mechanisms has not yet been achieved. Here, we wish to quantify how far the goal of a full list of S. cerevisiae gene functions still is. RESULTS The scientific literature about S. cerevisiae protein-coding genes has been mapped onto the yeast genome via the mentioning of names for genomic regions in scientific publications. The match was quantified with the ratio of a given gene name's occurrences to those of any gene names in the article. We find that ~ 230 elite genes with ≥ 75 full publication equivalents (FPEs, FPE = 1 is an idealized publication referring to just a single gene) command ~ 45% of all literature. At the same time, about two thirds of the genes (each with less than 10 FPEs) are described in just 12% of the literature (in average each such gene has just ~ 1.5% of the literature of an elite gene). About 600 genes have not been mentioned in any dedicated article. Compared with other groups of genes, the literature growth rates were highest for uncharacterized or understudied genes until late nineties of the twentieth century. Yet, these growth rates deteriorated and became negative thereafter. Thus, yeast function discovery for previously uncharacterized genes has returned to the level of ~ 1980. At the same time, literature for anyhow well-studied genes (with a threshold T10 (≥ 10 FPEs) and higher) remains steadily growing. CONCLUSIONS Did the early full genome sequencing of yeast boost gene function discovery? The data proves that the moment of publishing the full genome in reality coincides with the onset of decline of gene function discovery for previously uncharacterized genes. If the current status of literature about yeast molecular mechanisms can be extrapolated into the future, it will take about another ~ 50 years to complete the yeast gene function list. We found that a small group of scientific journals contributed extraordinarily to publishing early reports relevant to yeast gene function discoveries.
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Affiliation(s)
- Erwin Tantoso
- Agency for Science, Technology and Research (A*STAR), Bioinformatics Institute (BII), 30 Biopolis Street #07-01, Matrix Building, Singapore, 138671, Republic of Singapore.
- Agency for Science, Technology and Research (A*STAR), Genome Institute of Singapore (GIS), 60 Biopolis Street, Singapore, 138672, Republic of Singapore.
| | - Birgit Eisenhaber
- Agency for Science, Technology and Research (A*STAR), Bioinformatics Institute (BII), 30 Biopolis Street #07-01, Matrix Building, Singapore, 138671, Republic of Singapore.
- Agency for Science, Technology and Research (A*STAR), Genome Institute of Singapore (GIS), 60 Biopolis Street, Singapore, 138672, Republic of Singapore.
- LASA - Lausitz Advanced Scientific Applications gGmbH, Straße Der Einheit 2-24, 02943, Weißwasser, Federal Republic of Germany.
| | - Swati Sinha
- European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Lars Juhl Jensen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Frank Eisenhaber
- Agency for Science, Technology and Research (A*STAR), Bioinformatics Institute (BII), 30 Biopolis Street #07-01, Matrix Building, Singapore, 138671, Republic of Singapore.
- Agency for Science, Technology and Research (A*STAR), Genome Institute of Singapore (GIS), 60 Biopolis Street, Singapore, 138672, Republic of Singapore.
- LASA - Lausitz Advanced Scientific Applications gGmbH, Straße Der Einheit 2-24, 02943, Weißwasser, Federal Republic of Germany.
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Republic of Singapore.
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