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Zhang R, Fang J, Xie X, Carrico C, Meyer JG, Wei L, Bons J, Rose J, Riley R, Kwok R, Ashok Kumaar PV, Zhang Y, He W, Nishida Y, Liu X, Locasale JW, Schilling B, Verdin E. Regulation of urea cycle by reversible high-stoichiometry lysine succinylation. Nat Metab 2024; 6:550-566. [PMID: 38448615 DOI: 10.1038/s42255-024-01005-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 02/06/2024] [Indexed: 03/08/2024]
Abstract
The post-translational modification lysine succinylation is implicated in the regulation of various metabolic pathways. However, its biological relevance remains uncertain due to methodological difficulties in determining high-impact succinylation sites. Here, using stable isotope labelling and data-independent acquisition mass spectrometry, we quantified lysine succinylation stoichiometries in mouse livers. Despite the low overall stoichiometry of lysine succinylation, several high-stoichiometry sites were identified, especially upon deletion of the desuccinylase SIRT5. In particular, multiple high-stoichiometry lysine sites identified in argininosuccinate synthase (ASS1), a key enzyme in the urea cycle, are regulated by SIRT5. Mutation of the high-stoichiometry lysine in ASS1 to succinyl-mimetic glutamic acid significantly decreased its enzymatic activity. Metabolomics profiling confirms that SIRT5 deficiency decreases urea cycle activity in liver. Importantly, SIRT5 deficiency compromises ammonia tolerance, which can be reversed by the overexpression of wild-type, but not succinyl-mimetic, ASS1. Therefore, lysine succinylation is functionally important in ammonia metabolism.
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Affiliation(s)
- Ran Zhang
- Buck Institute for Research on Aging, Novato, CA, USA
- School of Life Sciences, Tsinghua University, Beijing, China
| | - Jingqi Fang
- Buck Institute for Research on Aging, Novato, CA, USA
| | - Xueshu Xie
- Buck Institute for Research on Aging, Novato, CA, USA
| | - Chris Carrico
- Buck Institute for Research on Aging, Novato, CA, USA
- Gladstone Institutes and University of California, San Francisco, San Francisco, CA, USA
| | - Jesse G Meyer
- Buck Institute for Research on Aging, Novato, CA, USA
- Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Lei Wei
- Buck Institute for Research on Aging, Novato, CA, USA
| | - Joanna Bons
- Buck Institute for Research on Aging, Novato, CA, USA
| | - Jacob Rose
- Buck Institute for Research on Aging, Novato, CA, USA
| | | | - Ryan Kwok
- Buck Institute for Research on Aging, Novato, CA, USA
| | | | - Yini Zhang
- Buck Institute for Research on Aging, Novato, CA, USA
| | - Wenjuan He
- Gladstone Institutes and University of California, San Francisco, San Francisco, CA, USA
| | - Yuya Nishida
- Gladstone Institutes and University of California, San Francisco, San Francisco, CA, USA
| | - Xiaojing Liu
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC, USA
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC, USA
| | - Jason W Locasale
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC, USA
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC, USA
| | | | - Eric Verdin
- Buck Institute for Research on Aging, Novato, CA, USA.
- Gladstone Institutes and University of California, San Francisco, San Francisco, CA, USA.
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Ubaida-Mohien C, Tanaka T, Tian Q, Moore Z, Moaddel R, Basisty N, Simonsick EM, Ferrucci L. Blood Biomarkers for Healthy Aging. Gerontology 2023; 69:1167-1174. [PMID: 37166337 PMCID: PMC11137618 DOI: 10.1159/000530795] [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: 11/02/2022] [Accepted: 03/22/2023] [Indexed: 05/12/2023] Open
Abstract
Measuring the abundance of biological molecules and their chemical modifications in blood and tissues has been the cornerstone of research and medical diagnoses for decades. Although the number and variety of molecules that can be measured have expanded exponentially, the blood biomarkers routinely assessed in medical practice remain limited to a few dozen, which have not substantially changed over the last 30-40 years. The discovery of novel biomarkers would allow, for example, risk stratification or monitoring of disease progression or the effectiveness of treatments and interventions, improving clinical practice in myriad ways. In this review, we combine the biomarker discovery concept with geroscience. Geroscience bridges aging research and translation to clinical applications by combining the framework of medical gerontology with high-technology medical research. With the development of geroscience and the rise of blood biomarkers, there has been a paradigm shift from disease prevention and cure to promoting health and healthy aging. New -omic technologies have played a role in the development of blood biomarkers, including epigenetic, proteomic, metabolomic, and lipidomic markers, which have emerged as correlates or predictors of health status, from disease to exceptional health.
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Affiliation(s)
- Ceereena Ubaida-Mohien
- Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, Maryland, USA
| | - Toshiko Tanaka
- Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, Maryland, USA
| | - Qu Tian
- Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, Maryland, USA
| | - Zenobia Moore
- Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, Maryland, USA
| | - Ruin Moaddel
- Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, Maryland, USA
| | - Nathan Basisty
- Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, Maryland, USA
| | - Eleanor M Simonsick
- Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, Maryland, USA
| | - Luigi Ferrucci
- Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, Maryland, USA
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Bons J, Rose J, Zhang R, Burton JB, Carrico C, Verdin E, Schilling B. In-depth analysis of the Sirtuin 5-regulated mouse brain malonylome and succinylome using library-free data-independent acquisitions. Proteomics 2023; 23:e2100371. [PMID: 36479818 PMCID: PMC10363399 DOI: 10.1002/pmic.202100371] [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: 06/23/2022] [Revised: 10/29/2022] [Accepted: 11/14/2022] [Indexed: 12/12/2022]
Abstract
Post-translational modifications (PTMs) dynamically regulate proteins and biological pathways, typically through the combined effects of multiple PTMs. Lysine residues are targeted for various PTMs, including malonylation and succinylation. However, PTMs offer specific challenges to mass spectrometry-based proteomics during data acquisition and processing. Thus, novel and innovative workflows using data-independent acquisition (DIA) ensure confident PTM identification, precise site localization, and accurate and robust label-free quantification. In this study, we present a powerful approach that combines antibody-based enrichment with comprehensive DIA acquisitions and spectral library-free data processing using directDIA (Spectronaut). Identical DIA data can be used to generate spectral libraries and comprehensively identify and quantify PTMs, reducing the amount of enriched sample and acquisition time needed, while offering a fully automated workflow. We analyzed brains from wild-type and Sirtuin 5 (SIRT5)-knock-out mice, and discovered and quantified 466 malonylated and 2211 succinylated peptides. SIRT5 regulation remodeled the acylomes by targeting 164 malonylated and 578 succinylated sites. Affected pathways included carbohydrate and lipid metabolisms, synaptic vesicle cycle, and neurodegenerative diseases. We found 48 common SIRT5-regulated malonylation and succinylation sites, suggesting potential PTM crosstalk. This innovative and efficient workflow offers deeper insights into the mouse brain lysine malonylome and succinylome.
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Affiliation(s)
- Joanna Bons
- Buck Institute for Research on Aging, Novato, California, USA
| | - Jacob Rose
- Buck Institute for Research on Aging, Novato, California, USA
| | - Ran Zhang
- Buck Institute for Research on Aging, Novato, California, USA
| | - Jordan B Burton
- Buck Institute for Research on Aging, Novato, California, USA
| | | | - Eric Verdin
- Buck Institute for Research on Aging, Novato, California, USA
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Affinity capture in bottom-up protein analysis - Overview of current status of proteolytic peptide capture using antibodies and molecularly imprinted polymers. Anal Chim Acta 2021; 1182:338714. [PMID: 34602193 DOI: 10.1016/j.aca.2021.338714] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 05/27/2021] [Accepted: 05/28/2021] [Indexed: 12/17/2022]
Abstract
Antibody-based affinity capture has become the gold standard in sample preparation for determination of low-abundance protein biomarkers in biological matrices prior to liquid chromatography-mass spectrometry (LC-MS) determination. This comprises both capture of intact proteins prior to the digestion step and capture of proteolytic peptides after digestion of the sample. The latter can be performed both using antibodies specifically developed to capture target proteolytic peptides, as well as by the less explored use of anti-protein antibodies to capture the proteolytic epitope peptide. Molecularly imprinted polymers (MIPs), also called plastic antibodies are another affinity-based approach emerging as sample preparation technique in LC-MS based protein biomarker analysis. The current review gives a critical and comprehensive overview of proteolytic peptide capture using antibodies and MIPs in LC-MS based protein biomarker determination during the last five years. The main emphasis is on capture of non-modified peptides, while a brief overview of affinity capture of peptides containing post-translational modifications (PTMs) is provided.
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Moaddel R, Ubaida‐Mohien C, Tanaka T, Lyashkov A, Basisty N, Schilling B, Semba RD, Franceschi C, Gorospe M, Ferrucci L. Proteomics in aging research: A roadmap to clinical, translational research. Aging Cell 2021; 20:e13325. [PMID: 33730416 PMCID: PMC8045948 DOI: 10.1111/acel.13325] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Revised: 12/31/2020] [Accepted: 01/18/2021] [Indexed: 02/06/2023] Open
Abstract
The identification of plasma proteins that systematically change with age and, independent of chronological age, predict accelerated decline of health is an expanding area of research. Circulating proteins are ideal translational "omics" since they are final effectors of physiological pathways and because physicians are accustomed to use information of plasma proteins as biomarkers for diagnosis, prognosis, and tracking the effectiveness of treatments. Recent technological advancements, including mass spectrometry (MS)-based proteomics, multiplexed proteomic assay using modified aptamers (SOMAscan), and Proximity Extension Assay (PEA, O-Link), have allowed for the assessment of thousands of proteins in plasma or other biological matrices, which are potentially translatable into new clinical biomarkers and provide new clues about the mechanisms by which aging is associated with health deterioration and functional decline. We carried out a detailed literature search for proteomic studies performed in different matrices (plasma, serum, urine, saliva, tissues) and species using multiple platforms. Herein, we identified 232 proteins that were age-associated across studies. Enrichment analysis of the 232 age-associated proteins revealed metabolic pathways previously connected with biological aging both in animal models and in humans, most remarkably insulin-like growth factor (IGF) signaling, mitogen-activated protein kinases (MAPK), hypoxia-inducible factor 1 (HIF1), cytokine signaling, Forkhead Box O (FOXO) metabolic pathways, folate metabolism, advance glycation end products (AGE), and receptor AGE (RAGE) metabolic pathway. Information on these age-relevant proteins, likely expanded and validated in longitudinal studies and examined in mechanistic studies, will be essential for patient stratification and the development of new treatments aimed at improving health expectancy.
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Affiliation(s)
- Ruin Moaddel
- Biomedical Research Centre National Institute on Aging, NIH Baltimore MD USA
| | | | - Toshiko Tanaka
- Biomedical Research Centre National Institute on Aging, NIH Baltimore MD USA
| | - Alexey Lyashkov
- Biomedical Research Centre National Institute on Aging, NIH Baltimore MD USA
| | | | | | - Richard D Semba
- Wilmer Eye Institute Johns Hopkins University School of Medicine Baltimore MD USA
| | - Claudio Franceschi
- University of Bologna and IRCCS Institute of Neurological Sciences Bologna Italy
| | - Myriam Gorospe
- Biomedical Research Centre National Institute on Aging, NIH Baltimore MD USA
| | - Luigi Ferrucci
- Biomedical Research Centre National Institute on Aging, NIH Baltimore MD USA
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Basisty N, Kale A, Patel S, Campisi J, Schilling B. The power of proteomics to monitor senescence-associated secretory phenotypes and beyond: toward clinical applications. Expert Rev Proteomics 2020; 17:297-308. [PMID: 32425074 DOI: 10.1080/14789450.2020.1766976] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
INTRODUCTION Cellular senescence is a rapidly growing field with potential relevance for the treatment of multiple human diseases. In the last decade, cellular senescence and the senescence-associated secretory phenotype (SASP) have emerged as central drivers of aging and many chronic diseases, including cancer, neurodegeneration, heart disease and osteoarthritis. Major efforts are underway to develop drugs that selectively eliminate senescent cells (senolytics) or alter the SASP (senomorphics) to treat age-related diseases in humans. The translation of senescence-targeting therapies into humans is still in early stages. Nonetheless, it is clear that proteomic approaches will facilitate the discovery of important SASP proteins, development of senescence- and SASP-derived biomarkers, and identification of therapeutic targets for senolytic and senomorphic drugs. AREAS COVERED We review recent proteomic studies of cellular senescence and their translational relevance and, particularly, characterization of the secretory phenotype and preclinical development of biomarkers (from 2008-2020, PubMed). We focus on emerging areas, such as the heterogeneity of senescent cells and the SASP, extracellular vesicles released by senescent cells, and validating biomarkers of aging in vivo. EXPERT OPINION Proteomic and multi-omic approaches will be important for the development of senescence-based biomarkers to facilitate and monitor future therapeutic interventions that target senescent cells.
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Affiliation(s)
- Nathan Basisty
- Buck Institute for Research on Aging, Novato , California, USA
| | - Abhijit Kale
- Buck Institute for Research on Aging, Novato , California, USA
| | - Sandip Patel
- Buck Institute for Research on Aging, Novato , California, USA
| | - Judith Campisi
- Buck Institute for Research on Aging, Novato , California, USA.,Lawrence Berkeley National Laboratory, University of California , Berkeley, USA
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