1
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Prus G, Satpathy S, Weinert BT, Narita T, Choudhary C. Global, site-resolved analysis of ubiquitylation occupancy and turnover rate reveals systems properties. Cell 2024; 187:2875-2892.e21. [PMID: 38626770 PMCID: PMC11136510 DOI: 10.1016/j.cell.2024.03.024] [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: 07/14/2023] [Revised: 12/19/2023] [Accepted: 03/19/2024] [Indexed: 04/18/2024]
Abstract
Ubiquitylation regulates most proteins and biological processes in a eukaryotic cell. However, the site-specific occupancy (stoichiometry) and turnover rate of ubiquitylation have not been quantified. Here we present an integrated picture of the global ubiquitylation site occupancy and half-life. Ubiquitylation site occupancy spans over four orders of magnitude, but the median ubiquitylation site occupancy is three orders of magnitude lower than that of phosphorylation. The occupancy, turnover rate, and regulation of sites by proteasome inhibitors are strongly interrelated, and these attributes distinguish sites involved in proteasomal degradation and cellular signaling. Sites in structured protein regions exhibit longer half-lives and stronger upregulation by proteasome inhibitors than sites in unstructured regions. Importantly, we discovered a surveillance mechanism that rapidly and site-indiscriminately deubiquitylates all ubiquitin-specific E1 and E2 enzymes, protecting them against accumulation of bystander ubiquitylation. The work provides a systems-scale, quantitative view of ubiquitylation properties and reveals general principles of ubiquitylation-dependent governance.
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Affiliation(s)
- Gabriela Prus
- Department of Proteomics, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Shankha Satpathy
- Department of Proteomics, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Brian T Weinert
- Department of Proteomics, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Takeo Narita
- Department of Proteomics, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Chunaram Choudhary
- Department of Proteomics, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark.
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2
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Reddien PW. The purpose and ubiquity of turnover. Cell 2024; 187:2657-2681. [PMID: 38788689 DOI: 10.1016/j.cell.2024.04.034] [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: 01/31/2024] [Revised: 03/19/2024] [Accepted: 04/24/2024] [Indexed: 05/26/2024]
Abstract
Turnover-constant component production and destruction-is ubiquitous in biology. Turnover occurs across organisms and scales, including for RNAs, proteins, membranes, macromolecular structures, organelles, cells, hair, feathers, nails, antlers, and teeth. For many systems, turnover might seem wasteful when degraded components are often fully functional. Some components turn over with shockingly high rates and others do not turn over at all, further making this process enigmatic. However, turnover can address fundamental problems by yielding powerful properties, including regeneration, rapid repair onset, clearance of unpredictable damage and errors, maintenance of low constitutive levels of disrepair, prevention of stable hazards, and transitions. I argue that trade-offs between turnover benefits and metabolic costs, combined with constraints on turnover, determine its presence and rates across distinct contexts. I suggest that the limits of turnover help explain aging and that turnover properties and the basis for its levels underlie this fundamental component of life.
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Affiliation(s)
- Peter W Reddien
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, MIT, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, MIT, Cambridge, MA 02139, USA.
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3
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Dear AJ, Garcia GA, Meisl G, Collins GA, Knowles TPJ, Goldberg AL. Maximum entropy determination of mammalian proteome dynamics. Proc Natl Acad Sci U S A 2024; 121:e2313107121. [PMID: 38652742 PMCID: PMC11067036 DOI: 10.1073/pnas.2313107121] [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: 08/02/2023] [Accepted: 03/04/2024] [Indexed: 04/25/2024] Open
Abstract
Full understanding of proteostasis and energy utilization in cells will require knowledge of the fraction of cell proteins being degraded with different half-lives and their rates of synthesis. We therefore developed a method to determine such information that combines mathematical analysis of protein degradation kinetics obtained in pulse-chase experiments with Bayesian data fitting using the maximum entropy principle. This approach will enable rapid analyses of whole-cell protein dynamics in different cell types, physiological states, and neurodegenerative disease. Using it, we obtained surprising insights about protein stabilities in cultured cells normally and upon activation of proteolysis by mTOR inhibition and increasing cAMP or cGMP. It revealed that >90% of protein content in dividing mammalian cell lines is long-lived, with half-lives of 24 to 200 h, and therefore comprises much of the proteins in daughter cells. The well-studied short-lived proteins (half-lives < 10 h) together comprise <2% of cell protein mass, but surprisingly account for 10 to 20% of measurable newly synthesized protein mass. Evolution thus appears to have minimized intracellular proteolysis except to rapidly eliminate misfolded and regulatory proteins.
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Affiliation(s)
- Alexander J. Dear
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA02115
- Department of Chemistry, University of Cambridge, CambridgeCB2 1EW, United Kingdom
| | - Gonzalo A. Garcia
- Department of Chemistry, University of Cambridge, CambridgeCB2 1EW, United Kingdom
| | - Georg Meisl
- Department of Chemistry, University of Cambridge, CambridgeCB2 1EW, United Kingdom
| | - Galen A. Collins
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA02115
- Department of Biochemistry, Molecular Biology, Entomology & Plant Pathology, Mississippi State University, Starkville, MS39762
| | - Tuomas P. J. Knowles
- Department of Chemistry, University of Cambridge, CambridgeCB2 1EW, United Kingdom
- Cavendish Laboratory, Department of Physics, University of Cambridge, CambridgeCB3 0HE, United Kingdom
| | - Alfred L. Goldberg
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA02115
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4
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Kim J, Byun I, Kim DY, Joh H, Kim HJ, Lee MJ. Targeted protein degradation directly engaging lysosomes or proteasomes. Chem Soc Rev 2024; 53:3253-3272. [PMID: 38369971 DOI: 10.1039/d3cs00344b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Targeted protein degradation (TPD) has been established as a viable alternative to attenuate the function of a specific protein of interest in both biological and clinical contexts. The unique TPD mode-of-action has allowed previously undruggable proteins to become feasible targets, expanding the landscape of "druggable" properties and "privileged" target proteins. As TPD continues to evolve, a range of innovative strategies, which do not depend on recruiting E3 ubiquitin ligases as in proteolysis-targeting chimeras (PROTACs), have emerged. Here, we present an overview of direct lysosome- and proteasome-engaging modalities and discuss their perspectives, advantages, and limitations. We outline the chemical composition, biochemical activity, and pharmaceutical characteristics of each degrader. These alternative TPD approaches not only complement the first generation of PROTACs for intracellular protein degradation but also offer unique strategies for targeting pathologic proteins located on the cell membrane and in the extracellular space.
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Affiliation(s)
- Jiseong Kim
- Department of Biochemistry & Molecular Biology, Seoul National University College of Medicine, Seoul 03080, Korea.
- Department of Biomedical Sciences, Seoul National University Graduate School, Seoul 03080, Korea
| | - Insuk Byun
- Department of Biochemistry & Molecular Biology, Seoul National University College of Medicine, Seoul 03080, Korea.
- Department of Biomedical Sciences, Seoul National University Graduate School, Seoul 03080, Korea
| | - Do Young Kim
- Department of Chemistry, College of Science, Korea University, Seoul 02841, Korea.
| | - Hyunhi Joh
- Department of Chemistry, College of Science, Korea University, Seoul 02841, Korea.
| | - Hak Joong Kim
- Department of Chemistry, College of Science, Korea University, Seoul 02841, Korea.
| | - Min Jae Lee
- Department of Biochemistry & Molecular Biology, Seoul National University College of Medicine, Seoul 03080, Korea.
- Department of Biomedical Sciences, Seoul National University Graduate School, Seoul 03080, Korea
- Department of Pathology and Laboratory Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
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5
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Seedhom MO, Dersh D, Holly J, Pavon-Eternod M, Wei J, Angel M, Shores L, David A, Santos J, Hickman H, Yewdell JW. Paradoxical imbalance between activated lymphocyte protein synthesis capacity and rapid division rate. eLife 2024; 12:RP89015. [PMID: 38512721 PMCID: PMC10957176 DOI: 10.7554/elife.89015] [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: 03/23/2024] Open
Abstract
Rapid lymphocyte cell division places enormous demands on the protein synthesis machinery. Flow cytometric measurement of puromycylated ribosome-associated nascent chains after treating cells or mice with translation initiation inhibitors reveals that ribosomes in resting lymphocytes in vitro and in vivo elongate at typical rates for mammalian cells. Intriguingly, elongation rates can be increased up to 30% by activation in vivo or fever temperature in vitro. Resting and activated lymphocytes possess abundant monosome populations, most of which actively translate in vivo, while in vitro, nearly all can be stalled prior to activation. Quantitating lymphocyte protein mass and ribosome count reveals a paradoxically high ratio of cellular protein to ribosomes insufficient to support their rapid in vivo division, suggesting that the activated lymphocyte proteome in vivo may be generated in an unusual manner. Our findings demonstrate the importance of a global understanding of protein synthesis in lymphocytes and other rapidly dividing immune cells.
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Affiliation(s)
- Mina O Seedhom
- National Institute of Allergy and Infectious DiseasesBethesdaUnited States
| | - Devin Dersh
- National Institute of Allergy and Infectious DiseasesBethesdaUnited States
| | - Jaroslav Holly
- National Institute of Allergy and Infectious DiseasesBethesdaUnited States
| | | | - Jiajie Wei
- National Institute of Allergy and Infectious DiseasesBethesdaUnited States
| | - Matthew Angel
- National Institute of Allergy and Infectious DiseasesBethesdaUnited States
| | - Lucas Shores
- National Institute of Allergy and Infectious DiseasesBethesdaUnited States
| | - Alexandre David
- CNRS UMR-5203; INSERM U661; UM1; UM2, Institut de Génomique FonctionnelleMontpellierFrance
| | - Jefferson Santos
- National Institute of Allergy and Infectious DiseasesBethesdaUnited States
| | - Heather Hickman
- National Institute of Allergy and Infectious DiseasesBethesdaUnited States
| | - Jonathan W Yewdell
- National Institute of Allergy and Infectious DiseasesBethesdaUnited States
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6
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Chen EP, Dutta S, Ho MH, DeMartino MP. Model-Based Virtual PK/PD Exploration and Machine Learning Approach to Define PK Drivers in Early Drug Discovery. J Med Chem 2024; 67:3727-3740. [PMID: 38375820 DOI: 10.1021/acs.jmedchem.3c02169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/21/2024]
Abstract
While poor translatability of preclinical efficacy models can be responsible for clinical phase II failures, misdefinition of the optimal PK properties required to achieve therapeutic efficacy can also be a contributing factor. In the present work, the pharmacological dependency of PK end points in driving efficacy is demonstrated for six common pharmacological processes via model-based analysis. The analysis shows that the response is driven by multiple pharmacology-specific PK end points that change with how the response is defined. Moreover, the results demonstrate that the most important chemical structural features influencing response are specific to both target and downstream pharmacology, meaning the design and screening criteria must be defined uniquely for each target and corresponding pharmacology. The model-based virtual exploration of PK/PD relationships presented in this work offers one approach to identify target pharmacology-specific PK drivers and the associated potency-ADME space early in discovery to increase the probability of success and, ultimately, clinical attrition.
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Affiliation(s)
- Emile P Chen
- Systems Modeling and Translational Biology, Computational Sciences, GSK, Collegeville, Pennsylvania 19426, United States
| | - Shayoni Dutta
- Systems Modeling and Translational Biology, Computational Sciences, GSK, Collegeville, Pennsylvania 19426, United States
| | - Ming-Hsun Ho
- Molecular Design, Computational Sciences, GSK, Collegeville, Pennsylvania 19426, United States
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7
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Baghdassarian HM, Lewis NE. Resource allocation in mammalian systems. Biotechnol Adv 2024; 71:108305. [PMID: 38215956 DOI: 10.1016/j.biotechadv.2023.108305] [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: 08/03/2023] [Revised: 12/17/2023] [Accepted: 12/18/2023] [Indexed: 01/14/2024]
Abstract
Cells execute biological functions to support phenotypes such as growth, migration, and secretion. Complementarily, each function of a cell has resource costs that constrain phenotype. Resource allocation by a cell allows it to manage these costs and optimize their phenotypes. In fact, the management of resource constraints (e.g., nutrient availability, bioenergetic capacity, and macromolecular machinery production) shape activity and ultimately impact phenotype. In mammalian systems, quantification of resource allocation provides important insights into higher-order multicellular functions; it shapes intercellular interactions and relays environmental cues for tissues to coordinate individual cells to overcome resource constraints and achieve population-level behavior. Furthermore, these constraints, objectives, and phenotypes are context-dependent, with cells adapting their behavior according to their microenvironment, resulting in distinct steady-states. This review will highlight the biological insights gained from probing resource allocation in mammalian cells and tissues.
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Affiliation(s)
- Hratch M Baghdassarian
- Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, CA 92093, USA; Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA
| | - Nathan E Lewis
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA; Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA.
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8
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Gustafsson J, Robinson JL, Zetterberg H, Nielsen J. Brain energy metabolism is optimized to minimize the cost of enzyme synthesis and transport. Proc Natl Acad Sci U S A 2024; 121:e2305035121. [PMID: 38315844 PMCID: PMC10873630 DOI: 10.1073/pnas.2305035121] [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: 04/08/2023] [Accepted: 12/22/2023] [Indexed: 02/07/2024] Open
Abstract
The energy metabolism of the brain is poorly understood partly due to the complex morphology of neurons and fluctuations in ATP demand over time. To investigate this, we used metabolic models that estimate enzyme usage per pathway, enzyme utilization over time, and enzyme transportation to evaluate how these parameters and processes affect ATP costs for enzyme synthesis and transportation. Our models show that the total enzyme maintenance energy expenditure of the human body depends on how glycolysis and mitochondrial respiration are distributed both across and within cell types in the brain. We suggest that brain metabolism is optimized to minimize the ATP maintenance cost by distributing the different ATP generation pathways in an advantageous way across cell types and potentially also across synapses within the same cell. Our models support this hypothesis by predicting export of lactate from both neurons and astrocytes during peak ATP demand, reproducing results from experimental measurements reported in the literature. Furthermore, our models provide potential explanation for parts of the astrocyte-neuron lactate shuttle theory, which is recapitulated under some conditions in the brain, while contradicting other aspects of the theory. We conclude that enzyme usage per pathway, enzyme utilization over time, and enzyme transportation are important factors for defining the optimal distribution of ATP production pathways, opening a broad avenue to explore in brain metabolism.
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Affiliation(s)
- Johan Gustafsson
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Jonathan L. Robinson
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
- BioInnovation Institute, CopenhagenDK-2200, Denmark
| | - Henrik Zetterberg
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, Sahlgrenska Academy at University of Gothenburg, Mölndal431 30, Sweden
- Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal431 30, Sweden
- Department of Neurodegenerative Disease, University College London Queen Square Institute of Neurology, LondonWC1E 6BT, United Kingdom
- United Kingdom Dementia Research Institute, University College London, LondonWC1E 6BT, United Kingdom
- Hong Kong Center for Neurodegenerative Diseases, Hong Kong999077, China
- Wisconsin Alzheimer’s Disease Research Center, University of Wisconsin School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI53792
| | - Jens Nielsen
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, Sahlgrenska Academy at University of Gothenburg, Mölndal431 30, Sweden
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9
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Conte L, Gonella F, Giansanti A, Kleidon A, Romano A. Modeling cell populations metabolism and competition under maximum power constraints. PLoS Comput Biol 2023; 19:e1011607. [PMID: 37939139 PMCID: PMC10659174 DOI: 10.1371/journal.pcbi.1011607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 11/20/2023] [Accepted: 10/16/2023] [Indexed: 11/10/2023] Open
Abstract
Ecological interactions are fundamental at the cellular scale, addressing the possibility of a description of cellular systems that uses language and principles of ecology. In this work, we use a minimal ecological approach that encompasses growth, adaptation and survival of cell populations to model cell metabolisms and competition under energetic constraints. As a proof-of-concept, we apply this general formulation to study the dynamics of the onset of a specific blood cancer-called Multiple Myeloma. We show that a minimal model describing antagonist cell populations competing for limited resources, as regulated by microenvironmental factors and internal cellular structures, reproduces patterns of Multiple Myeloma evolution, due to the uncontrolled proliferation of cancerous plasma cells within the bone marrow. The model is characterized by a class of regime shifts to more dissipative states for selectively advantaged malignant plasma cells, reflecting a breakdown of self-regulation in the bone marrow. The transition times obtained from the simulations range from years to decades consistently with clinical observations of survival times of patients. This irreversible dynamical behavior represents a possible description of the incurable nature of myelomas based on the ecological interactions between plasma cells and the microenvironment, embedded in a larger complex system. The use of ATP equivalent energy units in defining stocks and flows is a key to constructing an ecological model which reproduces the onset of myelomas as transitions between states of a system which reflects the energetics of plasma cells. This work provides a basis to construct more complex models representing myelomas, which can be compared with model ecosystems.
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Affiliation(s)
- Luigi Conte
- Department of Environmental Sciences, Informatics and Statistics, Ca’ Foscari University of Venice, Venezia Mestre, Italy
- Department of Physics, Sapienza University of Rome, Roma, Italy
- Centre for the Study of the Systemic Dynamics of Complex Diseases, Venezia Mestre, Italy
| | - Francesco Gonella
- Centre for the Study of the Systemic Dynamics of Complex Diseases, Venezia Mestre, Italy
- Department of Molecular Sciences and Nanosystems, Ca’ Foscari University of Venice, Venezia Mestre, Italy
- THE NEW INSTITUTE Centre for Environmental Humanities (NICHE), Venezia, Italy
| | - Andrea Giansanti
- Department of Physics, Sapienza University of Rome, Roma, Italy
- Istituto Nazionale di Fisica Nucleare, Roma, Italy
| | - Axel Kleidon
- Biospheric Theory and Modeling Group, Max Planck Institute for Biogeochemistry, Jena, Germany
| | - Alessandra Romano
- Centre for the Study of the Systemic Dynamics of Complex Diseases, Venezia Mestre, Italy
- Department of General Surgery and Medical-Surgical Specialties, University of Catania, Catania, Italy
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10
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Nishimura Y, Bittel AJ, Stead CA, Chen YW, Burniston JG. Facioscapulohumeral Muscular Dystrophy is Associated With Altered Myoblast Proteome Dynamics. Mol Cell Proteomics 2023; 22:100605. [PMID: 37353005 PMCID: PMC10392138 DOI: 10.1016/j.mcpro.2023.100605] [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: 12/15/2022] [Revised: 05/31/2023] [Accepted: 06/20/2023] [Indexed: 06/25/2023] Open
Abstract
Proteomic studies in facioscapulohumeral muscular dystrophy (FSHD) could offer new insight into disease mechanisms underpinned by post-transcriptional processes. We used stable isotope (deuterium oxide; D2O) labeling and peptide mass spectrometry to investigate the abundance and turnover rates of proteins in cultured muscle cells from two individuals affected by FSHD and their unaffected siblings (UASb). We measured the abundance of 4420 proteins and the turnover rate of 2324 proteins in each (n = 4) myoblast sample. FSHD myoblasts exhibited a greater abundance but slower turnover rate of subunits of mitochondrial respiratory complexes and mitochondrial ribosomal proteins, which may indicate an accumulation of "older" less viable mitochondrial proteins in myoblasts from individuals affected by FSHD. Treatment with a 2'-O-methoxyethyl modified antisense oligonucleotide targeting exon 3 of the double homeobox 4 (DUX4) transcript tended to reverse mitochondrial protein dysregulation in FSHD myoblasts, indicating the effect on mitochondrial proteins may be a DUX4-dependent mechanism. Our results highlight the importance of post-transcriptional processes and protein turnover in FSHD pathology and provide a resource for the FSHD research community to explore this burgeoning aspect of FSHD.
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Affiliation(s)
- Yusuke Nishimura
- Research Institute for Sport & Exercise Sciences, Liverpool John Moores University, Liverpool, United Kingdom
| | - Adam J Bittel
- Center for Genetic Medicine Research, Children's National Medical Center, Washington, District of Columbia, USA
| | - Connor A Stead
- Research Institute for Sport & Exercise Sciences, Liverpool John Moores University, Liverpool, United Kingdom
| | - Yi-Wen Chen
- Center for Genetic Medicine Research, Children's National Medical Center, Washington, District of Columbia, USA.
| | - Jatin G Burniston
- Research Institute for Sport & Exercise Sciences, Liverpool John Moores University, Liverpool, United Kingdom.
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11
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Zhang H, Ji S, Zhang K, Chen Y, Ming J, Kong F, Wang L, Wang S, Zou Z, Xiong Z, Xu K, Lin Z, Huang B, Liu L, Fan Q, Jin S, Deng H, Xie W. Stable maternal proteins underlie distinct transcriptome, translatome, and proteome reprogramming during mouse oocyte-to-embryo transition. Genome Biol 2023; 24:166. [PMID: 37443062 DOI: 10.1186/s13059-023-02997-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 06/27/2023] [Indexed: 07/15/2023] Open
Abstract
BACKGROUND The oocyte-to-embryo transition (OET) converts terminally differentiated gametes into a totipotent embryo and is critically controlled by maternal mRNAs and proteins, while the genome is silent until zygotic genome activation. How the transcriptome, translatome, and proteome are coordinated during this critical developmental window remains poorly understood. RESULTS Utilizing a highly sensitive and quantitative mass spectrometry approach, we obtain high-quality proteome data spanning seven mouse stages, from full-grown oocyte (FGO) to blastocyst, using 100 oocytes/embryos at each stage. Integrative analyses reveal distinct proteome reprogramming compared to that of the transcriptome or translatome. FGO to 8-cell proteomes are dominated by FGO-stockpiled proteins, while the transcriptome and translatome are more dynamic. FGO-originated proteins frequently persist to blastocyst while corresponding transcripts are already downregulated or decayed. Improved concordance between protein and translation or transcription is observed for genes starting translation upon meiotic resumption, as well as those transcribed and translated only in embryos. Concordance between protein and transcription/translation is also observed for proteins with short half-lives. We built a kinetic model that predicts protein dynamics by incorporating both initial protein abundance in FGOs and translation kinetics across developmental stages. CONCLUSIONS Through integrative analyses of datasets generated by ultrasensitive methods, our study reveals that the proteome shows distinct dynamics compared to the translatome and transcriptome during mouse OET. We propose that the remarkably stable oocyte-originated proteome may help save resources to accommodate the demanding needs of growing embryos. This study will advance our understanding of mammalian OET and the fundamental principles governing gene expression.
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Affiliation(s)
- Hongmei Zhang
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, New Cornerstone Science Laboratory, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Shuyan Ji
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, New Cornerstone Science Laboratory, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Ke Zhang
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, New Cornerstone Science Laboratory, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Yuling Chen
- School of Life Sciences, Tsinghua University, Beijing, China
| | - Jia Ming
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, New Cornerstone Science Laboratory, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Feng Kong
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, New Cornerstone Science Laboratory, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Lijuan Wang
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, New Cornerstone Science Laboratory, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Shun Wang
- School of Mathematics and Statistics, Wuhan University, Wuhan, China
- Hubei Key Laboratory of Computational Science, Wuhan University, Wuhan, China
| | - Zhuoning Zou
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, New Cornerstone Science Laboratory, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China
| | - Zhuqing Xiong
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, New Cornerstone Science Laboratory, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Kai Xu
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, New Cornerstone Science Laboratory, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Zili Lin
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, New Cornerstone Science Laboratory, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Bo Huang
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, School of Medicine, the First Affiliated Hospital, Zhejiang University, Hangzhou, 310002, China
| | - Ling Liu
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, New Cornerstone Science Laboratory, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Qiang Fan
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, New Cornerstone Science Laboratory, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Suoqin Jin
- School of Mathematics and Statistics, Wuhan University, Wuhan, China
| | - Haiteng Deng
- School of Life Sciences, Tsinghua University, Beijing, China
| | - Wei Xie
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, New Cornerstone Science Laboratory, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
- Tsinghua-Peking Center for Life Sciences, Beijing, China.
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12
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Sabatier M, Birsen R, Lauture L, Mouche S, Angelino P, Dehairs J, Goupille L, Boussaid I, Heiblig M, Boet E, Sahal A, Saland E, Santos JC, Armengol M, Fernández-Serrano M, Farge T, Cognet G, Simonetta F, Pignon C, Graffeuil A, Mazzotti C, Avet-Loiseau H, Delos O, Bertrand-Michel J, Chedru A, Dembitz V, Gallipoli P, Anstee NS, Loo S, Wei AH, Carroll M, Goubard A, Castellano R, Collette Y, Vergez F, Mansat-De Mas V, Bertoli S, Tavitian S, Picard M, Récher C, Bourges-Abella N, Granat F, Kosmider O, Sujobert P, Colsch B, Joffre C, Stuani L, Swinnen JV, Guillou H, Roué G, Hakim N, Dejean AS, Tsantoulis P, Larrue C, Bouscary D, Tamburini J, Sarry JE. C/EBPα Confers Dependence to Fatty Acid Anabolic Pathways and Vulnerability to Lipid Oxidative Stress-Induced Ferroptosis in FLT3-Mutant Leukemia. Cancer Discov 2023; 13:1720-1747. [PMID: 37012202 DOI: 10.1158/2159-8290.cd-22-0411] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 01/19/2023] [Accepted: 03/30/2023] [Indexed: 04/05/2023]
Abstract
Although transcription factor CCAAT-enhancer binding protein α (C/EBPα) is critical for normal and leukemic differentiation, its role in cell and metabolic homeostasis is largely unknown in cancer. Here, multiomics analyses uncovered a coordinated activation of C/EBPα and Fms-like tyrosine kinase 3 (FLT3) that increased lipid anabolism in vivo and in patients with FLT3-mutant acute myeloid leukemia (AML). Mechanistically, C/EBPα regulated the fatty acid synthase (FASN)-stearoyl-CoA desaturase (SCD) axis to promote fatty acid (FA) biosynthesis and desaturation. We further demonstrated that FLT3 or C/EBPα inactivation decreased monounsaturated FA incorporation to membrane phospholipids through SCD downregulation. Consequently, SCD inhibition enhanced susceptibility to lipid redox stress that was exploited by combining FLT3 and glutathione peroxidase 4 inhibition to trigger lipid oxidative stress, enhancing ferroptotic death of FLT3-mutant AML cells. Altogether, our study reveals a C/EBPα function in lipid homeostasis and adaptation to redox stress, and a previously unreported vulnerability of FLT3-mutant AML to ferroptosis with promising therapeutic application. SIGNIFICANCE FLT3 mutations are found in 30% of AML cases and are actionable by tyrosine kinase inhibitors. Here, we discovered that C/EBPα regulates FA biosynthesis and protection from lipid redox stress downstream mutant-FLT3 signaling, which confers a vulnerability to ferroptosis upon FLT3 inhibition with therapeutic potential in AML. This article is highlighted in the In This Issue feature, p. 1501.
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Affiliation(s)
- Marie Sabatier
- Centre de Recherches en Cancérologie de Toulouse, Université de Toulouse, Inserm U1037, CNRS U5077, Toulouse, France
- LabEx Toucan, Toulouse, France
- Équipe Labellisée Ligue Nationale Contre le Cancer 2018, Toulouse, France
| | - Rudy Birsen
- Translational Research Centre in Onco-Hematology, Faculty of Medicine, University of Geneva, and Swiss Cancer Center Leman, Geneva, Switzerland
- Université de Paris, Institut Cochin, CNRS U8104, Inserm U1016, Paris, France
- Equipe Labellisée Ligue Nationale Contre le Cancer, Paris, France
- Assistance Publique-Hôpitaux de Paris, Hôpitaux Universitaires Paris Centre, Service d'Hématologie Clinique, Paris, France
| | - Laura Lauture
- Centre de Recherches en Cancérologie de Toulouse, Université de Toulouse, Inserm U1037, CNRS U5077, Toulouse, France
- LabEx Toucan, Toulouse, France
- Équipe Labellisée Ligue Nationale Contre le Cancer 2018, Toulouse, France
| | - Sarah Mouche
- Translational Research Centre in Onco-Hematology, Faculty of Medicine, University of Geneva, and Swiss Cancer Center Leman, Geneva, Switzerland
| | - Paolo Angelino
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Jonas Dehairs
- Laboratory of Lipid Metabolism and Cancer, Department of Oncology, LKI-Leuven Cancer Institute, KU Leuven, Leuven, Belgium
| | - Léa Goupille
- Centre de Recherches en Cancérologie de Toulouse, Université de Toulouse, Inserm U1037, CNRS U5077, Toulouse, France
- LabEx Toucan, Toulouse, France
- Équipe Labellisée Ligue Nationale Contre le Cancer 2018, Toulouse, France
| | - Ismael Boussaid
- Université de Paris, Institut Cochin, CNRS U8104, Inserm U1016, Paris, France
- Equipe Labellisée Ligue Nationale Contre le Cancer, Paris, France
| | - Maël Heiblig
- Hospices Civils de Lyon, Hôpital Lyon Sud, Lyon, France
- CIRI, Inserm U1111 CNRS 5308, Université Lyon 1, Lyon, France
| | - Emeline Boet
- Centre de Recherches en Cancérologie de Toulouse, Université de Toulouse, Inserm U1037, CNRS U5077, Toulouse, France
- LabEx Toucan, Toulouse, France
- Équipe Labellisée Ligue Nationale Contre le Cancer 2018, Toulouse, France
| | - Ambrine Sahal
- Centre de Recherches en Cancérologie de Toulouse, Université de Toulouse, Inserm U1037, CNRS U5077, Toulouse, France
- LabEx Toucan, Toulouse, France
- Équipe Labellisée Ligue Nationale Contre le Cancer 2018, Toulouse, France
| | - Estelle Saland
- Centre de Recherches en Cancérologie de Toulouse, Université de Toulouse, Inserm U1037, CNRS U5077, Toulouse, France
- LabEx Toucan, Toulouse, France
- Équipe Labellisée Ligue Nationale Contre le Cancer 2018, Toulouse, France
| | - Juliana C Santos
- Lymphoma Translational Group, Josep Carreras Leukaemia Research Institute, Badalona, Spain
| | - Marc Armengol
- Lymphoma Translational Group, Josep Carreras Leukaemia Research Institute, Badalona, Spain
| | | | - Thomas Farge
- Centre de Recherches en Cancérologie de Toulouse, Université de Toulouse, Inserm U1037, CNRS U5077, Toulouse, France
- LabEx Toucan, Toulouse, France
- Équipe Labellisée Ligue Nationale Contre le Cancer 2018, Toulouse, France
| | - Guillaume Cognet
- Centre de Recherches en Cancérologie de Toulouse, Université de Toulouse, Inserm U1037, CNRS U5077, Toulouse, France
- LabEx Toucan, Toulouse, France
- Équipe Labellisée Ligue Nationale Contre le Cancer 2018, Toulouse, France
| | - Federico Simonetta
- Translational Research Centre in Onco-Hematology, Faculty of Medicine, University of Geneva, and Swiss Cancer Center Leman, Geneva, Switzerland
| | - Corentin Pignon
- Centre de Recherches en Cancérologie de Toulouse, Université de Toulouse, Inserm U1037, CNRS U5077, Toulouse, France
- Centre Hospitalier Universitaire de Toulouse, Institut Universitaire du Cancer de Toulouse Oncopole, Service d'Hématologie, Toulouse, France
| | - Antoine Graffeuil
- Centre de Recherches en Cancérologie de Toulouse, Université de Toulouse, Inserm U1037, CNRS U5077, Toulouse, France
- Centre Hospitalier Universitaire de Toulouse, Institut Universitaire du Cancer de Toulouse Oncopole, Service d'Hématologie, Toulouse, France
| | - Céline Mazzotti
- Centre de Recherches en Cancérologie de Toulouse, Université de Toulouse, Inserm U1037, CNRS U5077, Toulouse, France
- Centre Hospitalier Universitaire de Toulouse, Institut Universitaire du Cancer de Toulouse Oncopole, Service d'Hématologie, Toulouse, France
| | - Hervé Avet-Loiseau
- Centre de Recherches en Cancérologie de Toulouse, Université de Toulouse, Inserm U1037, CNRS U5077, Toulouse, France
- Centre Hospitalier Universitaire de Toulouse, Institut Universitaire du Cancer de Toulouse Oncopole, Service d'Hématologie, Toulouse, France
| | - Océane Delos
- MetaboHUB-MetaToul, National Infrastructure of Metabolomics and Fluxomics, University Paul Sabatier, Toulouse, France
| | - Justine Bertrand-Michel
- MetaboHUB-MetaToul, National Infrastructure of Metabolomics and Fluxomics, University Paul Sabatier, Toulouse, France
| | - Amélie Chedru
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé, MetaboHUB, Gif sur Yvette, France
| | - Vilma Dembitz
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
| | - Paolo Gallipoli
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
| | - Natasha S Anstee
- Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Australia
| | - Sun Loo
- Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Australia
- Clinical Haematology, Peter MacCallum Cancer Centre and Royal Melbourne Hospital, Melbourne, Australia
| | - Andrew H Wei
- Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Australia
- Clinical Haematology, Peter MacCallum Cancer Centre and Royal Melbourne Hospital, Melbourne, Australia
| | - Martin Carroll
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Armelle Goubard
- Aix-Marseille University, Inserm, CNRS, Institut Paoli-Calmettes, CRCM, Marseille, France
| | - Rémy Castellano
- Aix-Marseille University, Inserm, CNRS, Institut Paoli-Calmettes, CRCM, Marseille, France
| | - Yves Collette
- Aix-Marseille University, Inserm, CNRS, Institut Paoli-Calmettes, CRCM, Marseille, France
| | - François Vergez
- Centre de Recherches en Cancérologie de Toulouse, Université de Toulouse, Inserm U1037, CNRS U5077, Toulouse, France
- LabEx Toucan, Toulouse, France
- Équipe Labellisée Ligue Nationale Contre le Cancer 2018, Toulouse, France
- Centre Hospitalier Universitaire de Toulouse, Institut Universitaire du Cancer de Toulouse Oncopole, Service d'Hématologie, Toulouse, France
| | - Véronique Mansat-De Mas
- Centre de Recherches en Cancérologie de Toulouse, Université de Toulouse, Inserm U1037, CNRS U5077, Toulouse, France
- LabEx Toucan, Toulouse, France
- Équipe Labellisée Ligue Nationale Contre le Cancer 2018, Toulouse, France
- Centre Hospitalier Universitaire de Toulouse, Institut Universitaire du Cancer de Toulouse Oncopole, Service d'Hématologie, Toulouse, France
| | - Sarah Bertoli
- Centre de Recherches en Cancérologie de Toulouse, Université de Toulouse, Inserm U1037, CNRS U5077, Toulouse, France
- LabEx Toucan, Toulouse, France
- Équipe Labellisée Ligue Nationale Contre le Cancer 2018, Toulouse, France
- Centre Hospitalier Universitaire de Toulouse, Institut Universitaire du Cancer de Toulouse Oncopole, Service d'Hématologie, Toulouse, France
| | - Suzanne Tavitian
- Centre Hospitalier Universitaire de Toulouse, Institut Universitaire du Cancer de Toulouse Oncopole, Service d'Hématologie, Toulouse, France
| | - Muriel Picard
- Centre Hospitalier Universitaire de Toulouse, Institut Universitaire du Cancer de Toulouse Oncopole, Service de Réanimation, Toulouse, France
| | - Christian Récher
- Centre de Recherches en Cancérologie de Toulouse, Université de Toulouse, Inserm U1037, CNRS U5077, Toulouse, France
- LabEx Toucan, Toulouse, France
- Équipe Labellisée Ligue Nationale Contre le Cancer 2018, Toulouse, France
- Centre Hospitalier Universitaire de Toulouse, Institut Universitaire du Cancer de Toulouse Oncopole, Service d'Hématologie, Toulouse, France
| | | | - Fanny Granat
- Centre de Recherches en Cancérologie de Toulouse, Université de Toulouse, Inserm U1037, CNRS U5077, Toulouse, France
- LabEx Toucan, Toulouse, France
- Équipe Labellisée Ligue Nationale Contre le Cancer 2018, Toulouse, France
| | - Olivier Kosmider
- Université de Paris, Institut Cochin, CNRS U8104, Inserm U1016, Paris, France
- Equipe Labellisée Ligue Nationale Contre le Cancer, Paris, France
| | - Pierre Sujobert
- Hospices Civils de Lyon, Hôpital Lyon Sud, Lyon, France
- CIRI, Inserm U1111 CNRS 5308, Université Lyon 1, Lyon, France
| | - Benoit Colsch
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé, MetaboHUB, Gif sur Yvette, France
| | - Carine Joffre
- Centre de Recherches en Cancérologie de Toulouse, Université de Toulouse, Inserm U1037, CNRS U5077, Toulouse, France
- LabEx Toucan, Toulouse, France
- Équipe Labellisée Ligue Nationale Contre le Cancer 2018, Toulouse, France
| | - Lucille Stuani
- Centre de Recherches en Cancérologie de Toulouse, Université de Toulouse, Inserm U1037, CNRS U5077, Toulouse, France
- LabEx Toucan, Toulouse, France
- Équipe Labellisée Ligue Nationale Contre le Cancer 2018, Toulouse, France
| | - Johannes V Swinnen
- Laboratory of Lipid Metabolism and Cancer, Department of Oncology, LKI-Leuven Cancer Institute, KU Leuven, Leuven, Belgium
| | - Hervé Guillou
- Toxalim (Research Centre in Food Toxicology), Université de Toulouse, INRAE, ENVT, INP-Purpan, University Paul Sabatier, Toulouse, France
| | - Gael Roué
- Lymphoma Translational Group, Josep Carreras Leukaemia Research Institute, Badalona, Spain
| | - Nawad Hakim
- Institut Toulousain des Maladies Infectieuses et Inflammatoires (INFINITy), Inserm UMR1291, CNRS UMR5051, Université Toulouse III, Toulouse, France
| | - Anne S Dejean
- Institut Toulousain des Maladies Infectieuses et Inflammatoires (INFINITy), Inserm UMR1291, CNRS UMR5051, Université Toulouse III, Toulouse, France
| | - Petros Tsantoulis
- Translational Research Centre in Onco-Hematology, Faculty of Medicine, University of Geneva, and Swiss Cancer Center Leman, Geneva, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Clément Larrue
- Translational Research Centre in Onco-Hematology, Faculty of Medicine, University of Geneva, and Swiss Cancer Center Leman, Geneva, Switzerland
| | - Didier Bouscary
- Université de Paris, Institut Cochin, CNRS U8104, Inserm U1016, Paris, France
- Equipe Labellisée Ligue Nationale Contre le Cancer, Paris, France
- Assistance Publique-Hôpitaux de Paris, Hôpitaux Universitaires Paris Centre, Service d'Hématologie Clinique, Paris, France
| | - Jerome Tamburini
- Translational Research Centre in Onco-Hematology, Faculty of Medicine, University of Geneva, and Swiss Cancer Center Leman, Geneva, Switzerland
- Université de Paris, Institut Cochin, CNRS U8104, Inserm U1016, Paris, France
- Equipe Labellisée Ligue Nationale Contre le Cancer, Paris, France
| | - Jean-Emmanuel Sarry
- Centre de Recherches en Cancérologie de Toulouse, Université de Toulouse, Inserm U1037, CNRS U5077, Toulouse, France
- LabEx Toucan, Toulouse, France
- Équipe Labellisée Ligue Nationale Contre le Cancer 2018, Toulouse, France
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13
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Sarkar S, Rammohan J. Nearly maximal information gain due to time integration in central dogma reactions. iScience 2023; 26:106767. [PMID: 37235057 PMCID: PMC10206154 DOI: 10.1016/j.isci.2023.106767] [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: 09/27/2022] [Revised: 02/21/2023] [Accepted: 04/24/2023] [Indexed: 05/28/2023] Open
Abstract
Living cells process information about their environment through the central dogma processes of transcription and translation, which drive the cellular response to stimuli. Here, we study the transfer of information from environmental input to the transcript and protein expression levels. Evaluation of both experimental and analogous simulation data reveals that transcription and translation are not two simple information channels connected in series. Instead, we demonstrate that the central dogma reactions often create a time-integrating information channel, where the translation channel receives and integrates multiple outputs from the transcription channel. This information channel model of the central dogma provides new information-theoretic selection criteria for the central dogma rate constants. Using the data for four well-studied species we show that their central dogma rate constants achieve information gain because of time integration while also keeping the loss because of stochasticity in translation relatively low (<0.5 bits).
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Affiliation(s)
- Swarnavo Sarkar
- National Institute of Standards and Technology, Gaithersburg, MD 20899, USA
| | - Jayan Rammohan
- National Institute of Standards and Technology, Gaithersburg, MD 20899, USA
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14
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Paul AA, Szulc NA, Kobiela A, Brown SJ, Pokrzywa W, Gutowska-Owsiak D. In silico analysis of the profilaggrin sequence indicates alterations in the stability, degradation route, and intracellular protein fate in filaggrin null mutation carriers. Front Mol Biosci 2023; 10:1105678. [PMID: 37200867 PMCID: PMC10185843 DOI: 10.3389/fmolb.2023.1105678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 04/19/2023] [Indexed: 05/20/2023] Open
Abstract
Background: Loss of function mutation in FLG is the major genetic risk factor for atopic dermatitis (AD) and other allergic manifestations. Presently, little is known about the cellular turnover and stability of profilaggrin, the protein encoded by FLG. Since ubiquitination directly regulates the cellular fate of numerous proteins, their degradation and trafficking, this process could influence the concentration of filaggrin in the skin. Objective: To determine the elements mediating the interaction of profilaggrin with the ubiquitin-proteasome system (i.e., degron motifs and ubiquitination sites), the features responsible for its stability, and the effect of nonsense and frameshift mutations on profilaggrin turnover. Methods: The effect of inhibition of proteasome and deubiquitinases on the level and modifications of profilaggrin and processed products was assessed by immunoblotting. Wild-type profilaggrin sequence and its mutated variants were analysed in silico using the DEGRONOPEDIA and Clustal Omega tool. Results: Inhibition of proteasome and deubiquitinases stabilizes profilaggrin and its high molecular weight of presumably ubiquitinated derivatives. In silico analysis of the sequence determined that profilaggrin contains 18 known degron motifs as well as multiple canonical and non-canonical ubiquitination-prone residues. FLG mutations generate products with increased stability scores, altered usage of the ubiquitination marks, and the frequent appearance of novel degrons, including those promoting C-terminus-mediated degradation routes. Conclusion: The proteasome is involved in the turnover of profilaggrin, which contains multiple degrons and ubiquitination-prone residues. FLG mutations alter those key elements, affecting the degradation routes and the mutated products' stability.
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Affiliation(s)
- Argho Aninda Paul
- Experimental and Translational Immunology Group, Intercollegiate Faculty of Biotechnology of University of Gdansk and Medical University of Gdansk, University of Gdansk, Gdansk, Poland
| | - Natalia A. Szulc
- Laboratory of Protein Metabolism, International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland
| | - Adrian Kobiela
- Experimental and Translational Immunology Group, Intercollegiate Faculty of Biotechnology of University of Gdansk and Medical University of Gdansk, University of Gdansk, Gdansk, Poland
| | - Sara J. Brown
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
| | - Wojciech Pokrzywa
- Laboratory of Protein Metabolism, International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland
| | - Danuta Gutowska-Owsiak
- Experimental and Translational Immunology Group, Intercollegiate Faculty of Biotechnology of University of Gdansk and Medical University of Gdansk, University of Gdansk, Gdansk, Poland
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15
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Santo EE, Ribel‐Madsen R, Stroeken PJ, de Boer VCJ, Hansen NS, Commandeur M, Vaag AA, Versteeg R, Paik J, Westerhout EM. FOXO3A-short is a novel regulator of non-oxidative glucose metabolism associated with human longevity. Aging Cell 2023; 22:e13763. [PMID: 36617632 PMCID: PMC10014046 DOI: 10.1111/acel.13763] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 11/06/2022] [Accepted: 12/09/2022] [Indexed: 01/10/2023] Open
Abstract
Intronic single-nucleotide polymorphisms (SNPs) in FOXO3A are associated with human longevity. Currently, it is unclear how these SNPs alter FOXO3A functionality and human physiology, thereby influencing lifespan. Here, we identify a primate-specific FOXO3A transcriptional isoform, FOXO3A-Short (FOXO3A-S), encoding a major longevity-associated SNP, rs9400239 (C or T), within its 5' untranslated region. The FOXO3A-S mRNA is highly expressed in the skeletal muscle and has very limited expression in other tissues. We find that the rs9400239 variant influences the stability and functionality of the primarily nuclear protein(s) encoded by the FOXO3A-S mRNA. Assessment of the relationship between the FOXO3A-S polymorphism and peripheral glucose clearance during insulin infusion (Rd clamp) in a cohort of Danish twins revealed that longevity T-allele carriers have markedly faster peripheral glucose clearance rates than normal lifespan C-allele carriers. In vitro experiments in human myotube cultures utilizing overexpression of each allele showed that the C-allele represses glycolysis independently of PI3K signaling, while overexpression of the T-allele represses glycolysis only in a PI3K-inactive background. Supporting this finding inducible knockdown of the FOXO3A-S C-allele in cultured myotubes increases the glycolytic rate. We conclude that the rs9400239 polymorphism acts as a molecular switch which changes the identity of the FOXO3A-S-derived protein(s), which in turn alters the relationship between FOXO3A-S and insulin/PI3K signaling and glycolytic flux in the skeletal muscle. This critical difference endows carriers of the FOXO3A-S T-allele with consistently higher insulin-stimulated peripheral glucose clearance rates, which may contribute to their longer and healthier lifespans.
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Affiliation(s)
- Evan E. Santo
- Department of Pathology & Laboratory MedicineWeill Cornell MedicineNew YorkNew YorkUSA
| | - Rasmus Ribel‐Madsen
- The Novo Nordisk Foundation Center for Basic Metabolic ResearchClinical PharmacologyCopenhagenDenmark
- The Danish Diabetes AcademyOdenseDenmark
| | - Peter J. Stroeken
- Department of Oncogenomics, Academic Medical CenterUniversity of AmsterdamAmsterdamThe Netherlands
| | | | - Ninna S. Hansen
- Department of Biomedical Sciences, Endocrinology and MetabolismUniversity of CopenhagenCopenhagenDenmark
| | - Maaike Commandeur
- Department of Oncogenomics, Academic Medical CenterUniversity of AmsterdamAmsterdamThe Netherlands
| | - Allan A. Vaag
- Department of Biomedical Sciences, Endocrinology and MetabolismUniversity of CopenhagenCopenhagenDenmark
- Department of Clinical Sciences, Clinical Research CentreLund UniversityMalmöSweden
| | - Rogier Versteeg
- Department of Oncogenomics, Academic Medical CenterUniversity of AmsterdamAmsterdamThe Netherlands
| | - Jihye Paik
- Department of Pathology & Laboratory MedicineWeill Cornell MedicineNew YorkNew YorkUSA
| | - Ellen M. Westerhout
- Department of Oncogenomics, Academic Medical CenterUniversity of AmsterdamAmsterdamThe Netherlands
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16
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Abstract
Cellular protein turnover-the net result of protein synthesis and degradation-is crucial to maintain protein homeostasis and cellular function under steady-state conditions and to enable cells to remodel their proteomes upon a perturbation. In brain cells, proteins are continuously turned over at different rates depending on various factors including cell type, subcellular localization, cellular environment, and neuronal activity. Here we describe a workflow for the analysis of protein synthesis, degradation, and turnover in primary cultured rat neurons and glia using dynamic/pulsed SILAC and mass spectrometry.
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Affiliation(s)
- Aline R Dörrbaum
- Max Planck Institute for Brain Research, Frankfurt am Main, Germany
| | - Erin M Schuman
- Max Planck Institute for Brain Research, Frankfurt am Main, Germany.
| | - Julian D Langer
- Max Planck Institute for Brain Research, Frankfurt am Main, Germany.
- Max Planck Institute of Biophysics, Frankfurt am Main, Germany.
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17
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Gardner AP, Barbieri JT, Pellett S. How Botulinum Neurotoxin Light Chain A1 Maintains Stable Association with the Intracellular Neuronal Plasma Membrane. Toxins (Basel) 2022; 14:toxins14120814. [PMID: 36548711 PMCID: PMC9783275 DOI: 10.3390/toxins14120814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 11/17/2022] [Accepted: 11/18/2022] [Indexed: 11/23/2022] Open
Abstract
Botulinum neurotoxin serotype A (BoNT/A) is the most potent protein toxin for humans and is utilized as a therapy for numerous neurologic diseases. BoNT/A comprises a catalytic Light Chain (LC/A) and a Heavy Chain (HC/A) and includes eight subtypes (BoNT/A1-/A8). Previously we showed BoNT/A potency positively correlated with stable localization on the intracellular plasma membrane and identified a low homology domain (amino acids 268-357) responsible for LC/A1 stable co-localization with SNAP-25 on the plasma membrane, while LC/A3 was present in the cytosol of Neuro2A cells. In the present study, steady-state- and live-imaging of a cytosolic LC/A3 derivative (LC/A3V) engineered to contain individual structural elements of the A1 LDH showed that a 59 amino acid region (275-334) termed the MLD was sufficient to direct LC/A3V from the cytosol to the plasma membrane co-localized with SNAP-25. Informatics and experimental validation of the MLD-predicted R1 region (an α-helix, residues 275-300) and R2 region (a loop, α-helix, loop, residues 302-334) both contribute independent steps to the stable co-localization of LC/A1 with SNAP-25 on the plasma membrane of Neuro-2A cells. Understanding how these structural elements contribute to the overall association of LC/A1 on the plasma membrane may identify the molecular basis for the LC contribution of BoNT/A1 to high potency.
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Affiliation(s)
- Alexander P. Gardner
- Microbiology and Immunology, Medical College, Wisconsin 8701 Watertown Plank Road, Milwaukee, WI 53226, USA
| | - Joseph T. Barbieri
- Microbiology and Immunology, Medical College, Wisconsin 8701 Watertown Plank Road, Milwaukee, WI 53226, USA
- Correspondence: (J.T.B.); (S.P.)
| | - Sabine Pellett
- Department of Bacteriology, Microbial Sciences Building, University of Wisconsin-Madison, 1550 Linden Dr., Madison, WI 53706, USA
- Correspondence: (J.T.B.); (S.P.)
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18
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Osana S, Kitajima Y, Naoki S, Takada H, Murayama K, Kano Y, Nagatomi R. Little involvement of recycled-amino acids from proteasomal proteolysis in de novo protein synthesis. Biochem Biophys Res Commun 2022; 634:40-47. [DOI: 10.1016/j.bbrc.2022.09.113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Accepted: 09/28/2022] [Indexed: 11/27/2022]
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Kelley CP, Haerle MC, Wang ET. Negative autoregulation mitigates collateral RNase activity of repeat-targeting CRISPR-Cas13d in mammalian cells. Cell Rep 2022; 40:111226. [PMID: 35977479 PMCID: PMC9809062 DOI: 10.1016/j.celrep.2022.111226] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 04/29/2022] [Accepted: 07/26/2022] [Indexed: 01/05/2023] Open
Abstract
CRISPR-Cas13 RNA endonucleases show promise for programmable RNA knockdown. However, sequence-specific binding of Cas13 unleashes non-specific bystander RNA cleavage, or collateral activity, raising concerns for experiments and therapeutic applications. Although robust in cell-free and bacterial environments, collateral activity in mammalian cells remains disputed. We investigate Cas13d collateral activity in a therapeutic context for myotonic dystrophy type 1, caused by a transcribed CTG repeat expansion. We find that, when targeting CUGn RNA in mammalian cells, Cas13d depletes endogenous and transgenic RNAs, interferes with critical cellular processes, and activates stress response and apoptosis. Collateral effects also occur when targeting abundant endogenous transcripts. To minimize collateral activity for repeat-targeting approaches, we introduce GENO, an adeno-associated virus-compatible strategy that leverages guide RNA processing to control Cas13d expression. We argue that thorough assessment of collateral activity is necessary when applying Cas13 in mammalian cells and that GENO illustrates advantages of compact regulatory systems for Cas-based gene therapies.
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Affiliation(s)
- Chase P Kelley
- Department of Molecular Genetics & Microbiology, Center for NeuroGenetics, Genetics Institute, University of Florida, Gainesville, FL 32608, USA; Genetics and Genomics Graduate Program, University of Florida, Gainesville, FL 32608, USA
| | - Maja C Haerle
- Department of Molecular Genetics & Microbiology, Center for NeuroGenetics, Genetics Institute, University of Florida, Gainesville, FL 32608, USA
| | - Eric T Wang
- Department of Molecular Genetics & Microbiology, Center for NeuroGenetics, Genetics Institute, University of Florida, Gainesville, FL 32608, USA; Myology Institute, University of Florida, Gainesville, FL 32608, USA.
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20
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Ahmad HI, Ijaz N, Afzal G, Asif AR, ur Rehman A, Rahman A, Ahmed I, Yousaf M, Elokil A, Muhammad SA, Albogami SM, Alotaibi SS. Computational Insights into the Structural and Functional Impacts of nsSNPs of Bone Morphogenetic Proteins. BIOMED RESEARCH INTERNATIONAL 2022; 2022:4013729. [PMID: 35832847 PMCID: PMC9273450 DOI: 10.1155/2022/4013729] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Accepted: 06/15/2022] [Indexed: 12/12/2022]
Abstract
BMPs (bone morphogenetic proteins) are multipurpose (transforming growth factor)TGF-superfamily released cytokines. These glycoproteins, acting as disulfide-linked homo- or heterodimers, are highly potent regulators of bone and cartilage production and repair, cell proliferation throughout embryonic development, and bone homeostasis in the adults. Due to the fact that genetic variation might influence structural functions, this study is aimed to determine the pathogenic effect of nonsynonymous single-nucleotide polymorphisms (nsSNPs) in BMP genes. The implications of these variations, investigated using computational analysis and molecular models of the mature TGF-β domain, revealed the impact of modifications on the function of BMP protein. The three-dimensional (3D) structure analysis was performed on the nsSNP Y316S, V386G, E387G, C389G, and C391G nsSNP in the TGF-β domain of chicken BMP2 and H344P, S347P, V357A nsSNP in the TGF-β domain of chicken BMP4 protein that was anticipated to be harmful and of high risk. The ability of the proteins to perform variety of tasks interact with other molecules depends on their tertiary structural composition. The current analysis revealed the four most damaging variants (Y316S, V386G, E387G, C389G, and C391G), highly conserved and functional and are located in the TGF-beta domain of BMP2 and BMP4. The amino acid substitutions E387G, C389G, and C391G are discovered in the binding region. It was observed that the mutations in the TGF-beta domain caused significant changes in its structural organization including the substrate binding sites. Current findings will assist future research focused on the role of these variants in BMP function loss and their role in skeletal disorders, and this will possibly help to develop practical strategies for treating bone-related conditions.
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Affiliation(s)
- Hafiz Ishfaq Ahmad
- Department of Animal Breeding and Genetics, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Nabeel Ijaz
- Department of Clinical Science, Faculty of Veterinary Sciences, Bahauddin Zakariya University Multan, Pakistan
| | - Gulnaz Afzal
- Department of Zoology, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | - Akhtar Rasool Asif
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Huazhong Agricultural University, Wuhan, China
- University of Veterinary and Animal Sciences, Lahore, Sub-Campus Jhang, Pakistan
| | - Aziz ur Rehman
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Huazhong Agricultural University, Wuhan, China
- University of Veterinary and Animal Sciences, Lahore, Sub-Campus Jhang, Pakistan
| | - Abdur Rahman
- University of Veterinary and Animal Sciences, Lahore, Sub-Campus Jhang, Pakistan
- Department of Animal Nutrition, Afyon Kocatepe University, Turkey
| | - Irfan Ahmed
- Department of Animal Nutrition, Faculty of Veterinary and Animal Sciences, The Islamia University of Bahawalpur, Pakistan
| | - Muhammad Yousaf
- Department of Animal Nutrition, Faculty of Veterinary and Animal Sciences, The Islamia University of Bahawalpur, Pakistan
| | - Abdelmotaleb Elokil
- Department of Animal Production, Faculty of Agriculture, Benha University, Moshtohor 13736, Egypt
| | - Sayyed Aun Muhammad
- University of Veterinary and Animal Sciences, Lahore, Sub-Campus Jhang, Pakistan
| | - Sarah M. Albogami
- Department of Biotechnology, College of Science, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia
| | - Saqer S. Alotaibi
- Department of Biotechnology, College of Science, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia
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21
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Nissley DA, Jiang Y, Trovato F, Sitarik I, Narayan KB, To P, Xia Y, Fried SD, O’Brien EP. Universal protein misfolding intermediates can bypass the proteostasis network and remain soluble and less functional. Nat Commun 2022; 13:3081. [PMID: 35654797 PMCID: PMC9163053 DOI: 10.1038/s41467-022-30548-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 05/05/2022] [Indexed: 01/12/2023] Open
Abstract
Some misfolded protein conformations can bypass proteostasis machinery and remain soluble in vivo. This is an unexpected observation, as cellular quality control mechanisms should remove misfolded proteins. Three questions, then, are: how do long-lived, soluble, misfolded proteins bypass proteostasis? How widespread are such misfolded states? And how long do they persist? We address these questions using coarse-grain molecular dynamics simulations of the synthesis, termination, and post-translational dynamics of a representative set of cytosolic E. coli proteins. We predict that half of proteins exhibit misfolded subpopulations that bypass molecular chaperones, avoid aggregation, and will not be rapidly degraded, with some misfolded states persisting for months or longer. The surface properties of these misfolded states are native-like, suggesting they will remain soluble, while self-entanglements make them long-lived kinetic traps. In terms of function, we predict that one-third of proteins can misfold into soluble less-functional states. For the heavily entangled protein glycerol-3-phosphate dehydrogenase, limited-proteolysis mass spectrometry experiments interrogating misfolded conformations of the protein are consistent with the structural changes predicted by our simulations. These results therefore provide an explanation for how proteins can misfold into soluble conformations with reduced functionality that can bypass proteostasis, and indicate, unexpectedly, this may be a wide-spread phenomenon.
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Affiliation(s)
- Daniel A. Nissley
- grid.29857.310000 0001 2097 4281Department of Chemistry, Pennsylvania State University, University Park, PA 16802 USA
| | - Yang Jiang
- grid.29857.310000 0001 2097 4281Department of Chemistry, Pennsylvania State University, University Park, PA 16802 USA
| | - Fabio Trovato
- grid.29857.310000 0001 2097 4281Department of Chemistry, Pennsylvania State University, University Park, PA 16802 USA
| | - Ian Sitarik
- grid.29857.310000 0001 2097 4281Department of Chemistry, Pennsylvania State University, University Park, PA 16802 USA
| | - Karthik B. Narayan
- grid.29857.310000 0001 2097 4281Department of Chemistry, Pennsylvania State University, University Park, PA 16802 USA
| | - Philip To
- grid.21107.350000 0001 2171 9311Department of Chemistry, Johns Hopkins University, Baltimore, MD 21218 USA
| | - Yingzi Xia
- grid.21107.350000 0001 2171 9311Department of Chemistry, Johns Hopkins University, Baltimore, MD 21218 USA
| | - Stephen D. Fried
- grid.21107.350000 0001 2171 9311Department of Chemistry, Johns Hopkins University, Baltimore, MD 21218 USA ,grid.21107.350000 0001 2171 9311Thomas C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218 USA
| | - Edward P. O’Brien
- grid.29857.310000 0001 2097 4281Department of Chemistry, Pennsylvania State University, University Park, PA 16802 USA ,grid.29857.310000 0001 2097 4281Bioinformatics and Genomics Graduate Program, The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802 USA ,grid.29857.310000 0001 2097 4281Institute for Computational and Data Sciences, Pennsylvania State University, University Park, PA 16802 USA
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22
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Dickson ZW, Golding GB. Low complexity regions in mammalian proteins are associated with low protein abundance and high transcript abundance. Mol Biol Evol 2022; 39:6575407. [PMID: 35482425 PMCID: PMC9070799 DOI: 10.1093/molbev/msac087] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Low Complexity Regions (LCRs) are present in a surprisingly large number of eukaryotic proteins. These highly repetitive and compositionally biased sequences are often structurally disordered, bind promiscuously, and evolve rapidly. Frequently studied in terms of evolutionary dynamics, little is known about how LCRs affect the expression of the proteins which contain them. It would be expected that rapidly evolving LCRs are unlikely to be tolerated in strongly conserved, highly abundant proteins, leading to lower overall abundance in proteins which contain LCRs. To test this hypothesis and examine the associations of protein abundance and transcript abundance with the presence of LCRs, we have integrated high-throughput data from across mammals. We have found that LCRs are indeed associated with reduced protein abundance, but are also associated with elevated transcript abundance. These associations are qualitatively consistent across 12 human tissues and nine mammalian species. The differential impacts of LCRs on abundance at the protein and transcript level are not explained by differences in either protein degradation rates or the inefficiency of translation for LCR containing proteins. We suggest that rapidly evolving LCRs are a source of selective pressure on the regulatory mechanisms which maintain steady-state protein abundance levels.
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Affiliation(s)
- Zachery W Dickson
- Department of Biology, McMaster University, Hamilton, Ontario, Canada
| | - G Brian Golding
- Department of Biology, McMaster University, Hamilton, Ontario, Canada
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23
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Grycz K, Głowacka A, Ji B, Krzywdzińska K, Charzyńska A, Czarkowska-Bauch J, Gajewska-Woźniak O, Skup M. Regulation of perineuronal net components in the synaptic bouton vicinity on lumbar α-motoneurons in the rat after spinalization and locomotor training: New insights from spatio-temporal changes in gene, protein expression and WFA labeling. Exp Neurol 2022; 354:114098. [DOI: 10.1016/j.expneurol.2022.114098] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 03/31/2022] [Accepted: 04/24/2022] [Indexed: 11/25/2022]
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24
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Rusilowicz-Jones EV, Urbé S, Clague MJ. Protein degradation on the global scale. Mol Cell 2022; 82:1414-1423. [PMID: 35305310 DOI: 10.1016/j.molcel.2022.02.027] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Revised: 02/01/2022] [Accepted: 02/17/2022] [Indexed: 12/15/2022]
Abstract
Protein degradation occurs through proteasomal, endosomal, and lysosomal pathways. Technological advancements have allowed for the determination of protein copy numbers and turnover rates on a global scale, which has provided an overview of trends and rules governing protein degradation. Sharper chemical and gene-editing tools have enabled the specific perturbation of each degradation pathway, whose effects on protein dynamics can now be comprehensively analyzed. We review major studies and innovation in this field and discuss the interdependence between the major pathways of protein degradation.
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Affiliation(s)
- Emma V Rusilowicz-Jones
- Department of Molecular Physiology and Cell Signalling, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 3BX, UK
| | - Sylvie Urbé
- Department of Molecular Physiology and Cell Signalling, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 3BX, UK
| | - Michael J Clague
- Department of Molecular Physiology and Cell Signalling, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 3BX, UK.
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25
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Sadygov RG. Protein turnover models for LC-MS data of heavy water metabolic labeling. Brief Bioinform 2022; 23:6513431. [PMID: 35062023 PMCID: PMC8921656 DOI: 10.1093/bib/bbab598] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 12/12/2021] [Accepted: 12/26/2021] [Indexed: 01/23/2023] Open
Abstract
Protein turnover is vital for cellular functioning and is often associated with the pathophysiology of a variety of diseases. Metabolic labeling with heavy water followed by liquid chromatography coupled to mass spectrometry is a powerful tool to study in vivo protein turnover in high throughput and large scale. Heavy water is a cost-effective and easy to use labeling agent. It labels all nonessential amino acids. Due to its toxicity in high concentrations (20% or higher), small enrichments (8% or smaller) of heavy water are used with most organisms. The low concentration results in incomplete labeling of peptides/proteins. Therefore, the data processing is more challenging and requires accurate quantification of labeled and unlabeled forms of a peptide from overlapping mass isotopomer distributions. The work describes the bioinformatics aspects of the analysis of heavy water labeled mass spectral data, available software tools and current challenges and opportunities.
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Affiliation(s)
- Rovshan G Sadygov
- Corresponding author: Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555, USA. Tel.: (409)772-3287; E-mail:
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26
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Beller NC, Lukowski JK, Ludwig KR, Hummon AB. Spatial Stable Isotopic Labeling by Amino Acids in Cell Culture: Pulse-Chase Labeling of Three-Dimensional Multicellular Spheroids for Global Proteome Analysis. Anal Chem 2021; 93:15990-15999. [PMID: 34813286 DOI: 10.1021/acs.analchem.1c03461] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Three-dimensional cell cultures, or spheroids, are important model systems for cancer research because they recapitulate chemical and phenotypic aspects of in vivo tumors. Spheroids develop radially symmetric chemical gradients, resulting in distinct cellular populations. Stable isotopic labeling by amino acids in cell culture (SILAC) is a well-established approach to quantify protein expression and has previously been used in a pulse-chase format to evaluate temporal changes. In this article, we demonstrate that distinct isotopic signatures can be introduced into discrete spatial cellular populations, effectively tracking proteins to original locations in the spheroid, using a platform that we refer to as spatial SILAC. Spheroid populations were grown with light, medium, and heavy isotopic media, and the concentric shells of cells were harvested by serial trypsinization. Proteins were quantitatively analyzed by ultraperformance liquid chromatography-tandem mass spectrometry. The isotopic signatures correlated with the spatial location and the isotope position do not significantly impact the proteome of each individual layer. Spatial SILAC can be used to examine the proteomic changes in the different layers of the spheroid and to identify protein biomarkers throughout the structure. We show that SILAC labels can be discretely pulsed to discrete positions, without altering the spheroid's proteome, promising future combined pharmacodynamic and pharmacokinetic studies.
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Affiliation(s)
- Nicole C Beller
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Jessica K Lukowski
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Katelyn R Ludwig
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Amanda B Hummon
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States.,Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio 43210, United States
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27
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Venkataramanan S, Gadek M, Calviello L, Wilkins K, Floor SN. DDX3X and DDX3Y are redundant in protein synthesis. RNA (NEW YORK, N.Y.) 2021; 27:1577-1588. [PMID: 34535544 PMCID: PMC8594478 DOI: 10.1261/rna.078926.121] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 09/12/2021] [Indexed: 06/13/2023]
Abstract
DDX3 is a DEAD-box RNA helicase that regulates translation and is encoded by the X- and Y-linked paralogs DDX3X and DDX3Y While DDX3X is ubiquitously expressed in human tissues and essential for viability, DDX3Y is male-specific and shows lower and more variable expression than DDX3X in somatic tissues. Heterozygous genetic lesions in DDX3X mediate a class of developmental disorders called DDX3X syndrome, while loss of DDX3Y is implicated in male infertility. One possible explanation for female-bias in DDX3X syndrome is that DDX3Y encodes a polypeptide with different biochemical activity. In this study, we use ribosome profiling and in vitro translation to demonstrate that the X- and Y-linked paralogs of DDX3 play functionally redundant roles in translation. We find that transcripts that are sensitive to DDX3X depletion or mutation are rescued by complementation with DDX3Y. Our data indicate that DDX3X and DDX3Y proteins can functionally complement each other in the context of mRNA translation in human cells. DDX3Y is not expressed in a large fraction of the central nervous system. These findings suggest that expression differences, not differences in paralog-dependent protein synthesis, underlie the sex-bias of DDX3X-associated diseases.
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Affiliation(s)
- Srivats Venkataramanan
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, California 94143, USA
| | - Margaret Gadek
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, California 94143, USA
| | - Lorenzo Calviello
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, California 94143, USA
| | - Kevin Wilkins
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, California 94143, USA
| | - Stephen N Floor
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, California 94143, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California 94143, USA
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28
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Rolfs Z, Frey BL, Shi X, Kawai Y, Smith LM, Welham NV. An atlas of protein turnover rates in mouse tissues. Nat Commun 2021; 12:6778. [PMID: 34836951 PMCID: PMC8626426 DOI: 10.1038/s41467-021-26842-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 10/25/2021] [Indexed: 01/25/2023] Open
Abstract
Protein turnover is critical to cellular physiology as well as to the growth and maintenance of tissues. The unique synthesis and degradation rates of each protein help to define tissue phenotype, and knowledge of tissue- and protein-specific half-lives is directly relevant to protein-related drug development as well as the administration of medical therapies. Using stable isotope labeling and mass spectrometry, we determine the in vivo turnover rates of thousands of proteins-including those of the extracellular matrix-in a set of biologically important mouse tissues. We additionally develop a data visualization platform, named ApplE Turnover, that enables facile searching for any protein of interest in a tissue of interest and then displays its half-life, confidence interval, and supporting measurements. This extensive dataset and the corresponding visualization software provide a reference to guide future studies of mammalian protein turnover in response to physiologic perturbation, disease, or therapeutic intervention.
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Affiliation(s)
- Zach Rolfs
- grid.14003.360000 0001 2167 3675Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706 USA
| | - Brian L. Frey
- grid.14003.360000 0001 2167 3675Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706 USA
| | - Xudong Shi
- grid.14003.360000 0001 2167 3675Division of Otolaryngology–Head and Neck Surgery, Department of Surgery, University of Wisconsin School of Medicine and Public Health, Madison, WI 53792 USA
| | - Yoshitaka Kawai
- grid.14003.360000 0001 2167 3675Division of Otolaryngology–Head and Neck Surgery, Department of Surgery, University of Wisconsin School of Medicine and Public Health, Madison, WI 53792 USA ,grid.258799.80000 0004 0372 2033Present Address: Department of Otolaryngology–Head and Neck Surgery, Graduate School of Medicine, Kyoto University, Kyoto, 606-8507 Japan
| | - Lloyd M. Smith
- grid.14003.360000 0001 2167 3675Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706 USA
| | - Nathan V. Welham
- grid.14003.360000 0001 2167 3675Division of Otolaryngology–Head and Neck Surgery, Department of Surgery, University of Wisconsin School of Medicine and Public Health, Madison, WI 53792 USA
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29
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Li J, Cai Z, Vaites LP, Shen N, Mitchell DC, Huttlin EL, Paulo JA, Harry BL, Gygi SP. Proteome-wide mapping of short-lived proteins in human cells. Mol Cell 2021; 81:4722-4735.e5. [PMID: 34626566 DOI: 10.1016/j.molcel.2021.09.015] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 08/11/2021] [Accepted: 09/13/2021] [Indexed: 12/13/2022]
Abstract
Rapid protein degradation enables cells to quickly modulate protein abundance. Dysregulation of short-lived proteins plays essential roles in disease pathogenesis. A focused map of short-lived proteins remains understudied. Cycloheximide, a translational inhibitor, is widely used in targeted studies to measure degradation kinetics for short-lived proteins. Here, we combined cycloheximide chase assays with advanced quantitative proteomics to map short-lived proteins under translational inhibition in four human cell lines. Among 11,747 quantified proteins, we identified 1,017 short-lived proteins (half-lives ≤ 8 h). These short-lived proteins are less abundant, evolutionarily younger, and less thermally stable than other proteins. We quantified 103 proteins with different stabilities among cell lines. We showed that U2OS and HCT116 cells express truncated forms of ATRX and GMDS, respectively, which have lower stability than their full-length counterparts. This study provides a large-scale resource of human short-lived proteins under translational arrest, leading to untapped avenues of protein regulation for therapeutic interventions.
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Affiliation(s)
- Jiaming Li
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Zhenying Cai
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | | | - Ning Shen
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
| | - Dylan C Mitchell
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Edward L Huttlin
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Joao A Paulo
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Brian L Harry
- Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Pathology, University of Colorado, Anschutz Medical Campus, Aurora, CO 80045, USA.
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA.
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30
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Shrinivas K, Brenner MP. Phase separation in fluids with many interacting components. Proc Natl Acad Sci U S A 2021; 118:e2108551118. [PMID: 34725154 PMCID: PMC8609339 DOI: 10.1073/pnas.2108551118] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/03/2021] [Indexed: 01/23/2023] Open
Abstract
Fluids in natural systems, like the cytoplasm of a cell, often contain thousands of molecular species that are organized into multiple coexisting phases that enable diverse and specific functions. How interactions between numerous molecular species encode for various emergent phases is not well understood. Here, we leverage approaches from random-matrix theory and statistical physics to describe the emergent phase behavior of fluid mixtures with many species whose interactions are drawn randomly from an underlying distribution. Through numerical simulation and stability analyses, we show that these mixtures exhibit staged phase-separation kinetics and are characterized by multiple coexisting phases at steady state with distinct compositions. Random-matrix theory predicts the number of coexisting phases, validated by simulations with diverse component numbers and interaction parameters. Surprisingly, this model predicts an upper bound on the number of phases, derived from dynamical considerations, that is much lower than the limit from the Gibbs phase rule, which is obtained from equilibrium thermodynamic constraints. We design ensembles that encode either linear or nonmonotonic scaling relationships between the number of components and coexisting phases, which we validate through simulation and theory. Finally, inspired by parallels in biological systems, we show that including nonequilibrium turnover of components through chemical reactions can tunably modulate the number of coexisting phases at steady state without changing overall fluid composition. Together, our study provides a model framework that describes the emergent dynamical and steady-state phase behavior of liquid-like mixtures with many interacting constituents.
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Affiliation(s)
- Krishna Shrinivas
- NSF-Simons Center for Mathematical & Statistical Analysis of Biology, Harvard University, Cambridge, MA 02138;
| | - Michael P Brenner
- School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138
- Physics Department, Harvard University, Cambridge, MA 02138
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31
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Cai S, Kumar R, Singh BR. Clostridial Neurotoxins: Structure, Function and Implications to Other Bacterial Toxins. Microorganisms 2021; 9:2206. [PMID: 34835332 PMCID: PMC8618262 DOI: 10.3390/microorganisms9112206] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 10/19/2021] [Accepted: 10/19/2021] [Indexed: 01/20/2023] Open
Abstract
Gram-positive bacteria are ancient organisms. Many bacteria, including Gram-positive bacteria, produce toxins to manipulate the host, leading to various diseases. While the targets of Gram-positive bacterial toxins are diverse, many of those toxins use a similar mechanism to invade host cells and exert their functions. Clostridial neurotoxins produced by Clostridial tetani and Clostridial botulinum provide a classical example to illustrate the structure-function relationship of bacterial toxins. Here, we critically review the recent progress of the structure-function relationship of clostridial neurotoxins, including the diversity of the clostridial neurotoxins, the mode of actions, and the flexible structures required for the activation of toxins. The mechanism clostridial neurotoxins use for triggering their activity is shared with many other Gram-positive bacterial toxins, especially molten globule-type structures. This review also summarizes the implications of the molten globule-type flexible structures to other Gram-positive bacterial toxins. Understanding these highly dynamic flexible structures in solution and their role in the function of bacterial toxins not only fills in the missing link of the high-resolution structures from X-ray crystallography but also provides vital information for better designing antidotes against those toxins.
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Affiliation(s)
- Shuowei Cai
- Department of Chemistry and Biochemistry, University of Massachusetts Dartmouth, Dartmouth, MA 02747, USA
| | - Raj Kumar
- Botulinum Research Center, Institute of Advanced Sciences, Dartmouth, MA 02747, USA; (R.K.); (B.R.S.)
| | - Bal Ram Singh
- Botulinum Research Center, Institute of Advanced Sciences, Dartmouth, MA 02747, USA; (R.K.); (B.R.S.)
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Hark TJ, Savas JN. Using stable isotope labeling to advance our understanding of Alzheimer's disease etiology and pathology. J Neurochem 2021; 159:318-329. [PMID: 33434345 PMCID: PMC8273190 DOI: 10.1111/jnc.15298] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 01/07/2021] [Accepted: 01/08/2021] [Indexed: 12/18/2022]
Abstract
Stable isotope labeling with mass spectrometry (MS)-based proteomic analysis has become a powerful strategy to assess protein steady-state levels, protein turnover, and protein localization. Applying these analyses platforms to neurodegenerative disorders may uncover new aspects of the etiology of these devastating diseases. Recently, stable isotopes-MS has been used to investigate early pathological mechanisms of Alzheimer's disease (AD) with mouse models of AD-like pathology. In this review, we summarize these stable isotope-MS experimental designs and the recent application in the context of AD pathology. We also describe our current efforts aimed at using nuclear magnetic resonance (NMR) analysis of stable isotope-labeled amyloid fibrils from AD mouse model brains. Collectively, these methodologies offer new opportunities to study proteome changes in AD and other neurodegenerative diseases by elucidating mechanisms to target for treatment and prevention.
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Affiliation(s)
- Timothy J Hark
- Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Jeffrey N Savas
- Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
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33
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Aponte-Serrano JO, Weaver JJA, Sego TJ, Glazier JA, Shoemaker JE. Multicellular spatial model of RNA virus replication and interferon responses reveals factors controlling plaque growth dynamics. PLoS Comput Biol 2021; 17:e1008874. [PMID: 34695114 PMCID: PMC8608315 DOI: 10.1371/journal.pcbi.1008874] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 11/22/2021] [Accepted: 09/27/2021] [Indexed: 02/07/2023] Open
Abstract
Respiratory viruses present major public health challenges, as evidenced by the 1918 Spanish Flu, the 1957 H2N2, 1968 H3N2, and 2009 H1N1 influenza pandemics, and the ongoing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic. Severe RNA virus respiratory infections often correlate with high viral load and excessive inflammation. Understanding the dynamics of the innate immune response and its manifestations at the cell and tissue levels is vital to understanding the mechanisms of immunopathology and to developing strain-independent treatments. Here, we present a novel spatialized multicellular computational model of RNA virus infection and the type-I interferon-mediated antiviral response that it induces within lung epithelial cells. The model is built using the CompuCell3D multicellular simulation environment and is parameterized using data from influenza virus-infected cell cultures. Consistent with experimental observations, it exhibits either linear radial growth of viral plaques or arrested plaque growth depending on the local concentration of type I interferons. The model suggests that modifying the activity of signaling molecules in the JAK/STAT pathway or altering the ratio of the diffusion lengths of interferon and virus in the cell culture could lead to plaque growth arrest. The dependence of plaque growth arrest on diffusion lengths highlights the importance of developing validated spatial models of cytokine signaling and the need for in vitro measurement of these diffusion coefficients. Sensitivity analyses under conditions leading to continuous or arrested plaque growth found that plaque growth is more sensitive to variations of most parameters and more likely to have identifiable model parameters when conditions lead to plaque arrest. This result suggests that cytokine assay measurements may be most informative under conditions leading to arrested plaque growth. The model is easy to extend to include SARS-CoV-2-specific mechanisms or to use as a component in models linking epithelial cell signaling to systemic immune models.
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Affiliation(s)
- Josua O. Aponte-Serrano
- Department of Intelligent Systems Engineering, Indiana University, Bloomington, Indiana, United States of America
- Biocomplexity Institute, Indiana University, Bloomington, Indiana, United States of America
| | - Jordan J. A. Weaver
- Department of Chemical & Petroleum Engineering, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - T. J. Sego
- Department of Intelligent Systems Engineering, Indiana University, Bloomington, Indiana, United States of America
- Biocomplexity Institute, Indiana University, Bloomington, Indiana, United States of America
| | - James A. Glazier
- Department of Intelligent Systems Engineering, Indiana University, Bloomington, Indiana, United States of America
- Biocomplexity Institute, Indiana University, Bloomington, Indiana, United States of America
| | - Jason E. Shoemaker
- Department of Chemical & Petroleum Engineering, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
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Wang H, Zhong H, Gao C, Zang J, Yang D. The Distinct Properties of the Consecutive Disordered Regions Inside or Outside Protein Domains and Their Functional Significance. Int J Mol Sci 2021; 22:ijms221910677. [PMID: 34639018 PMCID: PMC8508753 DOI: 10.3390/ijms221910677] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 09/26/2021] [Accepted: 09/29/2021] [Indexed: 11/17/2022] Open
Abstract
The consecutive disordered regions (CDRs) are the basis for the formation of intrinsically disordered proteins, which contribute to various biological functions and increasing organism complexity. Previous studies have revealed that CDRs may be present inside or outside protein domains, but a comprehensive analysis of the property differences between these two types of CDRs and the proteins containing them is lacking. In this study, we investigated this issue from three viewpoints. Firstly, we found that in-domain CDRs are more hydrophilic and stable but have less stickiness and fewer post-translational modification sites compared with out-domain CDRs. Secondly, at the protein level, we found that proteins with only in-domain CDRs originated late, evolved rapidly, and had weak functional constraints, compared with the other two types of CDR-containing proteins. Proteins with only in-domain CDRs tend to be expressed spatiotemporal specifically, but they tend to have higher abundance and are more stable. Thirdly, we screened the CDR-containing protein domains that have a strong correlation with organism complexity. The CDR-containing domains tend to be evolutionarily young, or they changed from a domain without CDR to a CDR-containing domain during evolution. These results provide valuable new insights about the evolution and function of CDRs and protein domains.
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Affiliation(s)
| | | | | | | | - Dong Yang
- Correspondence: ; Tel.: +86-10-61777051
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35
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Abu Ahmad Y, Oknin-Vaisman A, Bitman-Lotan E, Orian A. From the Evasion of Degradation to Ubiquitin-Dependent Protein Stabilization. Cells 2021; 10:2374. [PMID: 34572023 PMCID: PMC8469536 DOI: 10.3390/cells10092374] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 08/30/2021] [Accepted: 09/04/2021] [Indexed: 12/11/2022] Open
Abstract
A hallmark of cancer is dysregulated protein turnover (proteostasis), which involves pathologic ubiquitin-dependent degradation of tumor suppressor proteins, as well as increased oncoprotein stabilization. The latter is due, in part, to mutation within sequences, termed degrons, which are required for oncoprotein recognition by the substrate-recognition enzyme, E3 ubiquitin ligase. Stabilization may also result from the inactivation of the enzymatic machinery that mediates the degradation of oncoproteins. Importantly, inactivation in cancer of E3 enzymes that regulates the physiological degradation of oncoproteins, results in tumor cells that accumulate multiple active oncoproteins with prolonged half-lives, leading to the development of "degradation-resistant" cancer cells. In addition, specific sequences may enable ubiquitinated proteins to evade degradation at the 26S proteasome. While the ubiquitin-proteasome pathway was originally discovered as central for protein degradation, in cancer cells a ubiquitin-dependent protein stabilization pathway actively translates transient mitogenic signals into long-lasting protein stabilization and enhances the activity of key oncoproteins. A central enzyme in this pathway is the ubiquitin ligase RNF4. An intimate link connects protein stabilization with tumorigenesis in experimental models as well as in the clinic, suggesting that pharmacological inhibition of protein stabilization has potential for personalized medicine in cancer. In this review, we highlight old observations and recent advances in our knowledge regarding protein stabilization.
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Affiliation(s)
| | | | | | - Amir Orian
- Rappaport Faculty of Medicine, R-TICC, Technion-IIT, Efron St. Bat-Galim, Haifa 3109610, Israel; (Y.A.A.); (A.O.-V.); (E.B.-L.)
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36
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A mistranslation-prone transcriptome underlying polyglutamine expansion diseases. Nat Rev Mol Cell Biol 2021; 22:583-584. [PMID: 33833432 DOI: 10.1038/s41580-021-00368-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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37
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Cascarina SM, Kaplan JP, Elder MR, Brookbank L, Ross ED. Generalizable Compositional Features Influencing the Proteostatic Fates of Polar Low-Complexity Domains. Int J Mol Sci 2021; 22:ijms22168944. [PMID: 34445649 PMCID: PMC8396281 DOI: 10.3390/ijms22168944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 08/11/2021] [Accepted: 08/16/2021] [Indexed: 11/25/2022] Open
Abstract
Protein aggregation is associated with a growing list of human diseases. A substantial fraction of proteins in eukaryotic proteomes constitutes a proteostasis network—a collection of proteins that work together to maintain properly folded proteins. One of the overarching functions of the proteostasis network is the prevention or reversal of protein aggregation. How proteins aggregate in spite of the anti-aggregation activity of the proteostasis machinery is incompletely understood. Exposed hydrophobic patches can trigger degradation by the ubiquitin-proteasome system, a key branch of the proteostasis network. However, in a recent study, we found that model glycine (G)-rich or glutamine/asparagine (Q/N)-rich prion-like domains differ in their susceptibility to detection and degradation by this system. Here, we expand upon this work by examining whether the features controlling the degradation of our model prion-like domains generalize broadly to G-rich and Q/N-rich domains. Experimentally, native yeast G-rich domains in isolation are sensitive to the degradation-promoting effects of hydrophobic residues, whereas native Q/N-rich domains completely resist these effects and tend to aggregate instead. Bioinformatic analyses indicate that native G-rich domains from yeast and humans tend to avoid degradation-promoting features, suggesting that the proteostasis network may act as a form of selection at the molecular level that constrains the sequence space accessible to G-rich domains. However, the sensitivity or resistance of G-rich and Q/N-rich domains, respectively, was not always preserved in their native protein contexts, highlighting that proteins can evolve other sequence features to overcome the intrinsic sensitivity of some LCDs to degradation.
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38
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Bomba-Warczak E, Edassery SL, Hark TJ, Savas JN. Long-lived mitochondrial cristae proteins in mouse heart and brain. J Cell Biol 2021; 220:212469. [PMID: 34259807 PMCID: PMC8282663 DOI: 10.1083/jcb.202005193] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 05/06/2021] [Accepted: 06/23/2021] [Indexed: 11/22/2022] Open
Abstract
Long-lived proteins (LLPs) have recently emerged as vital components of intracellular structures whose function is coupled to long-term stability. Mitochondria are multifaceted organelles, and their function hinges on efficient proteome renewal and replacement. Here, using metabolic stable isotope labeling of mice combined with mass spectrometry (MS)–based proteomic analysis, we demonstrate remarkable longevity for a subset of the mitochondrial proteome. We discovered that mitochondrial LLPs (mt-LLPs) can persist for months in tissues harboring long-lived cells, such as brain and heart. Our analysis revealed enrichment of mt-LLPs within the inner mitochondrial membrane, specifically in the cristae subcompartment, and demonstrates that the mitochondrial proteome is not turned over in bulk. Pioneering cross-linking experiments revealed that mt-LLPs are spatially restricted and copreserved within protein OXPHOS complexes, with limited subunit exchange throughout their lifetimes. This study provides an explanation for the exceptional mitochondrial protein lifetimes and supports the concept that LLPs provide key structural stability to multiple large and dynamic intracellular structures.
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Affiliation(s)
- Ewa Bomba-Warczak
- Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL
| | - Seby L Edassery
- Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL
| | - Timothy J Hark
- Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL
| | - Jeffrey N Savas
- Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL
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39
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Kong KYE, Fischer B, Meurer M, Kats I, Li Z, Rühle F, Barry JD, Kirrmaier D, Chevyreva V, San Luis BJ, Costanzo M, Huber W, Andrews BJ, Boone C, Knop M, Khmelinskii A. Timer-based proteomic profiling of the ubiquitin-proteasome system reveals a substrate receptor of the GID ubiquitin ligase. Mol Cell 2021; 81:2460-2476.e11. [PMID: 33974913 PMCID: PMC8189435 DOI: 10.1016/j.molcel.2021.04.018] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 03/15/2021] [Accepted: 04/19/2021] [Indexed: 01/01/2023]
Abstract
Selective protein degradation by the ubiquitin-proteasome system (UPS) is involved in all cellular processes. However, the substrates and specificity of most UPS components are not well understood. Here we systematically characterized the UPS in Saccharomyces cerevisiae. Using fluorescent timers, we determined how loss of individual UPS components affects yeast proteome turnover, detecting phenotypes for 76% of E2, E3, and deubiquitinating enzymes. We exploit this dataset to gain insights into N-degron pathways, which target proteins carrying N-terminal degradation signals. We implicate Ubr1, an E3 of the Arg/N-degron pathway, in targeting mitochondrial proteins processed by the mitochondrial inner membrane protease. Moreover, we identify Ylr149c/Gid11 as a substrate receptor of the glucose-induced degradation-deficient (GID) complex, an E3 of the Pro/N-degron pathway. Our results suggest that Gid11 recognizes proteins with N-terminal threonines, expanding the specificity of the GID complex. This resource of potential substrates and relationships between UPS components enables exploring functions of selective protein degradation.
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Affiliation(s)
| | - Bernd Fischer
- Computational Genome Biology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Matthias Meurer
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Ilia Kats
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Zhaoyan Li
- Institute of Molecular Biology (IMB), Mainz, Germany
| | - Frank Rühle
- Institute of Molecular Biology (IMB), Mainz, Germany
| | - Joseph D Barry
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Daniel Kirrmaier
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany; Cell Morphogenesis and Signal Transduction, German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Veronika Chevyreva
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Bryan-Joseph San Luis
- The Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Michael Costanzo
- The Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Wolfgang Huber
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Brenda J Andrews
- The Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Charles Boone
- The Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Michael Knop
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany; Cell Morphogenesis and Signal Transduction, German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance, Heidelberg, Germany.
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40
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Abstract
The nuclear envelope (NE) is continuous with the endoplasmic reticulum (ER), yet the NE carries out many functions distinct from those of bulk ER. This functional specialization depends on a unique protein composition that defines NE identity and must be both established and actively maintained. The NE undergoes extensive remodeling in interphase and mitosis, so mechanisms that seal NE holes and protect its unique composition are critical for maintaining its functions. New evidence shows that closure of NE holes relies on regulated de novo lipid synthesis, providing a link between lipid metabolism and generating and maintaining NE identity. Here, we review regulation of the lipid bilayers of the NE and suggest ways to generate lipid asymmetry across the NE despite its direct continuity with the ER. We also discuss the elusive mechanism of membrane fusion during nuclear pore complex (NPC) biogenesis. We propose a model in which NPC biogenesis is carefully controlled to ensure that a permeability barrier has been established before membrane fusion, thereby avoiding a major threat to compartmentalization.
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Affiliation(s)
- Shirin Bahmanyar
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520
| | - Christian Schlieker
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT 06520.,Department of Cell Biology, Yale School of Medicine, New Haven, CT 06520
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41
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Roboti P, O'Keefe S, Duah KB, Shi WQ, High S. Ipomoeassin-F disrupts multiple aspects of secretory protein biogenesis. Sci Rep 2021; 11:11562. [PMID: 34079010 PMCID: PMC8173012 DOI: 10.1038/s41598-021-91107-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 05/11/2021] [Indexed: 12/12/2022] Open
Abstract
The Sec61 complex translocates nascent polypeptides into and across the membrane of the endoplasmic reticulum (ER), providing access to the secretory pathway. In this study, we show that Ipomoeassin-F (Ipom-F), a selective inhibitor of protein entry into the ER lumen, blocks the in vitro translocation of certain secretory proteins and ER lumenal folding factors whilst barely affecting others such as albumin. The effects of Ipom-F on protein secretion from HepG2 cells are twofold: reduced ER translocation combined, in some cases, with defective ER lumenal folding. This latter issue is most likely a consequence of Ipom-F preventing the cell from replenishing its ER lumenal chaperones. Ipom-F treatment results in two cellular stress responses: firstly, an upregulation of stress-inducible cytosolic chaperones, Hsp70 and Hsp90; secondly, an atypical unfolded protein response (UPR) linked to the Ipom-F-mediated perturbation of ER function. Hence, although levels of spliced XBP1 and CHOP mRNA and ATF4 protein increase with Ipom-F, the accompanying increase in the levels of ER lumenal BiP and GRP94 seen with tunicamycin are not observed. In short, although Ipom-F reduces the biosynthetic load of newly synthesised secretory proteins entering the ER lumen, its effects on the UPR preclude the cell restoring ER homeostasis.
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Affiliation(s)
- Peristera Roboti
- Division of Molecular and Cellular Function, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, M13 9PT, UK.
| | - Sarah O'Keefe
- Division of Molecular and Cellular Function, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, M13 9PT, UK
| | - Kwabena B Duah
- Department of Chemistry, Ball State University, Muncie, IN, 47306, USA
| | - Wei Q Shi
- Department of Chemistry, Ball State University, Muncie, IN, 47306, USA
| | - Stephen High
- Division of Molecular and Cellular Function, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, M13 9PT, UK.
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42
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Komov L, Melamed Kadosh D, Barnea E, Admon A. The Effect of Interferons on Presentation of Defective Ribosomal Products as HLA Peptides. Mol Cell Proteomics 2021; 20:100105. [PMID: 34087483 PMCID: PMC8724922 DOI: 10.1016/j.mcpro.2021.100105] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 05/15/2021] [Accepted: 05/21/2021] [Indexed: 02/06/2023] Open
Abstract
A subset of class I major histocompatibility complex (MHC)-bound peptides is produced from immature proteins that are rapidly degraded after synthesis. These defective ribosomal products (DRiPs) have been implicated in early alert of the immune system about impending infections. Interferons are important cytokines, produced in response to viral infection, that modulate cellular metabolism and gene expression patterns, increase the presentation of MHC molecules, and induce rapid degradation of proteins and cell-surface presentation of their derived MHC peptides, thereby contributing to the battle against pathogen infections. This study evaluated the role of interferons in the induction of rapid degradation of DRiPs to modulate the repertoire of DRiP-derived MHC peptides. Cultured human breast cancer cells were treated with interferons, and the rates of synthesis and degradation of cellular protein and their degradation products were determined by LC-MS/MS analysis, following the rates of incorporation of heavy stable isotope–labeled amino acids (dynamic stable isotope labeling by amino acids in cell culture, dynamic SILAC) at several time points after the interferon application. Large numbers of MHC peptides that incorporated the heavy amino acids faster than their source proteins indicated that DRiP peptides were abundant in the MHC peptidome; interferon treatment increased by about twofold their relative proportions in the peptidome. Such typical DRiP-derived MHC peptides were from the surplus subunits of the proteasome and ribosome, which are degraded because of the transition to immunoproteasomes and a new composition of ribosomes incorporating protein subunits that are induced by the interferon. We conclude that degradation of surplus subunits induced by the interferon is a major source for DRiP–MHC peptides, a phenomenon relevant to coping with viral infections, where a rapid presentation of MHC peptides derived from excess viral proteins may help alert the immune system about the impending infection. Degradation products of surplus subunits are often presented as HLA peptides. Interferons increase degradation and presentation of such defective products. Dynamic SILAC facilitates identification of such HLA peptides. This cellular pathway provides alert to the immune system about viral infections.
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Affiliation(s)
- Liran Komov
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, Israel
| | | | - Eilon Barnea
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, Israel
| | - Arie Admon
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, Israel.
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43
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Karlsen J, Asplund-Samuelsson J, Jahn M, Vitay D, Hudson EP. Slow Protein Turnover Explains Limited Protein-Level Response to Diurnal Transcriptional Oscillations in Cyanobacteria. Front Microbiol 2021; 12:657379. [PMID: 34194405 PMCID: PMC8237939 DOI: 10.3389/fmicb.2021.657379] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 03/22/2021] [Indexed: 12/31/2022] Open
Abstract
Metabolically engineered cyanobacteria have the potential to mitigate anthropogenic CO2 emissions by converting CO2 into renewable fuels and chemicals. Yet, better understanding of metabolic regulation in cyanobacteria is required to develop more productive strains that can make industrial scale-up economically feasible. The aim of this study was to find the cause for the previously reported inconsistency between oscillating transcription and constant protein levels under day-night growth conditions. To determine whether translational regulation counteracts transcriptional changes, Synechocystis sp. PCC 6803 was cultivated in an artificial day-night setting and the level of transcription, translation and protein was measured across the genome at different time points using mRNA sequencing, ribosome profiling and quantitative proteomics. Furthermore, the effect of protein turnover on the amplitude of protein oscillations was investigated through in silico simulations using a protein mass balance model. Our experimental analysis revealed that protein oscillations were not dampened by translational regulation, as evidenced by high correlation between translational and transcriptional oscillations (r = 0.88) and unchanged protein levels. Instead, model simulations showed that these observations can be attributed to a slow protein turnover, which reduces the effect of protein synthesis oscillations on the protein level. In conclusion, these results suggest that cyanobacteria have evolved to govern diurnal metabolic shifts through allosteric regulatory mechanisms in order to avoid the energy burden of replacing the proteome on a daily basis. Identification and manipulation of such mechanisms could be part of a metabolic engineering strategy for overproduction of chemicals.
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Affiliation(s)
- Jan Karlsen
- Department of Protein Science, KTH Royal Institute of Technology, Stockholm, Sweden.,Science for Life Laboratory, Stockholm, Sweden
| | - Johannes Asplund-Samuelsson
- Department of Protein Science, KTH Royal Institute of Technology, Stockholm, Sweden.,Science for Life Laboratory, Stockholm, Sweden
| | - Michael Jahn
- Department of Protein Science, KTH Royal Institute of Technology, Stockholm, Sweden.,Science for Life Laboratory, Stockholm, Sweden
| | - Dóra Vitay
- Department of Protein Science, KTH Royal Institute of Technology, Stockholm, Sweden.,Science for Life Laboratory, Stockholm, Sweden.,Biosyntia ApS, Copenhagen, Denmark
| | - Elton P Hudson
- Department of Protein Science, KTH Royal Institute of Technology, Stockholm, Sweden.,Science for Life Laboratory, Stockholm, Sweden
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44
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Direct Conjugation of NEDD8 to the N-Terminus of a Model Protein Can Induce Degradation. Cells 2021; 10:cells10040854. [PMID: 33918652 PMCID: PMC8069691 DOI: 10.3390/cells10040854] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 04/05/2021] [Accepted: 04/08/2021] [Indexed: 12/28/2022] Open
Abstract
While the role of ubiquitin in protein degradation is well established, the role of other ubiquitin-like proteins (UBLs) in protein degradation is less clear. Neural precursor cell expressed developmentally down-regulated protein 8 (NEDD8) is the UBL with the highest level of amino acids identified when compared to ubiquitin. Here we tested if the N-terminal addition of NEDD8 to a protein of interest could lead to degradation. Mutation of critical glycine residues required for normal NEDD8 processing resulted in a non-cleavable fusion protein that was rapidly degraded within the cells by both the proteasome and autophagy. Both degradation pathways were dependent on a functional ubiquitin-conjugation system as treatment with MLN7243 increased levels of non-cleavable NEDD8-GFP. The degradation of non-cleavable, N-terminal NEDD8-GFP was not due to a failure of GFP folding as different NEDD8-GFP constructs with differing abilities to fold and fluoresce were similarly degraded. Though the fusion of NEDD8 to a protein resulted in degradation, treatment of cells with MLN4924, an inhibitor of the E1 activating enzyme for NEDD8, failed to prevent degradation of other destabilized substrates. Taken together these data suggest that under certain conditions, such as the model system described here, the covalent linkage of NEDD8 to a protein substrate may result in the target proteins degradation.
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45
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Das S, Barik D. Scaling of intrinsic noise in an autocratic reaction network. Phys Rev E 2021; 103:042403. [PMID: 34006004 DOI: 10.1103/physreve.103.042403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 03/16/2021] [Indexed: 11/07/2022]
Abstract
Biochemical reactions in living cells often produce stochastic trajectories due to the fluctuations of the finite number of the macromolecular species present inside the cell. A significant number of computational and theoretical studies have previously investigated stochasticity in small regulatory networks to understand its origin and regulation. At the systems level regulatory networks have been determined to be hierarchical resembling social networks. In order to determine the stochasticity in networks with hierarchical architecture, here we computationally investigated intrinsic noise in an autocratic reaction network in which only the upstream regulators regulate the downstream regulators. We studied the effects of the qualitative and quantitative nature of regulatory interactions on the stochasticity in the network. We established an unconventional scaling of noise with average abundance in which the noise passes through a minimum indicating that the network can be noisy both in the low and high abundance regimes. We determined that the bursty kinetics of the trajectories are responsible for such scaling. The scaling of noise remains intact for a mixed network that includes democratic subnetworks within the autocratic network.
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Affiliation(s)
- Soutrick Das
- School of Chemistry, University of Hyderabad, Gachibowli, 500046, Hyderabad, India
| | - Debashis Barik
- School of Chemistry, University of Hyderabad, Gachibowli, 500046, Hyderabad, India
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46
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Sadygov RG. Using Heavy Mass Isotopomers for Protein Turnover in Heavy Water Metabolic Labeling. J Proteome Res 2021; 20:2035-2041. [PMID: 33661639 DOI: 10.1021/acs.jproteome.0c00873] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Metabolic labeling followed by LC-MS-based proteomics is a powerful tool to study proteome dynamics in high-throughput experiments both in vivo and in vitro. High mass resolution and accuracy allow differentiation in isotope profiles and the quantification of partially labeled peptide species. Metabolic labeling duration introduces a time domain in which the gradual incorporation of labeled isotopes is recorded. Different stable isotopes are used for labeling. Labeling with heavy water has advantages because it is cost-effective and easy to use. The protein degradation rate constant has been modeled using exponential decay models for the relative abundances of mass isotopomers. The recently developed closed-form equations were applied to study the analytic behavior of the heavy mass isotopomers in the time domain of metabolic labeling. The predictions from the closed-form equations are compared with the practices that have been used to extract degradation rate constants from the time-course profiles of heavy mass isotopomers. It is shown that all mass isotopomers, except for the monoisotope, require data transformations to obtain the exponential depletion, which serves as a basis for the rate constant model. Heavy mass isotopomers may be preferable choices for modeling high-mass peptides or peptides with a high number of labeling sites. The results are also applicable to stable isotope labeling with other atom-based labeling agents.
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Affiliation(s)
- Rovshan G Sadygov
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, 301 University Boulevard, Galveston, Texas 77555, United States
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47
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Forés-Martos J, Forte A, García-Martínez J, Pérez-Ortín JE. A Trans-Omics Comparison Reveals Common Gene Expression Strategies in Four Model Organisms and Exposes Similarities and Differences between Them. Cells 2021; 10:334. [PMID: 33562654 PMCID: PMC7914595 DOI: 10.3390/cells10020334] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 01/29/2021] [Accepted: 02/01/2021] [Indexed: 12/01/2022] Open
Abstract
The ultimate goal of gene expression regulation is on the protein level. However, because the amounts of mRNAs and proteins are controlled by their synthesis and degradation rates, the cellular amount of a given protein can be attained by following different strategies. By studying omics data for six expression variables (mRNA and protein amounts, plus their synthesis and decay rates), we previously demonstrated the existence of common expression strategies (CESs) for functionally related genes in the yeast Saccharomyces cerevisiae. Here we extend that study to two other eukaryotes: the yeast Schizosaccharomyces pombe and cultured human HeLa cells. We also use genomic data from the model prokaryote Escherichia coli as an external reference. We show that six-variable profiles (6VPs) can be constructed for every gene and that these 6VPs are similar for genes with similar functions in all the studied organisms. The differences in 6VPs between organisms can be used to establish their phylogenetic relationships. The analysis of the correlations among the six variables supports the hypothesis that most gene expression control occurs in actively growing organisms at the transcription rate level, and that translation plays a minor role. We propose that living organisms use CESs for the genes acting on the same physiological pathways, especially for those belonging to stable macromolecular complexes, but CESs have been modeled by evolution to adapt to the specific life circumstances of each organism.
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Affiliation(s)
- Jaume Forés-Martos
- Instituto de Biotecnología y Biomedicina (Biotecmed), Universitat de València, C/Dr. Moliner 50, E46100 Burjassot, Spain;
| | - Anabel Forte
- Departamento de Estadística e Investigación Operativa, Facultad de Matemáticas, Universitat de València, C/Dr. Moliner 50, E46100 Burjassot, Spain;
| | - José García-Martínez
- Instituto de Biotecnología y Biomedicina (Biotecmed), Universitat de València, C/Dr. Moliner 50, E46100 Burjassot, Spain;
| | - José E. Pérez-Ortín
- Instituto de Biotecnología y Biomedicina (Biotecmed), Universitat de València, C/Dr. Moliner 50, E46100 Burjassot, Spain;
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48
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Salovska B, Zhu H, Gandhi T, Frank M, Li W, Rosenberger G, Wu C, Germain PL, Zhou H, Hodny Z, Reiter L, Liu Y. Isoform-resolved correlation analysis between mRNA abundance regulation and protein level degradation. Mol Syst Biol 2021; 16:e9170. [PMID: 32175694 PMCID: PMC7073818 DOI: 10.15252/msb.20199170] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2019] [Revised: 02/06/2020] [Accepted: 02/12/2020] [Indexed: 12/15/2022] Open
Abstract
Profiling of biological relationships between different molecular layers dissects regulatory mechanisms that ultimately determine cellular function. To thoroughly assess the role of protein post‐translational turnover, we devised a strategy combining pulse stable isotope‐labeled amino acids in cells (pSILAC), data‐independent acquisition mass spectrometry (DIA‐MS), and a novel data analysis framework that resolves protein degradation rate on the level of mRNA alternative splicing isoforms and isoform groups. We demonstrated our approach by the genome‐wide correlation analysis between mRNA amounts and protein degradation across different strains of HeLa cells that harbor a high grade of gene dosage variation. The dataset revealed that specific biological processes, cellular organelles, spatial compartments of organelles, and individual protein isoforms of the same genes could have distinctive degradation rate. The protein degradation diversity thus dissects the corresponding buffering or concerting protein turnover control across cancer cell lines. The data further indicate that specific mRNA splicing events such as intron retention significantly impact the protein abundance levels. Our findings support the tight association between transcriptome variability and proteostasis and provide a methodological foundation for studying functional protein degradation.
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Affiliation(s)
- Barbora Salovska
- Yale Cancer Biology Institute, Yale University, West Haven, CT, USA.,Department of Genome Integrity, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Hongwen Zhu
- Department of Analytical Chemistry and CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | | | - Max Frank
- European Molecular Biology Laboratory, Heidelberg, Germany
| | - Wenxue Li
- Yale Cancer Biology Institute, Yale University, West Haven, CT, USA
| | | | - Chongde Wu
- Yale Cancer Biology Institute, Yale University, West Haven, CT, USA
| | - Pierre-Luc Germain
- Institute for Neuroscience, D-HEST, ETH Zurich, Zurich, Switzerland.,Statistical Bioinformatics Lab, DMLS, University of Zürich, Zurich, Switzerland
| | - Hu Zhou
- Department of Analytical Chemistry and CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Zdenek Hodny
- Department of Genome Integrity, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | | | - Yansheng Liu
- Yale Cancer Biology Institute, Yale University, West Haven, CT, USA.,Department of Pharmacology, Yale University School of Medicine, New Haven, CT, USA
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49
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Swovick K, Firsanov D, Welle KA, Hryhorenko JR, Wise JP, George C, Sformo TL, Seluanov A, Gorbunova V, Ghaemmaghami S. Interspecies Differences in Proteome Turnover Kinetics Are Correlated With Life Spans and Energetic Demands. Mol Cell Proteomics 2021; 20:100041. [PMID: 33639418 PMCID: PMC7950207 DOI: 10.1074/mcp.ra120.002301] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 10/27/2020] [Accepted: 12/28/2020] [Indexed: 12/21/2022] Open
Abstract
Cells continually degrade and replace damaged proteins. However, the high energetic demand of protein turnover generates reactive oxygen species that compromise the long-term health of the proteome. Thus, the relationship between aging, protein turnover, and energetic demand remains unclear. Here, we used a proteomic approach to measure rates of protein turnover within primary fibroblasts isolated from a number of species with diverse life spans including the longest-lived mammal, the bowhead whale. We show that organismal life span is negatively correlated with turnover rates of highly abundant proteins. In comparison with mice, cells from long-lived naked mole rats have slower rates of protein turnover, lower levels of ATP production, and reduced reactive oxygen species levels. Despite having slower rates of protein turnover, naked mole rat cells tolerate protein misfolding stress more effectively than mouse cells. We suggest that in lieu of a rapid constitutive turnover, long-lived species may have evolved more energetically efficient mechanisms for selective detection and clearance of damaged proteins.
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Affiliation(s)
- Kyle Swovick
- Department of Biology, University of Rochester, Rochester, New York, USA
| | - Denis Firsanov
- Department of Biology, University of Rochester, Rochester, New York, USA
| | - Kevin A Welle
- Mass Spectrometry Resource Laboratory, University of Rochester, Rochester, New York, USA
| | - Jennifer R Hryhorenko
- Mass Spectrometry Resource Laboratory, University of Rochester, Rochester, New York, USA
| | - John P Wise
- Department of Pharmacology and Toxicology, Wise Laboratory for Environmental and Genetic Toxicology, University of Louisville, Louisville, Kentucky, USA
| | - Craig George
- North Slope Borough Department of Wildlife Management, Barrow, Alaska, USA
| | - Todd L Sformo
- North Slope Borough Department of Wildlife Management, Barrow, Alaska, USA; Institute of Arctic Biology, University of Alaska Fairbanks, Fairbanks, Alaska, USA
| | - Andrei Seluanov
- Department of Biology, University of Rochester, Rochester, New York, USA
| | - Vera Gorbunova
- Department of Biology, University of Rochester, Rochester, New York, USA
| | - Sina Ghaemmaghami
- Department of Biology, University of Rochester, Rochester, New York, USA; Mass Spectrometry Resource Laboratory, University of Rochester, Rochester, New York, USA.
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50
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Henninger JE, Oksuz O, Shrinivas K, Sagi I, LeRoy G, Zheng MM, Andrews JO, Zamudio AV, Lazaris C, Hannett NM, Lee TI, Sharp PA, Cissé II, Chakraborty AK, Young RA. RNA-Mediated Feedback Control of Transcriptional Condensates. Cell 2021; 184:207-225.e24. [PMID: 33333019 PMCID: PMC8128340 DOI: 10.1016/j.cell.2020.11.030] [Citation(s) in RCA: 263] [Impact Index Per Article: 87.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 08/09/2020] [Accepted: 11/16/2020] [Indexed: 12/11/2022]
Abstract
Regulation of biological processes typically incorporates mechanisms that initiate and terminate the process and, where understood, these mechanisms often involve feedback control. Regulation of transcription is a fundamental cellular process where the mechanisms involved in initiation have been studied extensively, but those involved in arresting the process are poorly understood. Modeling of the potential roles of RNA in transcriptional control suggested a non-equilibrium feedback control mechanism where low levels of RNA promote condensates formed by electrostatic interactions whereas relatively high levels promote dissolution of these condensates. Evidence from in vitro and in vivo experiments support a model where RNAs produced during early steps in transcription initiation stimulate condensate formation, whereas the burst of RNAs produced during elongation stimulate condensate dissolution. We propose that transcriptional regulation incorporates a feedback mechanism whereby transcribed RNAs initially stimulate but then ultimately arrest the process.
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Affiliation(s)
| | - Ozgur Oksuz
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Krishna Shrinivas
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Institute of Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; NSF-Simons Center for Mathematical & Statistical Analysis of Biology, Harvard University, Cambridge, MA 02138, USA
| | - Ido Sagi
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Gary LeRoy
- Howard Hughes Medical Institute, New York University School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA
| | - Ming M Zheng
- Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - J Owen Andrews
- Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Alicia V Zamudio
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Charalampos Lazaris
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Nancy M Hannett
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Tong Ihn Lee
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Phillip A Sharp
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Ibrahim I Cissé
- Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Arup K Chakraborty
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Institute of Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Ragon Institute of Massachusetts General Hospital, MIT and Harvard University, Cambridge, MA 02139, USA.
| | - Richard A Young
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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