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Yan Y, Sankar BS, Mirza B, Ng DCM, Pelletier AR, Huang SD, Wang W, Watson K, Wang D, Ping P. Missing Values in Longitudinal Proteome Dynamics Studies: Making a Case for Data Multiple Imputation. J Proteome Res 2024; 23:4151-4162. [PMID: 39189460 DOI: 10.1021/acs.jproteome.4c00263] [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] [Indexed: 08/28/2024]
Abstract
Temporal proteomics data sets are often confounded by the challenges of missing values. These missing data points, in a time-series context, can lead to fluctuations in measurements or the omission of critical events, thus hindering the ability to fully comprehend the underlying biomedical processes. We introduce a Data Multiple Imputation (DMI) pipeline designed to address this challenge in temporal data set turnover rate quantifications, enabling robust downstream analysis to gain novel discoveries. To demonstrate its utility and generalizability, we applied this pipeline to two use cases: a murine cardiac temporal proteomics data set and a human plasma temporal proteomics data set, both aimed at examining protein turnover rates. This DMI pipeline significantly enhanced the detection of protein turnover rate in both data sets, and furthermore, the imputed data sets captured new representation of proteins, leading to an augmented view of biological pathways, protein complex dynamics, as well as biomarker-disease associations. Importantly, DMI exhibited superior performance in benchmark data sets compared to single imputation methods (DSI). In summary, we have demonstrated that this DMI pipeline is effective at overcoming challenges introduced by missing values in temporal proteome dynamics studies.
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Affiliation(s)
- Yu Yan
- Departments of Physiology and Medicine, University of California, Los Angeles (UCLA) School of Medicine, Los Angeles, California 90095, United States
- NHLBI Integrated Cardiovascular Data Science Training Program, UCLA, Los Angeles, California 90095, United States
- NIH BRIDGE2AI Center & NHLBI Integrated Cardiovascular Data Science Training Program, UCLA, Suite 1-609, MRL Building, 675 Charles E. Young Drive South, Los Angeles, California 90095, United States
| | - Baradwaj Simha Sankar
- Departments of Physiology and Medicine, University of California, Los Angeles (UCLA) School of Medicine, Los Angeles, California 90095, United States
- NIH BRIDGE2AI Center & NHLBI Integrated Cardiovascular Data Science Training Program, UCLA, Suite 1-609, MRL Building, 675 Charles E. Young Drive South, Los Angeles, California 90095, United States
| | - Bilal Mirza
- Departments of Physiology and Medicine, University of California, Los Angeles (UCLA) School of Medicine, Los Angeles, California 90095, United States
- NHLBI Integrated Cardiovascular Data Science Training Program, UCLA, Los Angeles, California 90095, United States
| | - Dominic C M Ng
- Departments of Physiology and Medicine, University of California, Los Angeles (UCLA) School of Medicine, Los Angeles, California 90095, United States
- NHLBI Integrated Cardiovascular Data Science Training Program, UCLA, Los Angeles, California 90095, United States
- NIH BRIDGE2AI Center & NHLBI Integrated Cardiovascular Data Science Training Program, UCLA, Suite 1-609, MRL Building, 675 Charles E. Young Drive South, Los Angeles, California 90095, United States
| | - Alexander R Pelletier
- NHLBI Integrated Cardiovascular Data Science Training Program, UCLA, Los Angeles, California 90095, United States
- Department of Computer Science and Scalable Analytics Institute, UCLA School of Engineering, Los Angeles, California 90095, United States
| | - Sarah D Huang
- Departments of Physiology and Medicine, University of California, Los Angeles (UCLA) School of Medicine, Los Angeles, California 90095, United States
- NHLBI Integrated Cardiovascular Data Science Training Program, UCLA, Los Angeles, California 90095, United States
| | - Wei Wang
- NHLBI Integrated Cardiovascular Data Science Training Program, UCLA, Los Angeles, California 90095, United States
- Department of Computer Science and Scalable Analytics Institute, UCLA School of Engineering, Los Angeles, California 90095, United States
| | - Karol Watson
- Departments of Physiology and Medicine, University of California, Los Angeles (UCLA) School of Medicine, Los Angeles, California 90095, United States
- NIH BRIDGE2AI Center & NHLBI Integrated Cardiovascular Data Science Training Program, UCLA, Suite 1-609, MRL Building, 675 Charles E. Young Drive South, Los Angeles, California 90095, United States
| | - Ding Wang
- Departments of Physiology and Medicine, University of California, Los Angeles (UCLA) School of Medicine, Los Angeles, California 90095, United States
- NHLBI Integrated Cardiovascular Data Science Training Program, UCLA, Los Angeles, California 90095, United States
- NIH BRIDGE2AI Center & NHLBI Integrated Cardiovascular Data Science Training Program, UCLA, Suite 1-609, MRL Building, 675 Charles E. Young Drive South, Los Angeles, California 90095, United States
| | - Peipei Ping
- Departments of Physiology and Medicine, University of California, Los Angeles (UCLA) School of Medicine, Los Angeles, California 90095, United States
- NHLBI Integrated Cardiovascular Data Science Training Program, UCLA, Los Angeles, California 90095, United States
- NIH BRIDGE2AI Center & NHLBI Integrated Cardiovascular Data Science Training Program, UCLA, Suite 1-609, MRL Building, 675 Charles E. Young Drive South, Los Angeles, California 90095, United States
- Department of Computer Science and Scalable Analytics Institute, UCLA School of Engineering, Los Angeles, California 90095, United States
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Meadow ME, Broas S, Hoare M, Alimohammadi F, Welle KA, Swovick K, Hryhorenko JR, Martinez JC, Biashad SA, Seluanov A, Gorbunova V, Buchwalter A, Ghaemmaghami S. Proteome Birthdating Reveals Age-Selectivity of Protein Ubiquitination. Mol Cell Proteomics 2024; 23:100791. [PMID: 38797438 PMCID: PMC11260378 DOI: 10.1016/j.mcpro.2024.100791] [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: 12/14/2023] [Revised: 03/27/2024] [Accepted: 05/15/2024] [Indexed: 05/29/2024] Open
Abstract
Within a cell, proteins have distinct and highly variable half-lives. As a result, the molecular ages of proteins can range from seconds to years. How the age of a protein influences its environmental interactions is a largely unexplored area of biology. To investigate the age-selectivity of cellular pathways, we developed a methodology termed "proteome birthdating" that barcodes proteins based on their time of synthesis. We demonstrate that this approach provides accurate measurements of protein turnover kinetics from a single biological sample encoding multiple labeling time-points. As a first application of the birthdated proteome, we investigated the age distribution of the human ubiquitinome. Our results indicate that the vast majority of ubiquitinated proteins in a cell consist of newly synthesized proteins and that these young proteins constitute the bulk of the degradative flux through the proteasome. Rapidly ubiquitinated nascent proteins are enriched in cytosolic subunits of large protein complexes. Conversely, proteins destined for the secretory pathway and vesicular transport have older ubiquitinated populations. Our data also identify a smaller subset of older ubiquitinated cellular proteins that do not appear to be targeted to the proteasome for rapid degradation. Together, our data provide an age census of the human ubiquitinome and establish proteome birthdating as a robust methodology for investigating the protein age-selectivity of diverse cellular pathways.
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Affiliation(s)
- Michael E Meadow
- Department of Biology, University of Rochester, New York, USA; Medical Scientist Training Program, University of Rochester, New York, USA
| | - Sarah Broas
- Department of Biology, University of Rochester, New York, USA
| | - Margaret Hoare
- Department of Biology, University of Rochester, New York, USA
| | - Fatemeh Alimohammadi
- Department of Pharmacology and Physiology, University of Rochester Medical Center, Rochester, New York, USA
| | - Kevin A Welle
- University of Rochester Mass Spectrometry Resource Laboratory, New York, USA
| | - Kyle Swovick
- University of Rochester Mass Spectrometry Resource Laboratory, New York, USA
| | | | - John C Martinez
- Department of Biology, University of Rochester, New York, USA
| | | | - Andrei Seluanov
- Department of Biology, University of Rochester, New York, USA; Department of Medicine, University of Rochester Medical Center, Rochester, New York, USA
| | - Vera Gorbunova
- Department of Biology, University of Rochester, New York, USA; Department of Medicine, University of Rochester Medical Center, Rochester, New York, USA
| | - Abigail Buchwalter
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, California, USA
| | - Sina Ghaemmaghami
- Department of Biology, University of Rochester, New York, USA; University of Rochester Mass Spectrometry Resource Laboratory, New York, USA.
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3
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Masato A, Bubacco L. The αSynuclein half-life conundrum. Neurobiol Dis 2024; 196:106524. [PMID: 38705490 DOI: 10.1016/j.nbd.2024.106524] [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: 03/04/2024] [Revised: 04/22/2024] [Accepted: 05/02/2024] [Indexed: 05/07/2024] Open
Abstract
αSynuclein (αSyn) misfolding and aggregation frequently precedes neuronal loss associated with Parkinson's Disease (PD) and other Synucleinopathies. The progressive buildup of pathological αSyn species results from alterations on αSyn gene and protein sequence, increased local concentrations, variations in αSyn interactome and protein network. Therefore, under physiological conditions, it is mandatory to regulate αSyn proteostasis as an equilibrium among synthesis, trafficking, degradation and extracellular release. In this frame, a crucial parameter is protein half-life. It provides indications of the turnover of a specific protein and depends on mRNA synthesis and translation regulation, subcellular localization, function and clearance by the designated degradative pathways. For αSyn, the molecular mechanisms regulating its proteostasis in neurons have been extensively investigated in various cellular models, either using biochemical or imaging approaches. Nevertheless, a converging estimate of αSyn half-life has not emerged yet. Here, we discuss the challenges in studying αSyn proteostasis under physiological and pathological conditions, the advantages and disadvantages of the experimental strategies proposed so far, and the relevance of determining αSyn half-life from a translational perspective.
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Affiliation(s)
- Anna Masato
- UK Dementia Research Institute at University College London, London, United Kingdom.
| | - Luigi Bubacco
- Department of Biology, University of Padova, Padova, Italy; Centro Studi per la Neurodegenerazione (CESNE), University of Padova, Padova, Italy.
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Bizieff A, Cheng M, Chang K, Mohammed H, Ziari N, Nyangau E, Fitch M, Hellerstein MK. Changes in protein fluxes in skeletal muscle during sequential stages of muscle regeneration after acute injury in male mice. Sci Rep 2024; 14:13172. [PMID: 38849371 PMCID: PMC11161603 DOI: 10.1038/s41598-024-62115-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2024] [Accepted: 05/14/2024] [Indexed: 06/09/2024] Open
Abstract
Changes in protein turnover play an important role in dynamic physiological processes, including skeletal muscle regeneration, which occurs as an essential part of tissue repair after injury. The inability of muscle tissue to recapitulate this regenerative process can lead to the manifestation of clinical symptoms in various musculoskeletal diseases, including muscular dystrophies and pathological atrophy. Here, we employed a workflow that couples deuterated water (2H2O) administration with mass spectrometry (MS) to systematically measure in-vivo protein turnover rates across the muscle proteome in 8-week-old male C57BL6/J mice. We compared the turnover kinetics of over 100 proteins in response to cardiotoxin (CTX) induced muscle damage and regeneration at unique sequential stages along the regeneration timeline. This analysis is compared to gene expression data from mRNA-sequencing (mRNA-seq) from the same tissue. The data reveals quantitative protein flux signatures in response to necrotic damage, in addition to sequential differences in cell proliferation, energy metabolism, and contractile gene expression. Interestingly, the mRNA changes correlated poorly with changes in protein synthesis rates, consistent with post-transcriptional control mechanisms. In summary, the experiments described here reveal the signatures and timing of protein flux changes during skeletal muscle regeneration, as well as the inability of mRNA expression measurements to reveal changes in directly measured protein turnover rates. The results of this work described here provide a better understanding of the muscle regeneration process and could help to identify potential biomarkers or therapeutic targets.
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Affiliation(s)
- Alec Bizieff
- Division of Metabolic Biology, Department of Nutritional Sciences & Toxicology, University of California-Berkeley, Berkeley, CA, USA.
| | - Maggie Cheng
- Division of Metabolic Biology, Department of Nutritional Sciences & Toxicology, University of California-Berkeley, Berkeley, CA, USA
| | - Kelvin Chang
- Division of Metabolic Biology, Department of Nutritional Sciences & Toxicology, University of California-Berkeley, Berkeley, CA, USA
| | - Hussein Mohammed
- Division of Metabolic Biology, Department of Nutritional Sciences & Toxicology, University of California-Berkeley, Berkeley, CA, USA
| | - Naveed Ziari
- Division of Metabolic Biology, Department of Nutritional Sciences & Toxicology, University of California-Berkeley, Berkeley, CA, USA
| | - Edna Nyangau
- Division of Metabolic Biology, Department of Nutritional Sciences & Toxicology, University of California-Berkeley, Berkeley, CA, USA
| | - Mark Fitch
- Division of Metabolic Biology, Department of Nutritional Sciences & Toxicology, University of California-Berkeley, Berkeley, CA, USA
| | - Marc K Hellerstein
- Division of Metabolic Biology, Department of Nutritional Sciences & Toxicology, University of California-Berkeley, Berkeley, CA, USA
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5
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Gonzalez Ramirez C, Salvador SG, Patel RKR, Clark S, Miller NW, James LM, Ringelberg NW, Simon JM, Bennett J, Amaral DG, Burette AC, Philpot BD. Regional and cellular organization of the autism-associated protein UBE3A/E6AP and its antisense transcript in the brain of the developing rhesus monkey. Front Neuroanat 2024; 18:1410791. [PMID: 38873093 PMCID: PMC11169893 DOI: 10.3389/fnana.2024.1410791] [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: 04/01/2024] [Accepted: 05/17/2024] [Indexed: 06/15/2024] Open
Abstract
Angelman syndrome (AS) is a neurogenetic disorder caused by mutations or deletions in the maternally-inherited UBE3A allele, leading to a loss of UBE3A protein expression in neurons. The paternally-inherited UBE3A allele is epigenetically silenced in neurons during development by a noncoding transcript (UBE3A-ATS). The absence of neuronal UBE3A results in severe neurological symptoms, including speech and language impairments, intellectual disability, and seizures. While no cure exists, therapies aiming to restore UBE3A function-either by gene addition or by targeting UBE3A-ATS-are under development. Progress in developing these treatments relies heavily on inferences drawn from mouse studies about the function of UBE3A in the human brain. To aid translational efforts and to gain an understanding of UBE3A and UBE3A-ATS biology with greater relevance to human neurodevelopmental contexts, we investigated UBE3A and UBE3A-ATS expression in the developing brain of the rhesus macaque, a species that exhibits complex social behaviors, resembling aspects of human behavior to a greater degree than mice. Combining immunohistochemistry and in situ hybridization, we mapped UBE3A and UBE3A-ATS regional and cellular expression in normal prenatal, neonatal, and adolescent rhesus macaque brains. We show that key hallmarks of UBE3A biology, well-known in rodents, are also present in macaques, and suggest paternal UBE3A silencing in neurons-but not glial cells-in the macaque brain, with onset between gestational day 48 and 100. These findings support proposals that early-life, perhaps even prenatal, intervention is optimal for overcoming the maternal allele loss of UBE3A linked to AS.
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Affiliation(s)
- Chavely Gonzalez Ramirez
- Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Sarah G. Salvador
- Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Ridthi Kartik Rekha Patel
- Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Sarah Clark
- Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Noah W. Miller
- Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Lucas M. James
- Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Nicholas W. Ringelberg
- Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Jeremy M. Simon
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, United States
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, United States
| | - Jeffrey Bennett
- Department of Psychiatry and Behavioral Sciences, MIND Institute, Davis, CA, United States
- California National Primate Research Center, University of California, Davis, CA, United States
| | - David G. Amaral
- Department of Psychiatry and Behavioral Sciences, MIND Institute, Davis, CA, United States
- California National Primate Research Center, University of California, Davis, CA, United States
| | - Alain C. Burette
- Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Benjamin D. Philpot
- Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Carolina Institute for Developmental Disabilities, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
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Fan KT, Xu Y, Hegeman AD. Elevated Temperature Effects on Protein Turnover Dynamics in Arabidopsis thaliana Seedlings Revealed by 15N-Stable Isotope Labeling and ProteinTurnover Algorithm. Int J Mol Sci 2024; 25:5882. [PMID: 38892074 PMCID: PMC11172382 DOI: 10.3390/ijms25115882] [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: 05/04/2024] [Revised: 05/24/2024] [Accepted: 05/26/2024] [Indexed: 06/21/2024] Open
Abstract
Global warming poses a threat to plant survival, impacting growth and agricultural yield. Protein turnover, a critical regulatory mechanism balancing protein synthesis and degradation, is crucial for the cellular response to environmental changes. We investigated the effects of elevated temperature on proteome dynamics in Arabidopsis thaliana seedlings using 15N-stable isotope labeling and ultra-performance liquid chromatography-high resolution mass spectrometry, coupled with the ProteinTurnover algorithm. Analyzing different cellular fractions from plants grown under 22 °C and 30 °C growth conditions, we found significant changes in the turnover rates of 571 proteins, with a median 1.4-fold increase, indicating accelerated protein dynamics under thermal stress. Notably, soluble root fraction proteins exhibited smaller turnover changes, suggesting tissue-specific adaptations. Significant turnover alterations occurred with redox signaling, stress response, protein folding, secondary metabolism, and photorespiration, indicating complex responses enhancing plant thermal resilience. Conversely, proteins involved in carbohydrate metabolism and mitochondrial ATP synthesis showed minimal changes, highlighting their stability. This analysis highlights the intricate balance between proteome stability and adaptability, advancing our understanding of plant responses to heat stress and supporting the development of improved thermotolerant crops.
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Affiliation(s)
- Kai-Ting Fan
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei 115, Taiwan;
| | - Yuan Xu
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, USA
| | - Adrian D. Hegeman
- Departments of Horticultural Science and Plant and Microbial Biology, University of Minnesota, Twin Cities, MN 55108, USA
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Baeza J, Coons BE, Lin Z, Riley J, Mendoza M, Peranteau WH, Garcia BA. In utero pulse injection of isotopic amino acids quantifies protein turnover rates during murine fetal development. CELL REPORTS METHODS 2024; 4:100713. [PMID: 38412836 PMCID: PMC10921036 DOI: 10.1016/j.crmeth.2024.100713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 12/20/2023] [Accepted: 01/29/2024] [Indexed: 02/29/2024]
Abstract
Protein translational control is critical for ensuring that the fetus develops correctly and that necessary organs and tissues are formed and functional. We developed an in utero method to quantify tissue-specific protein dynamics by monitoring amino acid incorporation into the proteome after pulse injection. Fetuses of pregnant mice were injected with isotopically labeled lysine and arginine via the vitelline vein at various embyonic days, and organs and tissues were harvested. By analyzing the nascent proteome, unique signatures of each tissue were identified by hierarchical clustering. In addition, the quantified proteome-wide turnover rates were calculated between 3.81E-5 and 0.424 h-1. We observed similar protein turnover profiles for analyzed organs (e.g., liver vs. brain); however, their distributions of turnover rates vary significantly. The translational kinetic profiles of developing organs displayed differentially expressed protein pathways and synthesis rates, which correlated with known physiological changes during mouse development.
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Affiliation(s)
- Josue Baeza
- Department of Biochemistry & Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Barbara E Coons
- The Center for Fetal Research, Division of Pediatric General, Thoracis and Fetal Surgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Zongtao Lin
- Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - John Riley
- The Center for Fetal Research, Division of Pediatric General, Thoracis and Fetal Surgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Mariel Mendoza
- Department of Biochemistry & Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - William H Peranteau
- The Center for Fetal Research, Division of Pediatric General, Thoracis and Fetal Surgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.
| | - Benjamin A Garcia
- Department of Biochemistry & Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis, St. Louis, MO 63110, USA.
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Yuan F, Li Y, Zhou X, Meng P, Zou P. Spatially resolved mapping of proteome turnover dynamics with subcellular precision. Nat Commun 2023; 14:7217. [PMID: 37940635 PMCID: PMC10632371 DOI: 10.1038/s41467-023-42861-8] [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: 10/22/2022] [Accepted: 10/23/2023] [Indexed: 11/10/2023] Open
Abstract
Cellular activities are commonly associated with dynamic proteomic changes at the subcellular level. Although several techniques are available to quantify whole-cell protein turnover dynamics, such measurements often lack sufficient spatial resolution at the subcellular level. Herein, we report the development of prox-SILAC method that combines proximity-dependent protein labeling (APEX2/HRP) with metabolic incorporation of stable isotopes (pulse-SILAC) to map newly synthesized proteins with subcellular spatial resolution. We apply prox-SILAC to investigate proteome dynamics in the mitochondrial matrix and the endoplasmic reticulum (ER) lumen. Our analysis reveals a highly heterogeneous distribution in protein turnover dynamics within macromolecular machineries such as the mitochondrial ribosome and respiratory complexes I-V, thus shedding light on their mechanism of hierarchical assembly. Furthermore, we investigate the dynamic changes of ER proteome when cells are challenged with stress or undergoing stimulated differentiation, identifying subsets of proteins with unique patterns of turnover dynamics, which may play key regulatory roles in alleviating stress or promoting differentiation. We envision that prox-SILAC could be broadly applied to profile protein turnover at various subcellular compartments, under both physiological and pathological conditions.
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Affiliation(s)
- Feng Yuan
- Academy for Advanced Interdisciplinary Studies, PKU-Tsinghua Center for Life Science, Peking University, Beijing, 100871, China
| | - Yi Li
- College of Chemistry and Molecular Engineering, Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, PKU-IDG/McGovern Institute for Brain Research, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University, Beijing, 100871, China
| | - Xinyue Zhou
- Academy for Advanced Interdisciplinary Studies, PKU-Tsinghua Center for Life Science, Peking University, Beijing, 100871, China
| | - Peiyuan Meng
- College of Chemistry and Molecular Engineering, Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, PKU-IDG/McGovern Institute for Brain Research, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University, Beijing, 100871, China
| | - Peng Zou
- Academy for Advanced Interdisciplinary Studies, PKU-Tsinghua Center for Life Science, Peking University, Beijing, 100871, China.
- College of Chemistry and Molecular Engineering, Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, PKU-IDG/McGovern Institute for Brain Research, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University, Beijing, 100871, China.
- Chinese Institute for Brain Research (CIBR), Beijing, 102206, China.
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Leem YH, Kim DY, Park JE, Kim HS. Necrosulfonamide exerts neuroprotective effect by inhibiting necroptosis, neuroinflammation, and α-synuclein oligomerization in a subacute MPTP mouse model of Parkinson's disease. Sci Rep 2023; 13:8783. [PMID: 37258791 DOI: 10.1038/s41598-023-35975-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 05/26/2023] [Indexed: 06/02/2023] Open
Abstract
Parkinson's disease (PD) is an incurable movement disorder characterized by dopaminergic cell loss, neuroinflammation, and α-synuclein pathology. Herein, we investigated the therapeutic effects of necrosulfonamide (NSA), a specific inhibitor of mixed lineage kinase domain-like protein (MLKL), in a subacute 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) mouse model of PD. MLKL is an executor of necroptosis, a programmed cell death pathway that causes inflammation. Repeated administration of NSA resulted in the recovery of impaired motor performance and dopaminergic degeneration. Furthermore, NSA inhibited the phosphorylation, ubiquitylation, and oligomerization of MLKL, all of which are associated with MLKL cell death-inducing activity in dopaminergic cells in the substantia nigra (SN). NSA also inhibited microglial activation and reactive astrogliosis as well as the MPTP-induced expression of proinflammatory molecules such as tumor necrosis factor-α, interleukin-1β, inducible nitric oxide synthase, and cystatin F. Furthermore, NSA inhibited α-synuclein oligomerization and phosphorylation in the SN of MPTP-treated mice by inhibiting the activity of glycogen synthase kinase 3β and matrix metalloproteinase-3. In conclusion, NSA has anti-necroptotic, anti-inflammatory, and anti-synucleinopathic effects on PD pathology. Therefore, NSA is a potential therapeutic candidate for PD.
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Affiliation(s)
- Yea-Hyun Leem
- Department of Molecular Medicine and Inflammation-Cancer Microenvironment Research Center, School of Medicine, Ewha Womans University, 808-1 Magok-Dong, Gangseo-gu, Seoul, 07804, South Korea
| | - Do-Yeon Kim
- Department of Molecular Medicine and Inflammation-Cancer Microenvironment Research Center, School of Medicine, Ewha Womans University, 808-1 Magok-Dong, Gangseo-gu, Seoul, 07804, South Korea
| | - Jung-Eun Park
- Department of Molecular Medicine and Inflammation-Cancer Microenvironment Research Center, School of Medicine, Ewha Womans University, 808-1 Magok-Dong, Gangseo-gu, Seoul, 07804, South Korea
| | - Hee-Sun Kim
- Department of Molecular Medicine and Inflammation-Cancer Microenvironment Research Center, School of Medicine, Ewha Womans University, 808-1 Magok-Dong, Gangseo-gu, Seoul, 07804, South Korea.
- Department of Brain and Cognitive Sciences, Ewha Womans University, Seoul, South Korea.
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Baeza J, Coons BE, Lin Z, Riley J, Mendoza M, Peranteau WH, Garcia BA. In utero pulse injection of isotopic amino acids quantifies protein turnover rates during murine fetal development. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.18.541242. [PMID: 37293076 PMCID: PMC10245746 DOI: 10.1101/2023.05.18.541242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Protein translational control is highly regulated step in the gene expression program during mammalian development that is critical for ensuring that the fetus develops correctly and that all of the necessary organs and tissues are formed and functional. Defects in protein expression during fetal development can lead to severe developmental abnormalities or premature death. Currently, quantitative techniques to monitor protein synthesis rates in a developing fetus (in utero) are limited. Here, we developed a novel in utero stable isotope labeling approach to quantify tissue-specific protein dynamics of the nascent proteome during mouse fetal development. Fetuses of pregnant C57BL/6J mice were injected with isotopically labeled lysine (Lys8) and arginine (Arg10) via the vitelline vein at various gestational days. After treatment, fetal organs/tissues including brain, liver, lung, and heart were harvested for sample preparation and proteomic analysis. We show that the mean incorporation rate for injected amino acids into all organs was 17.50 ± 0.6%. By analyzing the nascent proteome, unique signatures of each tissue were identified by hierarchical clustering. In addition, the quantified proteome-wide turnover rates (kobs) were calculated between 3.81E-5 and 0.424 hour-1. We observed similar protein turnover profiles for analyzed organs (e.g., liver versus brain), however, their distributions of turnover rates vary significantly. The translational kinetic profiles of developing organs displayed differentially expressed protein pathways and synthesis rates which correlated with known physiological changes during mouse development.
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Affiliation(s)
- Josue Baeza
- Department of Biochemistry & Biophysics, University of Pennsylvania, Philadelphia, PA 19104
- Contributed equally to this work
| | - Barbara E. Coons
- The Center for Fetal Research, Division of Pediatric General, Thoracis and Fetal Surgery, Children’s Hospital of Philadelphia, Philadelphia, PA 19104
- Contributed equally to this work
| | - Zongtao Lin
- Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis, St. Louis, MO 63110
| | - John Riley
- The Center for Fetal Research, Division of Pediatric General, Thoracis and Fetal Surgery, Children’s Hospital of Philadelphia, Philadelphia, PA 19104
| | - Mariel Mendoza
- Department of Biochemistry & Biophysics, University of Pennsylvania, Philadelphia, PA 19104
| | - William H. Peranteau
- The Center for Fetal Research, Division of Pediatric General, Thoracis and Fetal Surgery, Children’s Hospital of Philadelphia, Philadelphia, PA 19104
| | - Benjamin A Garcia
- Department of Biochemistry & Biophysics, University of Pennsylvania, Philadelphia, PA 19104
- Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis, St. Louis, MO 63110
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11
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Deberneh HM, Abdelrahman DR, Verma SK, Linares JJ, Murton AJ, Russell WK, Kuyumcu-Martinez MN, Miller BF, Sadygov RG. Quantifying label enrichment from two mass isotopomers increases proteome coverage for in vivo protein turnover using heavy water metabolic labeling. Commun Chem 2023; 6:72. [PMID: 37069333 PMCID: PMC10110577 DOI: 10.1038/s42004-023-00873-x] [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: 10/03/2022] [Accepted: 03/31/2023] [Indexed: 04/19/2023] Open
Abstract
Heavy water metabolic labeling followed by liquid chromatography coupled with mass spectrometry is a powerful high throughput technique for measuring the turnover rates of individual proteins in vivo. The turnover rate is obtained from the exponential decay modeling of the depletion of the monoisotopic relative isotope abundance. We provide theoretical formulas for the time course dynamics of six mass isotopomers and use the formulas to introduce a method that utilizes partial isotope profiles, only two mass isotopomers, to compute protein turnover rate. The use of partial isotope profiles alleviates the interferences from co-eluting contaminants in complex proteome mixtures and improves the accuracy of the estimation of label enrichment. In five different datasets, the technique consistently doubles the number of peptides with high goodness-of-fit characteristics of the turnover rate model. We also introduce a software tool, d2ome+, which automates the protein turnover estimation from partial isotope profiles.
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Affiliation(s)
- Henock M Deberneh
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, TX, USA
| | - Doaa R Abdelrahman
- Department of Surgery, The University of Texas Medical Branch, Galveston, TX, USA
- Sealy Center on Aging, The University of Texas Medical Branch, Galveston, TX, USA
| | - Sunil K Verma
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, TX, USA
| | - Jennifer J Linares
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, TX, USA
| | - Andrew J Murton
- Department of Surgery, The University of Texas Medical Branch, Galveston, TX, USA
- Sealy Center on Aging, The University of Texas Medical Branch, Galveston, TX, USA
| | - William K Russell
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, TX, USA
| | - Muge N Kuyumcu-Martinez
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, TX, USA
- Department of Neuroscience, Cell Biology and Anatomy, The University of Texas Medical Branch, Galveston, TX, USA
- Department of Molecular Physiology and Biological Physics, The University of Virginia, Charlottesville, VA, USA
| | - Benjamin F Miller
- Oklahoma Medical Research Foundation, Oklahoma Nathan Shock Center, Oklahoma Center for Geosciences, Harold Hamm Diabetes Center, Oklahoma City, OK, USA
- Oklahoma City Veterans Association, Oklahoma City, OK, USA
| | - Rovshan G Sadygov
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, TX, USA.
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12
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Garcia A, Gaju O, Bowerman AF, Buck SA, Evans JR, Furbank RT, Gilliham M, Millar AH, Pogson BJ, Reynolds MP, Ruan Y, Taylor NL, Tyerman SD, Atkin OK. Enhancing crop yields through improvements in the efficiency of photosynthesis and respiration. THE NEW PHYTOLOGIST 2023; 237:60-77. [PMID: 36251512 PMCID: PMC10100352 DOI: 10.1111/nph.18545] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 09/15/2022] [Indexed: 06/06/2023]
Abstract
The rate with which crop yields per hectare increase each year is plateauing at the same time that human population growth and other factors increase food demand. Increasing yield potential (Y p ) of crops is vital to address these challenges. In this review, we explore a component ofY p that has yet to be optimised - that being improvements in the efficiency with which light energy is converted into biomass (ε c ) via modifications to CO2 fixed per unit quantum of light (α), efficiency of respiratory ATP production (ε prod ) and efficiency of ATP use (ε use ). For α, targets include changes in photoprotective machinery, ribulose bisphosphate carboxylase/oxygenase kinetics and photorespiratory pathways. There is also potential forε prod to be increased via targeted changes to the expression of the alternative oxidase and mitochondrial uncoupling pathways. Similarly, there are possibilities to improveε use via changes to the ATP costs of phloem loading, nutrient uptake, futile cycles and/or protein/membrane turnover. Recently developed high-throughput measurements of respiration can serve as a proxy for the cumulative energy cost of these processes. There are thus exciting opportunities to use our growing knowledge of factors influencing the efficiency of photosynthesis and respiration to create a step-change in yield potential of globally important crops.
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Affiliation(s)
- Andres Garcia
- ARC Centre of Excellence in Plant Energy Biology, Research School of BiologyThe Australian National UniversityCanberraACT2601Australia
- Division of Plant Sciences, Research School of BiologyAustralian National UniversityCanberraACT2601Australia
| | - Oorbessy Gaju
- ARC Centre of Excellence in Plant Energy Biology, Research School of BiologyThe Australian National UniversityCanberraACT2601Australia
- College of Science, Lincoln Institute for Agri‐Food TechnologyUniversity of LincolnLincolnshireLN2 2LGUK
| | - Andrew F. Bowerman
- ARC Centre of Excellence in Plant Energy Biology, Research School of BiologyThe Australian National UniversityCanberraACT2601Australia
- Division of Plant Sciences, Research School of BiologyAustralian National UniversityCanberraACT2601Australia
| | - Sally A. Buck
- ARC Centre of Excellence in Plant Energy Biology, Research School of BiologyThe Australian National UniversityCanberraACT2601Australia
- Division of Plant Sciences, Research School of BiologyAustralian National UniversityCanberraACT2601Australia
| | - John R. Evans
- Division of Plant Sciences, Research School of BiologyAustralian National UniversityCanberraACT2601Australia
- ARC Centre of Excellence for Translational Photosynthesis, Research School of BiologyThe Australian National UniversityCanberraACT2601Australia
| | - Robert T. Furbank
- Division of Plant Sciences, Research School of BiologyAustralian National UniversityCanberraACT2601Australia
- ARC Centre of Excellence for Translational Photosynthesis, Research School of BiologyThe Australian National UniversityCanberraACT2601Australia
| | - Matthew Gilliham
- ARC Centre of Excellence in Plant Energy Biology, School of Agriculture, Food and Wine & Waite Research InstituteUniversity of AdelaideGlen OsmondSA5064Australia
| | - A. Harvey Millar
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences & Institute of AgricultureThe University of Western AustraliaCrawleyWA6009Australia
| | - Barry J. Pogson
- ARC Centre of Excellence in Plant Energy Biology, Research School of BiologyThe Australian National UniversityCanberraACT2601Australia
- Division of Plant Sciences, Research School of BiologyAustralian National UniversityCanberraACT2601Australia
| | - Matthew P. Reynolds
- International Maize and Wheat Improvement Center (CIMMYT)Km. 45, Carretera Mexico, El BatanTexcoco56237Mexico
| | - Yong‐Ling Ruan
- Division of Plant Sciences, Research School of BiologyAustralian National UniversityCanberraACT2601Australia
| | - Nicolas L. Taylor
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences & Institute of AgricultureThe University of Western AustraliaCrawleyWA6009Australia
| | - Stephen D. Tyerman
- ARC Centre of Excellence in Plant Energy Biology, School of Agriculture, Food and Wine & Waite Research InstituteUniversity of AdelaideGlen OsmondSA5064Australia
| | - Owen K. Atkin
- ARC Centre of Excellence in Plant Energy Biology, Research School of BiologyThe Australian National UniversityCanberraACT2601Australia
- Division of Plant Sciences, Research School of BiologyAustralian National UniversityCanberraACT2601Australia
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13
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Label-free quantitative proteomics and stress responses in pigs-The case of short or long road transportation. PLoS One 2022; 17:e0277950. [PMID: 36417452 PMCID: PMC9683611 DOI: 10.1371/journal.pone.0277950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 11/07/2022] [Indexed: 11/25/2022] Open
Abstract
Ethical livestock production is currently a major concern for consumers. In parallel, research has shown that transport duration is an important factor affecting animal welfare and has a negative impact on the final product quality and on the production cost. This study applied proteomics methods to the animal stress/welfare problem in pigs muscle-exudate with the aim to identify proteins indicative of molecular processes underpinning transport stress and to better characterise this species as a biomedical model. A broader perspective of the problem was obtained by applying label-free LC-MS to characterise the proteome response to transport stress (short or long road transportation) in pigs within the same genetic line. A total of 1,464 proteins were identified, following statistical analysis 66 proteins clearly separating pigs subject to short road transportation and pigs subject long road transportation. These proteins were mainly involved in cellular and metabolic processes. Catalase and stress-induced phosphoprotein-1 were further confirmed by Western blot as being involved in the process of self-protection of the cells in response to stress. This study provide an insight into the molecular processes that are involved in pig adaptability to transport stress and are a step-forward for the development of an objective evaluation method of stress in order to improve animal care and management in farm animals.
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14
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Cold-Induced Physiological and Biochemical Alternations and Proteomic Insight into the Response of Saccharum spontaneum to Low Temperature. Int J Mol Sci 2022; 23:ijms232214244. [PMID: 36430736 PMCID: PMC9692960 DOI: 10.3390/ijms232214244] [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: 11/01/2022] [Revised: 11/15/2022] [Accepted: 11/15/2022] [Indexed: 11/19/2022] Open
Abstract
Sugarcane, a cash crop, is easily affected by low temperature, which results in a decrease in yield and sugar production. Breeding a new variety with cold tolerance is an essential strategy to reduce loss from cold stress. The identification of germplasms and genes/proteins with cold tolerance is a vital step in breeding sugarcane varieties with cold tolerance via a conventional program and molecular technology. In this study, the physiological and biochemical indices of 22 genotypes of S. spontaneum were measured, and the membership function analysis method was used to comprehensively evaluate the cold tolerance ability of these genotypes. The physiological and biochemical indices of these S. spontaneum genotypes showed a sophisticated response to low temperature. On the basis of the physiological and chemical indices, the genotypes were classified into different cold tolerance groups. Then, the high-tolerance genotype 1027 and the low-tolerance genotype 3217 were selected for DIA-based proteomic analysis by subjecting them to low temperature. From the four comparison groups, 1123, 1341, 751, and 1693 differentially abundant proteins (DAPs) were identified, respectively. The DAPs based on genotypes or treatments participated in distinct metabolic pathways. Through detailed analysis of the DAPs, some proteins related to protein homeostasis, carbohydrate and energy metabolism, amino acid transport and metabolism, signal transduction, and the cytoskeleton may be involved in sugarcane tolerance to cold stress. Furthermore, five important proteins related to cold tolerance were discovered for the first time in this study. This work not only provides the germplasms and candidate target proteins for breeding sugarcane varieties with cold tolerance via a conventional program and molecular breeding, but also helps to accelerate the determination of the molecular mechanism underlying cold tolerance in sugarcane.
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15
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Mahrou B, Pirhanov A, Alijanvand MH, Cho YK, Shin YJ. Degradation-driven protein level oscillation in the yeast Saccharomyces cerevisiae. Biosystems 2022; 219:104717. [PMID: 35690291 DOI: 10.1016/j.biosystems.2022.104717] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 06/03/2022] [Accepted: 06/03/2022] [Indexed: 11/02/2022]
Abstract
Generating robust, predictable perturbations in cellular protein levels will advance our understanding of protein function and enable the control of physiological outcomes in biotechnology applications. Timed periodic changes in protein levels play a critical role in the cell division cycle, cellular stress response, and development. Here we report the generation of robust protein level oscillations by controlling the protein degradation rate in the yeast Saccharomyces cerevisiae. Using a photo-sensitive degron and red fluorescent proteins as reporters, we show that under constitutive transcriptional induction, repeated triangular protein level oscillations as fast as 5-10 min-scale can be generated by modulating the protein degradation rate. Consistent with oscillations generated though transcriptional control, we observed a continuous decrease in the magnitude of oscillations as the input modulation frequency increased, indicating low-pass filtering of input perturbation. By using two red fluorescent proteins with distinct maturation times, we show that the oscillations in protein level is largely unaffected by delays originating from functional protein formation. Our study demonstrates the potential for repeated control of protein levels by controlling the protein degradation rate without altering the transcription rate.
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Affiliation(s)
- Bahareh Mahrou
- Biomedical Engineering Department, University of Connecticut, Storrs, CT, 06269, USA; Electrical Engineering Department, University of Connecticut, Storrs, CT, 06069, USA.
| | - Azady Pirhanov
- Biomedical Engineering Department, University of Connecticut, Storrs, CT, 06269, USA
| | - Moluk Hadi Alijanvand
- Department of Epidemiology and Biostatistics, School of Health, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Yong Ku Cho
- Biomedical Engineering Department, University of Connecticut, Storrs, CT, 06269, USA; Chemical and Biomolecular Engineering Department, University of Connecticut, Storrs, CT, 06269, USA.
| | - Yong-Jun Shin
- Biomedical Engineering Department, University of Connecticut, Storrs, CT, 06269, USA
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16
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Isolation and Characterization of Antimicrobial Peptides Isolated from Fagonia bruguieri. Appl Biochem Biotechnol 2022; 194:4319-4332. [PMID: 35041129 DOI: 10.1007/s12010-022-03818-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/31/2021] [Indexed: 01/08/2023]
Abstract
The majority of pathogenic microorganisms have developed resistance to commercial antibiotics. It causes the risk of illness relapse with current antimicrobial therapy regimens; additional and/or different antibacterial drugs are needed to treat diseases caused by these pathogenic microorganisms. The applied analysis in the present study was purification and characterization of plant peptides isolated from the leaves of Fagonia bruguieri as well as their antibacterial activities against Gram-positive bacteria, Staphylococcus aureus, Bacillus subtilis, Micrococcus luteus, and methicillin-resistant Staphylococcus aureus, in addition to Gram-negative bacteria, Escherichia coli and Pseudomonas aeruginosa. The minimum inhibitory concentration for the isolated peptide ranges from 25 to 62.5 mg/mL. The methanolic solvent was used for the extraction followed by reversed-phase high-performance liquid chromatography for purification of peptides. Eventually, the peptide characterization and identification were also determined by MALDI-TOF/TOF and SEM analysis. This study paves a way to the effective antimicrobials from the plant resources.
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17
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Linking post-translational modifications and protein turnover by site-resolved protein turnover profiling. Nat Commun 2022; 13:165. [PMID: 35013197 PMCID: PMC8748498 DOI: 10.1038/s41467-021-27639-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Accepted: 12/02/2021] [Indexed: 12/21/2022] Open
Abstract
Proteome-wide measurements of protein turnover have largely ignored the impact of post-translational modifications (PTMs). To address this gap, we employ stable isotope labeling and mass spectrometry to measure the turnover of >120,000 peptidoforms including >33,000 phosphorylated, acetylated, and ubiquitinated peptides for >9,000 native proteins. This site-resolved protein turnover (SPOT) profiling discloses global and site-specific differences in turnover associated with the presence or absence of PTMs. While causal relationships may not always be immediately apparent, we speculate that PTMs with diverging turnover may distinguish states of differential protein stability, structure, localization, enzymatic activity, or protein-protein interactions. We show examples of how the turnover data may give insights into unknown functions of PTMs and provide a freely accessible online tool that allows interrogation and visualisation of all turnover data. The SPOT methodology is applicable to many cell types and modifications, offering the potential to prioritize PTMs for future functional investigations. Post-translational modifications (PTMs) can regulate cellular protein function but their global impact on protein turnover is largely unknown. Here, the authors develop proteomic workflows to profile PTM-resolved protein turnover and analyze the effects of phosphorylation, acetylation and ubiquitination.
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18
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Andrews B, Murphy AE, Stofella M, Maslen S, Almeida-Souza L, Skehel JM, Skene NG, Sobott F, Frank RAW. Multidimensional dynamics of the proteome in the neurodegenerative and aging mammalian brain. Mol Cell Proteomics 2021; 21:100192. [PMID: 34979241 PMCID: PMC8816717 DOI: 10.1016/j.mcpro.2021.100192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 12/03/2021] [Accepted: 12/29/2021] [Indexed: 11/18/2022] Open
Abstract
The amount of any given protein in the brain is determined by the rates of its synthesis and destruction, which are regulated by different cellular mechanisms. Here, we combine metabolic labeling in live mice with global proteomic profiling to simultaneously quantify both the flux and amount of proteins in mouse models of neurodegeneration. In multiple models, protein turnover increases were associated with increasing pathology. This method distinguishes changes in protein expression mediated by synthesis from those mediated by degradation. In the AppNL-F knockin mouse model of Alzheimer’s disease, increased turnover resulted from imbalances in both synthesis and degradation, converging on proteins associated with synaptic vesicle recycling (Dnm1, Cltc, Rims1) and mitochondria (Fis1, Ndufv1). In contrast to disease models, aging in wild-type mice caused a widespread decrease in protein recycling associated with a decrease in autophagic flux. Overall, this simple multidimensional approach enables a comprehensive mapping of proteome dynamics and identifies affected proteins in mouse models of disease and other live animal test settings. Multidimensional proteomic screen to detect imbalances in mouse models of disease. Increased proteome turnover in multiple symptomatic neurodegeneration mouse models. Healthy aging is associated with a global decrease in protein turnover.
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Affiliation(s)
- Byron Andrews
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Alan E Murphy
- UK Dementia Research Institute, Department of Brain Sciences, Imperial College London, W12 0BZ, UK
| | - Michele Stofella
- Astbury Centre of Molecular Structural Biology, Faculty of Biological Sciences, University of Leeds, LS2 9JT, UK
| | - Sarah Maslen
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Leonardo Almeida-Souza
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK; Helsinki Institute of Life Science - HiLIFE, Institute of Biotechnology and Faculty of Biological and Environmental Sciences, University of Helsinki, Viikinkaari 5, 00790, Helsinki, Finland
| | - J Mark Skehel
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Nathan G Skene
- UK Dementia Research Institute, Department of Brain Sciences, Imperial College London, W12 0BZ, UK
| | - Frank Sobott
- Astbury Centre of Molecular Structural Biology, Faculty of Biological Sciences, University of Leeds, LS2 9JT, UK
| | - René A W Frank
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK; Astbury Centre of Molecular Structural Biology, Faculty of Biological Sciences, University of Leeds, LS2 9JT, UK.
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19
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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: 21] [Impact Index Per Article: 7.0] [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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20
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Pinto VB, Almeida VC, Pereira-Lima ÍA, Vale EM, Araújo WL, Silveira V, Viana JMS. Deciphering the major metabolic pathways associated with aluminum tolerance in popcorn roots using label-free quantitative proteomics. PLANTA 2021; 254:132. [PMID: 34821986 DOI: 10.1007/s00425-021-03786-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Accepted: 11/10/2021] [Indexed: 06/13/2023]
Abstract
Al responsive proteins are associated with starch, sucrose, and other carbohydrate metabolic pathways. Sucrose synthase is a candidate to Al tolerance. Al responses are regulated at transcriptional and post-transcriptional levels. Aluminum toxicity is one of the important abiotic stresses that affects worldwide crop production. The soluble form of aluminum (Al3+) inhibits root growth by altering water and nutrient uptake, a process that also reduces plant growth and development. Under long-term Al3+ exposure, plants can activate several tolerance mechanisms. To date, no reports of large-scale proteomic data concerning maize responses to this ion have been published. To investigate the post-transcriptional regulation in response to Al toxicity, we performed label-free quantitative proteomics for comparative analysis of two Al-contrasting popcorn inbred lines and an Al-tolerant commercial hybrid during 72 h under Al-stress conditions. A total of 489 differentially accumulated proteins (DAPs) were identified in the Al-sensitive inbred line, 491 in the Al-tolerant inbred line, and 277 in the commercial hybrid. Among them, 120 DAPs were co-expressed in both Al tolerant genotypes. Bioinformatics analysis indicated that starch, sucrose, and other components of carbohydrate metabolism and glycolysis/gluconeogenesis are the biochemical processes regulated in response to Al toxicity. Sucrose synthase accumulation and an increase in sucrose content and starch degradation suggest that these components may enhance popcorn tolerance to Al stress. The accumulation of citrate synthase suggests a key role for this enzyme in the detoxification process in the Al-tolerant inbred line. The integration of transcriptomic and proteomic data indicates that the Al tolerance response presents a complex regulatory network into the transcription and translation dynamics of popcorn root development.
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Affiliation(s)
- Vitor Batista Pinto
- Departamento de Biologia Geral, Universidade Federal de Viçosa (UFV), Viçosa, MG, 36570-900, Brazil.
- Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia (CBB), Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Av. Alberto Lamego, 2000, Campos dos Goytacazes, RJ, 28013-602, Brazil.
- Setor de Genômica e Proteômica. CBB, Unidade de Biologia Integrativa, UENF, Campos dos Goytacazes, RJ, Brazil.
| | - Vinicius Costa Almeida
- Departamento de Biologia Geral, Universidade Federal de Viçosa (UFV), Viçosa, MG, 36570-900, Brazil
| | - Ítalo A Pereira-Lima
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa (UFV), Viçosa, MG, 36570-900, Brazil
| | - Ellen Moura Vale
- Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia (CBB), Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Av. Alberto Lamego, 2000, Campos dos Goytacazes, RJ, 28013-602, Brazil
- Setor de Genômica e Proteômica. CBB, Unidade de Biologia Integrativa, UENF, Campos dos Goytacazes, RJ, Brazil
| | - Wagner L Araújo
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa (UFV), Viçosa, MG, 36570-900, Brazil
| | - Vanildo Silveira
- Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia (CBB), Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Av. Alberto Lamego, 2000, Campos dos Goytacazes, RJ, 28013-602, Brazil
- Setor de Genômica e Proteômica. CBB, Unidade de Biologia Integrativa, UENF, Campos dos Goytacazes, RJ, Brazil
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21
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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: 57] [Impact Index Per Article: 19.0] [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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22
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Chepyala SR, Liu X, Yang K, Wu Z, Breuer AM, Cho JH, Li Y, Mancieri A, Jiao Y, Zhang H, Peng J. JUMPt: Comprehensive Protein Turnover Modeling of In Vivo Pulse SILAC Data by Ordinary Differential Equations. Anal Chem 2021; 93:13495-13504. [PMID: 34587451 DOI: 10.1021/acs.analchem.1c02309] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Recent advances in mass spectrometry (MS)-based proteomics allow the measurement of turnover rates of thousands of proteins using dynamic labeling methods, such as pulse stable isotope labeling by amino acids in cell culture (pSILAC). However, when applying the pSILAC strategy to multicellular animals (e.g., mice), the labeling process is significantly delayed by native amino acids recycled from protein degradation in vivo, raising a challenge of defining accurate protein turnover rates. Here, we report JUMPt, a software package using a novel ordinary differential equation (ODE)-based mathematical model to determine reliable rates of protein degradation. The uniqueness of JUMPt is to consider amino acid recycling and fit the kinetics of the labeling amino acid (e.g., Lys) and whole proteome simultaneously to derive half-lives of individual proteins. Multiple settings in the software are designed to enable simple to comprehensive data inputs for precise analysis of half-lives with flexibility. We examined the software by studying the turnover of thousands of proteins in the pSILAC brain and liver tissues. The results were largely consistent with the proteome turnover measurements from previous studies. The long-lived proteins are enriched in the integral membrane, myelin sheath, and mitochondrion in the brain. In summary, the ODE-based JUMPt software is an effective proteomics tool for analyzing large-scale protein turnover, and the software is publicly available on GitHub (https://github.com/JUMPSuite/JUMPt) to the research community.
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Affiliation(s)
- Surendhar Reddy Chepyala
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States.,Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Xueyan Liu
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Ka Yang
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States.,Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Zhiping Wu
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States.,Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Alex M Breuer
- Department of Information Services, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Ji-Hoon Cho
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Yuxin Li
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Ariana Mancieri
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States.,Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Yun Jiao
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States.,Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Hui Zhang
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Junmin Peng
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States.,Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States.,Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
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23
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Kapitanov GI, Chabot JR, Narula J, Roy M, Neubert H, Palandra J, Farrokhi V, Johnson JS, Webster R, Jones HM. A Mechanistic Site-Of-Action Model: A Tool for Informing Right Target, Right Compound, And Right Dose for Therapeutic Antagonistic Antibody Programs. FRONTIERS IN BIOINFORMATICS 2021; 1:731340. [DOI: 10.3389/fbinf.2021.731340] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 08/23/2021] [Indexed: 11/13/2022] Open
Abstract
Quantitative modeling is increasingly utilized in the drug discovery and development process, from the initial stages of target selection, through clinical studies. The modeling can provide guidance on three major questions–is this the right target, what are the right compound properties, and what is the right dose for moving the best possible candidate forward. In this manuscript, we present a site-of-action modeling framework which we apply to monoclonal antibodies against soluble targets. We give a comprehensive overview of how we construct the model and how we parametrize it and include several examples of how to apply this framework for answering the questions postulated above. The utilities and limitations of this approach are discussed.
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24
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Global Proteome Profiling to Assess Changes in Protein Abundance Using Isobaric Labeling and Liquid Chromatography-Tandem Mass Spectrometry. Methods Mol Biol 2021. [PMID: 34432251 DOI: 10.1007/978-1-0716-1665-9_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Protein degradation is a critical component of all facets of cell biology, and recently methods have been developed to make use of targeted protein degradation as both an investigative tool and a potential therapeutic avenue. Mass spectrometry-based proteomic studies have allowed detailed characterization of changes in protein level and the biology underlying growth, development, and disease. Current methods and instrumentation allow identification and quantitative analysis of thousands of proteins in a single assay. The method described here involves cell lysis and digestion to peptides, labeling peptides with isobaric tagging TMT reagents, basic reversed phase fractionation, and liquid chromatography-tandem mass spectrometry analysis of the enriched peptides.
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25
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Marcotti S, Sánchez-Sánchez BJ, Serna-Morales E, Dragu A, Díaz-de-la-Loza MDC, Matsubayashi Y, Stramer BM. Protocol for intervention-free quantification of protein turnover rate by steady-state modeling. STAR Protoc 2021; 2:100377. [PMID: 33786460 PMCID: PMC7988239 DOI: 10.1016/j.xpro.2021.100377] [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] [Indexed: 11/05/2022] Open
Abstract
Protein turnover rate is difficult to obtain experimentally. This protocol shows how to mathematically model turnover rates in an intervention-free manner given the ability to quantify mRNA and protein expression from initiation to homeostasis. This approach can be used to calculate production and degradation rates and to infer protein half-life. This model was successfully employed to quantify turnover during Drosophila embryogenesis, and we hypothesize that it will be applicable to diverse in vivo or in vitro systems. For complete details on the use and execution of this protocol, please refer to Matsubayashi et al. (2020).
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Affiliation(s)
- Stefania Marcotti
- Randall Centre for Cell and Molecular Biophysics, King’s College London, London SE1 1UL, UK
| | | | - Eduardo Serna-Morales
- Randall Centre for Cell and Molecular Biophysics, King’s College London, London SE1 1UL, UK
| | - Anca Dragu
- Randall Centre for Cell and Molecular Biophysics, King’s College London, London SE1 1UL, UK
| | | | - Yutaka Matsubayashi
- Randall Centre for Cell and Molecular Biophysics, King’s College London, London SE1 1UL, UK
| | - Brian Marc Stramer
- Randall Centre for Cell and Molecular Biophysics, King’s College London, London SE1 1UL, UK
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26
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Martínez-Gómez MG, Roberts BM. Metabolic Adaptations to Weight Loss: A Brief Review. J Strength Cond Res 2021; 36:2970-2981. [PMID: 33677461 DOI: 10.1519/jsc.0000000000003991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
ABSTRACT Martínez-Gómez, MG and Roberts, BM. Metabolic adaptations to weight loss: A brief review. J Strength Cond Res XX(X): 000-000, 2021-As the scientific literature has continuously shown, body mass loss attempts do not always follow a linear fashion nor always go as expected even when the intervention is calculated with precise tools. One of the main reasons why this tends to happen relies on our body's biological drive to regain the body mass we lose to survive. This phenomenon has been referred to as "metabolic adaptation" many times in the literature and plays a very relevant role in the management of obesity and human weight loss. This review will provide insights into some of the theoretical models for the etiology of metabolic adaptation as well as a quick look into the physiological and endocrine mechanisms that underlie it. Nutritional strategies and dietetic tools are thus necessary to confront these so-called adaptations to body mass loss. Among some of these strategies, we can highlight increasing protein needs, opting for high-fiber foods or programming-controlled diet refeeds, and diet breaks over a large body mass loss phase. Outside the nutritional aspects, it might be wise to increase the physical activity and thus the energy flux of an individual when possible to maintain diet-induced body mass loss in the long term. This review will examine these protocols and their viability in the context of adherence and sustainability for the individual toward successful body mass loss.
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Affiliation(s)
- Mario G Martínez-Gómez
- CarloSportNutrition, Spain; and University of Alabama at Birmingham, Birmingham, Alabama
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27
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Kudriaeva AA, Livneh I, Baranov MS, Ziganshin RH, Tupikin AE, Zaitseva SO, Kabilov MR, Ciechanover A, Belogurov AA. In-depth characterization of ubiquitin turnover in mammalian cells by fluorescence tracking. Cell Chem Biol 2021; 28:1192-1205.e9. [PMID: 33675681 DOI: 10.1016/j.chembiol.2021.02.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 12/29/2020] [Accepted: 02/11/2021] [Indexed: 01/01/2023]
Abstract
Despite almost 40 years having passed from the initial discovery of ubiquitin (Ub), fundamental questions related to its intracellular metabolism are still enigmatic. Here we utilized fluorescent tracking for monitoring ubiquitin turnover in mammalian cells, resulting in obtaining qualitatively new data. In the present study we report (1) short Ub half-life estimated as 4 h; (2) for a median of six Ub molecules per substrate as a dynamic equilibrium between Ub ligases and deubiquitinated enzymes (DUBs); (3) loss on average of one Ub molecule per four acts of engagement of polyubiquitinated substrate by the proteasome; (4) direct correlation between incorporation of Ub into the distinct type of chains and Ub half-life; and (5) critical influence of the single lysine residue K27 on the stability of the whole Ub molecule. Concluding, our data provide a comprehensive understanding of ubiquitin-proteasome system dynamics on the previously unreachable state of the art.
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Affiliation(s)
- Anna A Kudriaeva
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997 Moscow, Russian Federation
| | - Ido Livneh
- Technion Integrated Cancer Center, The Rappaport Faculty of Medicine and Research Institute, Technion-Israel Institute of Technology, 3109602 Haifa, Israel
| | - Mikhail S Baranov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997 Moscow, Russian Federation; Pirogov Russian National Research Medical University, Ostrovitianov 1, 117997 Moscow, Russian Federation
| | - Rustam H Ziganshin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997 Moscow, Russian Federation
| | - Alexey E Tupikin
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Lavrentieva 8, 630090 Novosibirsk, Russian Federation
| | - Snizhana O Zaitseva
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997 Moscow, Russian Federation
| | - Marsel R Kabilov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Lavrentieva 8, 630090 Novosibirsk, Russian Federation
| | - Aaron Ciechanover
- Technion Integrated Cancer Center, The Rappaport Faculty of Medicine and Research Institute, Technion-Israel Institute of Technology, 3109602 Haifa, Israel
| | - Alexey A Belogurov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997 Moscow, Russian Federation; Lomonosov Moscow State University, Leninskie Gory, 119991 Moscow, Russian Federation.
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28
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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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29
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Ross AB, Langer JD, Jovanovic M. Proteome Turnover in the Spotlight: Approaches, Applications, and Perspectives. Mol Cell Proteomics 2020; 20:100016. [PMID: 33556866 PMCID: PMC7950106 DOI: 10.1074/mcp.r120.002190] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 11/25/2020] [Accepted: 11/30/2020] [Indexed: 01/17/2023] Open
Abstract
In all cells, proteins are continuously synthesized and degraded to maintain protein homeostasis and modify gene expression levels in response to stimuli. Collectively, the processes of protein synthesis and degradation are referred to as protein turnover. At a steady state, protein turnover is constant to maintain protein homeostasis, but in dynamic responses, proteins change their rates of synthesis and degradation to adjust their proteomes to internal or external stimuli. Thus, probing the kinetics and dynamics of protein turnover lends insight into how cells regulate essential processes such as growth, differentiation, and stress response. Here, we outline historical and current approaches to measuring the kinetics of protein turnover on a proteome-wide scale in both steady-state and dynamic systems, with an emphasis on metabolic tracing using stable isotope-labeled amino acids. We highlight important considerations for designing proteome turnover experiments, key biological findings regarding the conserved principles of proteome turnover regulation, and future perspectives for both technological and biological investigation.
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Affiliation(s)
- Alison Barbara Ross
- Department of Biological Sciences, Columbia University, New York, New York, USA
| | - Julian David Langer
- Proteomics, Max Planck Institute of Biophysics, Frankfurt am Main, Germany; Proteomics, Max Planck Institute for Brain Research, Frankfurt am Main, Germany.
| | - Marko Jovanovic
- Department of Biological Sciences, Columbia University, New York, New York, USA.
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30
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Li J, Nadeem M, Chen L, Wang M, Wan M, Qiu L, Wang X. Differential proteomic analysis of soybean anthers by iTRAQ under high-temperature stress. J Proteomics 2020; 229:103968. [PMID: 32911126 DOI: 10.1016/j.jprot.2020.103968] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Revised: 08/14/2020] [Accepted: 08/31/2020] [Indexed: 02/07/2023]
Abstract
High-temperature has severe impacts on the functionality and development of soybean male reproductive organs. However, the molecular mechanism of thermo-tolerance in soybean remains unclear. In this study, a differential proteomic analysis was conducted between the anthers of heat-tolerant (JD21) and heat-sensitive (HD14) cultivars using an iTRAQ based approach. In total, 371, 479, and 417 differentially abundant proteins were identified between HD14 anthers treated with high-temperature stress vs HD14 anthers in the natural field conditions, JD21 anthers treated with high-temperature stress vs JD21 anthers in the natural field conditions, and HD14 vs JD21 anthers treated with high-temperature stress, respectively. The differentially abundant proteins associated with thermo-tolerance were predominantly involved in carbohydrate and energy metabolism, protein synthesis and degradation, nitrogen assimilation, and ROS detoxification. Sixteen common differentially abundant proteins were involved in known protein-protein interaction networks in three comparisons associated with heat, which may strongly influence anther growth and development. The qRT-PCR analysis validated the reliability of the iTRAQ results. In conclusion, the heat-tolerant cultivar performed better under stress than heat-sensitive cultivar through modulation of HSP family proteins, pectinesterase, profilin, S-adenosylmethionine synthase, peroxidase, GST, peptidylprolyl isomerase, and disulfide-isomerase. The results provide novel insight into the mechanism of high-temperature stress response of soybean. SIGNIFICANCE: In recent years, with the high temperature (HT) stress brought by climate change frequently occurs at anthesis and negatively affects soybean productivity. The molecular mechanism underlying the response of soybean anthers to HT is a relatively complex process and thus difficult to elucidate; however, it is possible to identify differentially expressed genes or proteins between heat-sensitive and heat-tolerant cultivars under HT stress. The potential candidate genes or proteins may then be utilized in elucidating the molecular mechanism underlying the response of soybean to HT stress, as well as provide genetic resource for the improvement of heat-tolerant characteristics in soybean. In present study, quantitative and qualitative proteomic changes occurring in anthers were compared between the heat-tolerant (JD21) and heat-sensitive (HD14) cultivars under HT stress using iTRAQ-based proteomics strategy. Our results provide new insight into translational alterations in HT-resistant and HT-sensitive soybean cultivars under HT stress, which helps to address the underlying molecular mechanism of soybean in response to HT stress.
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Affiliation(s)
- Jiajia Li
- School of Agronomy, Anhui Agricultural University, Hefei 230036, China
| | - Muhammad Nadeem
- School of Agronomy, Anhui Agricultural University, Hefei 230036, China
| | - Linying Chen
- School of Agronomy, Anhui Agricultural University, Hefei 230036, China
| | - Minghua Wang
- School of Agronomy, Anhui Agricultural University, Hefei 230036, China
| | - Mingyue Wan
- School of Agronomy, Anhui Agricultural University, Hefei 230036, China
| | - Lijuan Qiu
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Key Laboratory of Crop Gene Resource and Germplasm Enhancement (MOA), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Xiaobo Wang
- School of Agronomy, Anhui Agricultural University, Hefei 230036, China.
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31
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Lissandrello CA, Santos JA, Hsi P, Welch M, Mott VL, Kim ES, Chesin J, Haroutunian NJ, Stoddard AG, Czarnecki A, Coppeta JR, Freeman DK, Flusberg DA, Balestrini JL, Tandon V. High-throughput continuous-flow microfluidic electroporation of mRNA into primary human T cells for applications in cellular therapy manufacturing. Sci Rep 2020; 10:18045. [PMID: 33093518 PMCID: PMC7582186 DOI: 10.1038/s41598-020-73755-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 09/21/2020] [Indexed: 02/08/2023] Open
Abstract
Implementation of gene editing technologies such as CRISPR/Cas9 in the manufacture of novel cell-based therapeutics has the potential to enable highly-targeted, stable, and persistent genome modifications without the use of viral vectors. Electroporation has emerged as a preferred method for delivering gene-editing machinery to target cells, but a major challenge remaining is that most commercial electroporation machines are built for research and process development rather than for large-scale, automated cellular therapy manufacturing. Here we present a microfluidic continuous-flow electrotransfection device designed for precise, consistent, and high-throughput genetic modification of target cells in cellular therapy manufacturing applications. We optimized our device for delivery of mRNA into primary human T cells and demonstrated up to 95% transfection efficiency with minimum impact on cell viability and expansion potential. We additionally demonstrated processing of samples comprising up to 500 million T cells at a rate of 20 million cells/min. We anticipate that our device will help to streamline the production of autologous therapies requiring on the order of 10[Formula: see text]-10[Formula: see text] cells, and that it is well-suited to scale for production of trillions of cells to support emerging allogeneic therapies.
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Affiliation(s)
| | - Jose A Santos
- The Charles Stark Draper Laboratory, Inc., Cambridge, MA, 02139, USA
| | - Peter Hsi
- The Charles Stark Draper Laboratory, Inc., Cambridge, MA, 02139, USA
| | - Michaela Welch
- The Charles Stark Draper Laboratory, Inc., Cambridge, MA, 02139, USA
| | - Vienna L Mott
- The Charles Stark Draper Laboratory, Inc., Cambridge, MA, 02139, USA
| | - Ernest S Kim
- The Charles Stark Draper Laboratory, Inc., Cambridge, MA, 02139, USA
| | - Jordan Chesin
- The Charles Stark Draper Laboratory, Inc., Cambridge, MA, 02139, USA
| | | | - Aaron G Stoddard
- The Charles Stark Draper Laboratory, Inc., Cambridge, MA, 02139, USA
| | - Andrew Czarnecki
- The Charles Stark Draper Laboratory, Inc., Cambridge, MA, 02139, USA
| | | | - Daniel K Freeman
- The Charles Stark Draper Laboratory, Inc., Cambridge, MA, 02139, USA
| | | | | | - Vishal Tandon
- The Charles Stark Draper Laboratory, Inc., Cambridge, MA, 02139, USA.
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32
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Yang T, Yeoh LM, Tutor MV, Dixon MW, McMillan PJ, Xie SC, Bridgford JL, Gillett DL, Duffy MF, Ralph SA, McConville MJ, Tilley L, Cobbold SA. Decreased K13 Abundance Reduces Hemoglobin Catabolism and Proteotoxic Stress, Underpinning Artemisinin Resistance. Cell Rep 2020; 29:2917-2928.e5. [PMID: 31775055 DOI: 10.1016/j.celrep.2019.10.095] [Citation(s) in RCA: 94] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 09/08/2019] [Accepted: 10/23/2019] [Indexed: 01/09/2023] Open
Abstract
Increased tolerance of Plasmodium falciparum to front-line artemisinin antimalarials (ARTs) is associated with mutations in Kelch13 (K13), although the precise role of K13 remains unclear. Here, we show that K13 mutations result in decreased expression of this protein, while mislocalization of K13 mimics resistance-conferring mutations, pinpointing partial loss of function of K13 as the relevant molecular event. K13-GFP is associated with ∼170 nm diameter doughnut-shaped structures at the parasite periphery, consistent with the location and dimensions of cytostomes. Moreover, the hemoglobin-peptide profile of ring-stage parasites is reduced when K13 is mislocalized. We developed a pulse-SILAC approach to quantify protein turnover and observe less disruption to protein turnover following ART exposure when K13 is mislocalized. Our findings suggest that K13 regulates digestive vacuole biogenesis and the uptake/degradation of hemoglobin and that ART resistance is mediated by a decrease in heme-dependent drug activation, less proteotoxicity, and increased survival of parasite ring stages.
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Affiliation(s)
- Tuo Yang
- Department of Biochemistry and Molecular Biology, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Lee M Yeoh
- Department of Microbiology and Immunology, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Madel V Tutor
- Department of Biochemistry and Molecular Biology, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Matthew W Dixon
- Department of Biochemistry and Molecular Biology, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Paul J McMillan
- Department of Biochemistry and Molecular Biology, The University of Melbourne, Melbourne, VIC 3010, Australia; Biological Optical Microscopy Platform, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Stanley C Xie
- Department of Biochemistry and Molecular Biology, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Jessica L Bridgford
- Department of Biochemistry and Molecular Biology, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - David L Gillett
- Department of Biochemistry and Molecular Biology, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Michael F Duffy
- Department of Microbiology and Immunology, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Stuart A Ralph
- Department of Biochemistry and Molecular Biology, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Malcolm J McConville
- Department of Biochemistry and Molecular Biology, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Leann Tilley
- Department of Biochemistry and Molecular Biology, The University of Melbourne, Melbourne, VIC 3010, Australia.
| | - Simon A Cobbold
- Department of Biochemistry and Molecular Biology, The University of Melbourne, Melbourne, VIC 3010, Australia.
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Purification and characterization of antimicrobial peptide fractions of Junipers seravschanica. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2020. [DOI: 10.1016/j.bcab.2020.101554] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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34
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Kinetically distinct processing pathways diversify the CD8 + T cell response to a single viral epitope. Proc Natl Acad Sci U S A 2020; 117:19399-19407. [PMID: 32719124 DOI: 10.1073/pnas.2004372117] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The source proteins from which CD8+ T cell-activating peptides are derived remain enigmatic. Glycoproteins are particularly challenging in this regard owing to several potential trafficking routes within the cell. By engineering a glycoprotein-derived epitope to contain an N-linked glycosylation site, we determined that optimal CD8+ T cell expansion and function were induced by the peptides that are rapidly produced from the exceedingly minor fraction of protein mislocalized to the cytosol. In contrast, peptides derived from the much larger fraction that undergoes translocation and quality control are produced with delayed kinetics and induce suboptimal CD8+ T cell responses. This dual system of peptide generation enhances CD8+ T cell participation in diversifying both antigenicity and the kinetics of peptide display.
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35
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Jia X, Qin H, Bose SK, Liu T, He J, Xie S, Ye M, Yin H. Proteomics analysis reveals the defense priming effect of chitosan oligosaccharides in Arabidopsis-Pst DC3000 interaction. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2020; 149:301-312. [PMID: 32120172 DOI: 10.1016/j.plaphy.2020.01.037] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2019] [Revised: 01/29/2020] [Accepted: 01/30/2020] [Indexed: 05/02/2023]
Abstract
Chitosan oligosaccharides (COS) worked effectively in multiple plant-pathogen interactions as plant immunity regulator, however, due to the complexity of the COS-induced immune signaling network, the topic requires further investigation. In the present study, quantitative analysis of proteins was performed to investigate the underlying mechanism of COS induced resistance to Pseudomonas syringae pv. tomato DC3000 (Pst DC3000) in Arabidopsis thaliana. 4303 proteins were successfully quantified, 186, 217 and 207 proteins were differently regulated in mock + Pst, COS, and COS + Pst treated plants, respectively, compared with mock plants. From detailed functional and hierarchical clustering analysis, a priming effect of COS on plant immune system by pre-regulated the key proteins related to signaling transduction, defense response, cell wall biosynthesis and modification, plant growth and development, gene transcription and translation, which confers enhanced resistance when Pst DC3000 infection in Arabidopsis. Moreover, RACK1B which has the potential to be the key kinase receptor for COS signals was found out by protein-protein interaction network analysis of COS responsive proteins. In conclusion, COS treatment enable plant to fine-tuning its defense mechanisms for a more rapid and stronger response to future pathogen attacks, which obviously enhances plants defensive capacity that makes COS worked effectively in multiple plant-pathogen interactions.
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Affiliation(s)
- Xiaochen Jia
- Dalian Engineering Research Center for Carbohydrate Agricultural Preparations, Liaoning Provincial Key Laboratory of Carbohydrates, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Hongqiang Qin
- Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R & A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Santosh Kumar Bose
- Dalian Engineering Research Center for Carbohydrate Agricultural Preparations, Liaoning Provincial Key Laboratory of Carbohydrates, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Tongmei Liu
- Dalian Engineering Research Center for Carbohydrate Agricultural Preparations, Liaoning Provincial Key Laboratory of Carbohydrates, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Jinxia He
- Dalian Engineering Research Center for Carbohydrate Agricultural Preparations, Liaoning Provincial Key Laboratory of Carbohydrates, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Shangqiang Xie
- Dalian Engineering Research Center for Carbohydrate Agricultural Preparations, Liaoning Provincial Key Laboratory of Carbohydrates, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Mingliang Ye
- Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R & A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China.
| | - Heng Yin
- Dalian Engineering Research Center for Carbohydrate Agricultural Preparations, Liaoning Provincial Key Laboratory of Carbohydrates, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China.
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36
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Rožman K, Alexander EM, Ogorevc E, Bozovičar K, Sosič I, Aldrich CC, Gobec S. Psoralen Derivatives as Inhibitors of Mycobacterium tuberculosis Proteasome. Molecules 2020; 25:E1305. [PMID: 32178473 PMCID: PMC7144120 DOI: 10.3390/molecules25061305] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 03/06/2020] [Accepted: 03/10/2020] [Indexed: 12/19/2022] Open
Abstract
Protein degradation is a fundamental process in all living organisms. An important part of this system is a multisubunit, barrel-shaped protease complex called the proteasome. This enzyme is directly responsible for the proteolysis of ubiquitin- or pup-tagged proteins to smaller peptides. In this study, we present a series of 92 psoralen derivatives, of which 15 displayed inhibitory potency against the Mycobacterium tuberculosis proteasome in low micromolar concentrations. The best inhibitors, i.e., 8, 11, 13 and 15, exhibited a mixed type of inhibition and overall good inhibitory potency in biochemical assays. N-(cyanomethyl)acetamide 8 (Ki = 5.6 µM) and carboxaldehyde-based derivative 15 (Ki = 14.9 µM) were shown to be reversible inhibitors of the enzyme. On the other hand, pyrrolidine-2,5-dione esters 11 and 13 irreversibly inhibited the enzyme with Ki values of 4.2 µM and 1.1 µM, respectively. In addition, we showed that an established immunoproteasome inhibitor, PR-957, is a noncompetitive irreversible inhibitor of the mycobacterial proteasome (Ki = 5.2 ± 1.9 µM, kinact/Ki = 96 ± 41 M-1·s-1). These compounds represent interesting hit compounds for further optimization in the development of new drugs for the treatment of tuberculosis.
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Affiliation(s)
- Kaja Rožman
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva 7, SI-1000 Ljubljana, Slovenia; (K.R.); (E.O.); (K.B.); (I.S.)
- Department of Medicinal Chemistry, University of Minnesota, 308 Harvard Street Southeast, Minneapolis, MN 55455, USA; (E.M.A.); (C.C.A.)
| | - Evan M. Alexander
- Department of Medicinal Chemistry, University of Minnesota, 308 Harvard Street Southeast, Minneapolis, MN 55455, USA; (E.M.A.); (C.C.A.)
| | - Eva Ogorevc
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva 7, SI-1000 Ljubljana, Slovenia; (K.R.); (E.O.); (K.B.); (I.S.)
| | - Krištof Bozovičar
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva 7, SI-1000 Ljubljana, Slovenia; (K.R.); (E.O.); (K.B.); (I.S.)
| | - Izidor Sosič
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva 7, SI-1000 Ljubljana, Slovenia; (K.R.); (E.O.); (K.B.); (I.S.)
| | - Courtney C. Aldrich
- Department of Medicinal Chemistry, University of Minnesota, 308 Harvard Street Southeast, Minneapolis, MN 55455, USA; (E.M.A.); (C.C.A.)
| | - Stanislav Gobec
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva 7, SI-1000 Ljubljana, Slovenia; (K.R.); (E.O.); (K.B.); (I.S.)
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37
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Cheng C, Liu Y, Fang W, Tao J, Yang Z, Yin Y. iTRAQ-based proteomic and physiological analyses of mustard sprouts in response to heat stress. RSC Adv 2020; 10:6052-6062. [PMID: 35497421 PMCID: PMC9049219 DOI: 10.1039/c9ra10089j] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Accepted: 01/30/2020] [Indexed: 12/02/2022] Open
Abstract
Heat stress has been proved to increase the content of melatonin in plants. In the present study, a combination of methods including physiological and biochemical, gene transcription and proteomic were used to investigate the melatonin accumulation mechanisms in mustard sprouts under heat treatment during the germination period. It was revealed that the heat treatment can significantly affect sprout growth, antioxidant enzyme activity and melatonin content in mustard sprouts. Meanwhile, the expression of melatonin key synthase genes, such as tryptophan decarboxylase genes (BjTDC 1, BjTDC 2) and serotonin N-acetyltransferase genes (BjSNAT 1), were significantly induced by heat stress, which coincided with the trend of melatonin content. Under the heat stress, a total of 172 differential abundance proteins were confidently identified in mustard sprouts and participated in many physiological processes. Functional classification analysis showed that the defense/pressure, energy and nucleotide metabolism, protein biosynthesis, signal transduction and transcription etc. were largely induced. Heat treatment stimulated a defense response at the protein level by regulating the growth and physiological metabolism in mustard sprouts. The results in this work provided novel deep insights into the proteins' response to heat stress, which will certainly promote further understanding of the heat-tolerance mechanism of mustard sprouts.
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Affiliation(s)
- Chao Cheng
- College of Food Science and Engerning, Yangzhou University Yangzhou Jiangsu 210095 People's Republic of China +86-514-89786551 +86-514-89786551
| | - Yin Liu
- College of Food Science and Engerning, Yangzhou University Yangzhou Jiangsu 210095 People's Republic of China +86-514-89786551 +86-514-89786551
| | - Weiming Fang
- College of Food Science and Engerning, Yangzhou University Yangzhou Jiangsu 210095 People's Republic of China +86-514-89786551 +86-514-89786551
| | - Jun Tao
- College of Food Science and Engerning, Yangzhou University Yangzhou Jiangsu 210095 People's Republic of China +86-514-89786551 +86-514-89786551
| | - Zhengfei Yang
- College of Food Science and Engerning, Yangzhou University Yangzhou Jiangsu 210095 People's Republic of China +86-514-89786551 +86-514-89786551
| | - Yongqi Yin
- College of Food Science and Engerning, Yangzhou University Yangzhou Jiangsu 210095 People's Republic of China +86-514-89786551 +86-514-89786551
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38
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Seryl-tRNA synthetase is involved in methionine stimulation of β-casein synthesis in bovine mammary epithelial cells. Br J Nutr 2019; 123:489-498. [PMID: 31711551 PMCID: PMC7015878 DOI: 10.1017/s0007114519002885] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Despite the well-characterised mechanisms of amino acids (AA) regulation of milk protein synthesis in mammary glands (MG), the underlying specific AA regulatory machinery in bovine MG remains further elucidated. As methionine (Met) is one of the most important essential and limiting AA for dairy cows, it is crucial to expand how Met exerts its regulatory effects on dairy milk protein synthesis. Our previous work detected the potential regulatory role of seryl-tRNA synthetase (SARS) in essential AA (EAA)-stimulated bovine casein synthesis. Here, we investigated whether and how SARS participates in Met stimulation of casein production in bovine mammary epithelial cells (BMEC). With or without RNA interference against SARS, BMEC were treated with the medium in the absence (containing all other EAA and devoid of Met alone)/presence (containing 0·6 mm of Met in the medium devoid of Met alone) of Met. The protein abundance of β-casein and members of the mammalian target of rapamycin (mTOR) and general control nonderepressible 2 (GCN2) pathways was determined by immunoblot assay after 6 h treatment, the cell viability and cell cycle progression were determined by cell counting and propidium iodide-staining assay after 24 h treatment, and protein turnover was determined by l-[ring-3H5]phenylalanine isotope tracing assay after 48 h treatment. In the absence of Met, there was a general reduction in cell viability, total protein synthesis and β-casein production; in contrast, total protein degradation was enhanced. SARS knockdown strengthened these changes. Finally, SARS may work to promote Met-stimulated β-casein synthesis via affecting mTOR and GCN2 routes in BMEC.
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39
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Yang L, Cao Y, Zhao J, Fang Y, Liu N, Zhang Y. Multidimensional Proteomics Identifies Declines in Protein Homeostasis and Mitochondria as Early Signals for Normal Aging and Age-associated Disease in Drosophila. Mol Cell Proteomics 2019; 18:2078-2088. [PMID: 31434710 PMCID: PMC6773560 DOI: 10.1074/mcp.ra119.001621] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 08/19/2019] [Indexed: 12/13/2022] Open
Abstract
Aging is characterized by a gradual deterioration in proteome. However, how protein dynamics that changes with normal aging and in disease is less well understood. Here, we profiled the snapshots of aging proteome in Drosophila, from head and muscle tissues of post-mitotic somatic cells, and the testis of mitotically-active cells. Our data demonstrated that dysregulation of proteome homeostasis, or proteostasis, might be a common feature associated with age. We further used pulsed metabolic stable isotope labeling analysis to characterize protein synthesis. Interestingly, this study determined an age-modulated decline in protein synthesis with age, particularly in the pathways related to mitochondria, neurotransmission, and proteostasis. Importantly, this decline became dramatically accelerated in Pink1 mutants, a Drosophila model of human age-related Parkinson's disease. Taken together, our multidimensional proteomic study revealed tissue-specific protein dynamics with age, highlighting mitochondrial and proteostasis-related proteins. We suggest that declines in proteostasis and mitochondria early in life are critical signals prior to the onset of aging and aging-associated diseases.
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Affiliation(s)
- Lu Yang
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 26 Qiuyue Rd., Pudong, Shanghai, 201210, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ye Cao
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 26 Qiuyue Rd., Pudong, Shanghai, 201210, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jing Zhao
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 26 Qiuyue Rd., Pudong, Shanghai, 201210, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yanshan Fang
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 26 Qiuyue Rd., Pudong, Shanghai, 201210, China
| | - Nan Liu
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 26 Qiuyue Rd., Pudong, Shanghai, 201210, China.
| | - Yaoyang Zhang
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 26 Qiuyue Rd., Pudong, Shanghai, 201210, China.
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40
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Eldeeb MA, Siva-Piragasam R, Ragheb MA, Esmaili M, Salla M, Fahlman RP. A molecular toolbox for studying protein degradation in mammalian cells. J Neurochem 2019; 151:520-533. [PMID: 31357232 DOI: 10.1111/jnc.14838] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2019] [Revised: 07/03/2019] [Accepted: 07/24/2019] [Indexed: 12/14/2022]
Abstract
Protein degradation is a crucial regulatory process in maintaining cellular proteostasis. The selective degradation of intracellular proteins controls diverse cellular and biochemical processes in all kingdoms of life. Targeted protein degradation is implicated in controlling the levels of regulatory proteins as well as eliminating misfolded and any otherwise abnormal proteins. Deregulation of protein degradation is concomitant with the progression of various neurodegenerative disorders such as Parkinson's and Alzheimer's diseases. Thus, methods of measuring metabolic half-lives of proteins greatly influence our understanding of the diverse functions of proteins in mammalian cells including neuronal cells. Historically, protein degradation rates have been studied via exploiting methods that estimate overall protein degradation or focus on few individual proteins. Notably, with the recent technical advances and developments in proteomic and imaging techniques, it is now possible to measure degradation rates of a large repertoire of defined proteins and analyze the degradation profile in a detailed spatio-temporal manner, with the aim of determining proteome-wide protein stabilities upon different physiological conditions. Herein, we discuss some of the classical and novel methods for determining protein degradation rates highlighting the crucial role of some state of art approaches in deciphering the global impact of dynamic nature of targeted degradation of cellular proteins. This article is part of the Special Issue "Proteomics".
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Affiliation(s)
- Mohamed A Eldeeb
- Department of Chemistry (Biochemistry Division), Faculty of Science, Cairo University, Giza, Egypt.,Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montreal, Quebec, Canada
| | | | - Mohamed A Ragheb
- Department of Chemistry (Biochemistry Division), Faculty of Science, Cairo University, Giza, Egypt
| | - Mansoore Esmaili
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada
| | - Mohamed Salla
- Department of Biological Sciences, Lebanese International University, Bekaa, Lebanon
| | - Richard P Fahlman
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada
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41
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Zalzman M, Meltzer WA, Portney BA, Brown RA, Gupta A. The Role of Ubiquitination and SUMOylation in Telomere Biology. Curr Issues Mol Biol 2019; 35:85-98. [PMID: 31422934 DOI: 10.21775/cimb.035.085] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Telomeres are a unique structure of DNA repeats covered by proteins at the ends of the chromosomes that protect the coding regions of the genome and function as a biological clock. They require a tight regulation of the factors covering and protecting their structure, as they are shortened with each cell division to limit the ability of cells to replicate uncontrollably. Additionally, they protect the chromosome ends from DNA damage responses and thereby, prevent genomic instability. Telomere dysfunction can lead to chromosomal abnormalities and cancer. Therefore, dysregulation of any of the factors that regulate the integrity of the telomeres will have implications to chromosomal stability, replicative lifespan and may lead to cell transformation. This review will cover the main factors participating in the normal function of the telomeres and how these are regulated by the ubiquitin and SUMO systems. Accumulating evidence indicate that the ubiquitin and SUMO pathways are significant regulators of the shelterin complex and other chromatin modifiers, which are important for telomere structure integrity. Furthermore, the crosstalk between these two pathways has been reported in telomeric DNA repair. A better understanding of the factors contributing to telomere biology, and how they are regulated, is important for the design of new strategies for cancer therapies and regenerative medicine.
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Affiliation(s)
- Michal Zalzman
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - W Alex Meltzer
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Benjamin A Portney
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Robert A Brown
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Aditi Gupta
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD, USA
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42
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Liu Z, Zou L, Chen C, Zhao H, Yan Y, Wang C, Liu X. iTRAQ-based quantitative proteomic analysis of salt stress in Spica Prunellae. Sci Rep 2019; 9:9590. [PMID: 31270436 PMCID: PMC6610069 DOI: 10.1038/s41598-019-46043-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 06/20/2019] [Indexed: 01/03/2023] Open
Abstract
Spica Prunellae is an important Chinese herbal medicine. Because of its good curative effect on various diseases, this herb is consumed in large quantities in clinical applications. The metabolites of Spica Prunellae are known to change under salt stress; however, the difference in protein levels of Spica Prunellae between saline and normal conditions is unclear. In this study, we used proteomics techniques to identify differentially expressed proteins in Spica Prunellae under different saline conditions. (iTRAQ) MS/MS was used to detect statistically significant changes in protein between salt stress and normal conditions. Ultimately, we detected 1,937 proteins, 89 of which were detected in two different comparison. Based on GO, STRING and KEGG analyses, 35 significantly differentially expressed proteins were selected for further analysis. The results of functional and signal pathway analyses indicated that the cellular protein and carbohydrate metabolism of Spica Prunellae was weaker, calcium ion transport was higher, photosynthesis was higher, and protein production was faster under saline conditions than under normal conditions. This study provides useful information for studying the causes of differences in secondary metabolites in Spica Prunellae under salt stress and the protein mechanisms related to their quality.
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Affiliation(s)
- Zixiu Liu
- College of pharmacy, Nanjing University of Chinese Medicine, Nanjing, China.,Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing, China.,National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing, China.,Department of Pharmacy, No. 454 Hospital of PLA, Nanjing, China
| | - Lisi Zou
- College of pharmacy, Nanjing University of Chinese Medicine, Nanjing, China.,Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing, China.,National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing, China
| | - Cuihua Chen
- College of pharmacy, Nanjing University of Chinese Medicine, Nanjing, China.,Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing, China.,National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing, China
| | - Hui Zhao
- College of pharmacy, Nanjing University of Chinese Medicine, Nanjing, China.,Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing, China.,National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing, China
| | - Ying Yan
- College of pharmacy, Nanjing University of Chinese Medicine, Nanjing, China.,Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing, China.,National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing, China
| | - Chengcheng Wang
- College of pharmacy, Nanjing University of Chinese Medicine, Nanjing, China.,Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing, China.,National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing, China
| | - Xunhong Liu
- College of pharmacy, Nanjing University of Chinese Medicine, Nanjing, China. .,Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing, China. .,National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing, China.
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43
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Alderman SL, Crossley DA, Elsey RM, Gillis TE. Hypoxia-induced reprogramming of the cardiac phenotype in American alligators (Alligator mississippiensis) revealed by quantitative proteomics. Sci Rep 2019; 9:8592. [PMID: 31197188 PMCID: PMC6565670 DOI: 10.1038/s41598-019-45023-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 05/29/2019] [Indexed: 02/06/2023] Open
Abstract
Hypoxic exposure during development can have a profound influence on offspring physiology, including cardiac dysfunction, yet many reptile embryos naturally experience periods of hypoxia in buried nests. American alligators experimentally exposed to developmental hypoxia demonstrate morphological and functional changes to the heart that persist into later life stages; however, the molecular bases of these changes remain unknown. We tested if targeted and persistent changes in steady-state protein expression underlie this hypoxic heart phenotype, using isobaric tags for relative and absolute quantitation (iTRAQ) proteomics. Alligator eggs were reared under normoxia or 10% hypoxia, then either sampled (embryo) or returned to normoxia for 2 years (juvenile). Three salient findings emerge from the integrated analysis of the 145 differentially expressed proteins in hypoxia-reared animals: (1) significant protein-protein interaction networks were identified only in up-regulated proteins, indicating that the effects of developmental hypoxia are stimulatory and directed; (2) the up-regulated proteins substantially enriched processes related to protein turnover, cellular organization, and metabolic pathways, supporting increased resource allocation towards building and maintaining a higher functioning heart; and (3) the juvenile cardiac proteome retained many of the signature changes observed in embryonic hearts, supporting long-term reprogramming of cardiac myocytes induced by hypoxia during critical periods of development.
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Affiliation(s)
- Sarah L Alderman
- Department of Integrative Biology, University of Guelph, Guelph, Ontario, N1G 2W1, Canada.
| | - Dane A Crossley
- Developmental Integrative Biology Research Group, Department of Biological Sciences, University of North Texas, Denton, Texas, 76203-5017, USA
| | - Ruth M Elsey
- Louisiana Department of Wildlife and Fisheries, Rockefeller Wildlife Refuge, Grand Chenier, Louisiana, 70643, USA
| | - Todd E Gillis
- Department of Integrative Biology, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
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44
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Grandi P, Bantscheff M. Advanced proteomics approaches to unravel protein homeostasis. DRUG DISCOVERY TODAY. TECHNOLOGIES 2019; 31:99-108. [PMID: 31200865 DOI: 10.1016/j.ddtec.2019.02.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 02/03/2019] [Accepted: 02/05/2019] [Indexed: 05/22/2023]
Abstract
Quantitative proteomics methods are instrumental in measuring the interplay between protein synthesis and protein degradation in cells and tissues in different conditions and substantially contribute to the understanding of control mechanisms for protein homeostasis. Proteomics and chemoproteomics approaches enable the characterization of small molecule modifiers of protein degradation for therapeutic applications. Here, we review recent developments and applications of mass spectrometry-based (chemo-)proteomics methods for the study of cellular homeostasis.
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Affiliation(s)
- Paola Grandi
- Cellzome GmbH, GlaxoSmithKline, Meyerhofstrasse 1, 69117 Heidelberg, Germany.
| | - Marcus Bantscheff
- Cellzome GmbH, GlaxoSmithKline, Meyerhofstrasse 1, 69117 Heidelberg, Germany.
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45
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Tsuji JS, Chang ET, Gentry PR, Clewell HJ, Boffetta P, Cohen SM. Dose-response for assessing the cancer risk of inorganic arsenic in drinking water: the scientific basis for use of a threshold approach. Crit Rev Toxicol 2019; 49:36-84. [DOI: 10.1080/10408444.2019.1573804] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
| | - Ellen T. Chang
- Exponent, Inc., Menlo Park, CA and Stanford Cancer Institute, Stanford, CA, USA
| | | | | | - Paolo Boffetta
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Samuel M. Cohen
- Havlik-Wall Professor of Oncology, Department of Pathology and Microbiology and the Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, USA
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iTRAQ-based quantitative proteomics analysis of cold stress-induced mechanisms in grafted watermelon seedlings. J Proteomics 2019; 192:311-320. [DOI: 10.1016/j.jprot.2018.09.012] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 09/05/2018] [Accepted: 09/20/2018] [Indexed: 12/21/2022]
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47
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Pulse SILAC Approaches to the Measurement of Cellular Dynamics. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1140:575-583. [DOI: 10.1007/978-3-030-15950-4_34] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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48
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Abstract
Idiopathic pulmonary fibrosis (IPF) is an extremely aggressive lung disease that develops almost exclusively in older individuals, carries a very poor prognosis, and lacks any truly effective therapies. The current conceptual model is that IPF develops because of an age-related decline in the ability of the lung epithelium to regenerate after injury, largely due to death or senescence of epithelial progenitor cells in the distal airways. This loss of regenerative capacity is thought to initiate a chronic and ineffective wound-healing response, characterized by persistent, low-grade lung inflammation and sustained production of collagen and other extracellular matrix materials. Despite recent advances in our understanding of IPF pathobiology, there remains a pressing need to further delineate underlying mechanisms to develop more effective therapies for this disease. In this review, we build the case that many of the manifestations of IPF result from a failure of cells to effectively manage their proteome. We propose that epithelial progenitor cells, as well as immune cells and fibroblasts, become functionally impaired, at least in part, because of an accumulation or a loss in the expression of various crucial proteins. Further, we propose that central to this defect is the dysregulation of the ubiquitin-proteasome system (UPS), which is the major protein-degradation system in eukaryotic cells. Lastly, borrowing concepts from other fields, we discuss how targeting the UPS system could be employed as a novel treatment for IPF and perhaps for other fibrotic lung diseases as well.
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Affiliation(s)
- Willy Roque
- Center for Translational Medicine and Jane and Leonard Korman Lung Center, Thomas Jefferson University, Philadelphia, PA, USA
| | - Ross Summer
- Center for Translational Medicine and Jane and Leonard Korman Lung Center, Thomas Jefferson University, Philadelphia, PA, USA
| | - Freddy Romero
- Center for Translational Medicine and Jane and Leonard Korman Lung Center, Thomas Jefferson University, Philadelphia, PA, USA
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Zhao X, Zhang Y, Wang M, Fang X, Cai X. Comparative proteomic analysis of latex from Euphorbia kansui laticifers at different development stages with and without UV-B treatment via iTRAQ-coupled two-dimensional liquid chromatography-MS/MS. FUNCTIONAL PLANT BIOLOGY : FPB 2019; 47:67-79. [PMID: 31818367 DOI: 10.1071/fp19033] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 08/30/2019] [Indexed: 06/10/2023]
Abstract
Euphorbia kansui Liou, an endemic species in China, is well-known in traditional Chinese medicine. All parts of E. kansui contain white latex, which is the protoplasm constituent of specialised cells known as laticifers. The latex contains many proteins with various biological functions. In the present study, isobaric tagging for relative and absolute quantitation (iTRAQ) and MS technology combined with western blot and quantitative real-time PCR analysis were used to identify latex proteins and analyse differentially accumulated proteins in laticifers at different development stages, with and without UV-B treatment according to the E. kansui transcriptome database and the NCBI Euphorbiaceae RefSeq protein database. A total of 322 latex proteins were successfully identified. Proteasome subunits, ubiquitinated proteins, vacuolar ATP synthase (V-ATPase) and lysosomal enzymes decreased, keeping the content at a higher level in laticifers in the early development stage. These results suggest that the ubiquitin-proteasome pathway and the lysosome autophagy pathway were involved in the partial degradation of laticifer cytoplasm. In addition, terpenoid biosynthesis-related proteins, 14-3-3 protein, V-ATPase and lysosomal enzymes increased under UV-B treatment, which showed that partial cytoplasmic degradation is positively correlated with secondary metabolite synthesis in the development of E. kansui laticifers. Besides, UV-B radiation can increase plant resistance by promoting laticifer development in E. kansui. This information provides a basis for further exploration of E. kansui laticifer development, and terpenoid synthesis and regulation.
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Affiliation(s)
- Xueyan Zhao
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Northwest University, Xi'an, 710069, China; and Collaborative Innovation Center of Green Manufacturing Technology for Traditional Chinese Medicine in Shaanxi Province, School of Pharmacy, Shaanxi Institute of International Trade and Commerce, Xianyang, 712046, China
| | - Yue Zhang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Northwest University, Xi'an, 710069, China
| | - Meng Wang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Northwest University, Xi'an, 710069, China
| | - Xiaoai Fang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Northwest University, Xi'an, 710069, China
| | - Xia Cai
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Northwest University, Xi'an, 710069, China; and Corresponding author.
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50
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Bensaddek D, Nicolas A, Lamond AI. Signal enhanced proteomics: a biological perspective on dissecting the functional organisation of cell proteomes. Curr Opin Chem Biol 2018; 48:114-122. [PMID: 30551035 DOI: 10.1016/j.cbpa.2018.10.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 10/07/2018] [Accepted: 10/10/2018] [Indexed: 01/28/2023]
Abstract
Proteomes are highly dynamic and can respond rapidly to environmental and cellular signals. Within cells, proteins often form distinct pools with different functions and properties. However, in quantitative proteomics studies it is common to measure averaged values for proteins that do not reflect variations that may occur between different protein isoforms, different subcellular compartments, or in cells at different cell cycle stages and so on. Here we review experimental approaches that can be used to enhance the signal from specific pools of protein that may otherwise be obscured through averaging across protein populations. This signal enhancement can help to reveal functions associated with specific protein pools, providing insight into the regulation of cellular processes. We review different strategies for proteomic signal enhancement, with a focus on the analysis of protein pools in different subcellular locations. We describe how MS-based proteome analyses can be combined with a general physico-chemical cell fractionation procedure that can be applied to many cultured cell lines.
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Affiliation(s)
- Dalila Bensaddek
- Laboratory of Quantitative Proteomics, Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
| | - Armel Nicolas
- Laboratory of Quantitative Proteomics, Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
| | - Angus I Lamond
- Laboratory of Quantitative Proteomics, Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK.
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