1
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Calis S, Gevaert K. The role of Nα-terminal acetylation in protein conformation. FEBS J 2024. [PMID: 38923676 DOI: 10.1111/febs.17209] [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: 03/28/2024] [Accepted: 06/12/2024] [Indexed: 06/28/2024]
Abstract
Especially in higher eukaryotes, the N termini of proteins are subject to enzymatic modifications, with the acetylation of the alpha-amino group of nascent polypeptides being a prominent one. In recent years, the specificities and substrates of the enzymes responsible for this modification, the Nα-terminal acetyltransferases, have been mapped in several proteomic studies. Aberrant expression of, and mutations in these enzymes were found to be associated with several human diseases, explaining the growing interest in protein Nα-terminal acetylation. With some enzymes, such as the Nα-terminal acetyltransferase A complex having thousands of possible substrates, researchers are now trying to decipher the functional outcome of Nα-terminal protein acetylation. In this review, we zoom in on one possible functional consequence of Nα-terminal protein acetylation; its effect on protein folding. Using selected examples of proteins associated with human diseases such as alpha-synuclein and huntingtin, here, we discuss the sometimes contradictory findings of the effects of Nα-terminal protein acetylation on protein (mis)folding and aggregation.
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Affiliation(s)
- Sam Calis
- VIB Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Belgium
| | - Kris Gevaert
- VIB Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Belgium
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2
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Manav N, Jit BP, Kataria B, Sharma A. Cellular and epigenetic perspective of protein stability and its implications in the biological system. Epigenomics 2024:1-22. [PMID: 38884355 DOI: 10.1080/17501911.2024.2351788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 04/30/2024] [Indexed: 06/18/2024] Open
Abstract
Protein stability is a fundamental prerequisite in both experimental and therapeutic applications. Current advancements in high throughput experimental techniques and functional ontology approaches have elucidated that impairment in the structure and stability of proteins is intricately associated with the cause and cure of several diseases. Therefore, it is paramount to deeply understand the physical and molecular confounding factors governing the stability of proteins. In this review article, we comprehensively investigated the evolution of protein stability, examining its emergence over time, its relationship with organizational aspects and the experimental methods used to understand it. Furthermore, we have also emphasized the role of Epigenetics and its interplay with post-translational modifications (PTMs) in regulating the stability of proteins.
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Affiliation(s)
- Nisha Manav
- Department of Biochemistry, All India Institute of Medical Sciences New Delhi, Ansari Nagar, 110029, India
| | - Bimal Prasad Jit
- Department of Biochemistry, All India Institute of Medical Sciences New Delhi, Ansari Nagar, 110029, India
| | - Babita Kataria
- Department of Medical Oncology, National Cancer Institute, All India Institute of Medical Sciences, Jhajjar, 124105, India
| | - Ashok Sharma
- Department of Biochemistry, All India Institute of Medical Sciences New Delhi, Ansari Nagar, 110029, India
- Department of Biochemistry, National Cancer Institute, All India Institute of Medical Sciences, Jhajjar, 124105, India
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3
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Ray B, Rungratanawanich W, LeFort KR, Chidambaram SB, Song BJ. Mitochondrial Aldehyde Dehydrogenase 2 (ALDH2) Protects against Binge Alcohol-Mediated Gut and Brain Injury. Cells 2024; 13:927. [PMID: 38891060 PMCID: PMC11171926 DOI: 10.3390/cells13110927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Revised: 05/16/2024] [Accepted: 05/24/2024] [Indexed: 06/21/2024] Open
Abstract
Mitochondrial aldehyde dehydrogenase-2 (ALDH2) metabolizes acetaldehyde to acetate. People with ALDH2 deficiency and Aldh2-knockout (KO) mice are more susceptible to alcohol-induced tissue damage. However, the underlying mechanisms behind ALDH2-related gut-associated brain damage remain unclear. Age-matched young female Aldh2-KO and C57BL/6J wild-type (WT) mice were gavaged with binge alcohol (4 g/kg/dose, three doses) or dextrose (control) at 12 h intervals. Tissues and sera were collected 1 h after the last ethanol dose and evaluated by histological and biochemical analyses of the gut and hippocampus and their extracts. For the mechanistic study, mouse neuroblast Neuro2A cells were exposed to ethanol with or without an Aldh2 inhibitor (Daidzin). Binge alcohol decreased intestinal tight/adherens junction proteins but increased oxidative stress-mediated post-translational modifications (PTMs) and enterocyte apoptosis, leading to elevated gut leakiness and endotoxemia in Aldh2-KO mice compared to corresponding WT mice. Alcohol-exposed Aldh2-KO mice also showed higher levels of hippocampal brain injury, oxidative stress-related PTMs, and neuronal apoptosis than the WT mice. Additionally, alcohol exposure reduced Neuro2A cell viability with elevated oxidative stress-related PTMs and apoptosis, all of which were exacerbated by Aldh2 inhibition. Our results show for the first time that ALDH2 plays a protective role in binge alcohol-induced brain injury partly through the gut-brain axis, suggesting that ALDH2 is a potential target for attenuating alcohol-induced tissue injury.
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Affiliation(s)
- Bipul Ray
- Section of Molecular Pharmacology and Toxicology, National Institute on Alcohol Abuse and Alcoholism, Bethesda, MD 20892, USA; (B.R.); (W.R.); (K.R.L.)
| | - Wiramon Rungratanawanich
- Section of Molecular Pharmacology and Toxicology, National Institute on Alcohol Abuse and Alcoholism, Bethesda, MD 20892, USA; (B.R.); (W.R.); (K.R.L.)
| | - Karli R. LeFort
- Section of Molecular Pharmacology and Toxicology, National Institute on Alcohol Abuse and Alcoholism, Bethesda, MD 20892, USA; (B.R.); (W.R.); (K.R.L.)
| | - Saravana Babu Chidambaram
- Department of Pharmacology, JSS College of Pharmacy, and Center for Experimental Pharmacology and Toxicology, JSS Academy of Higher Education & Research, Mysuru 570015, India;
| | - Byoung-Joon Song
- Section of Molecular Pharmacology and Toxicology, National Institute on Alcohol Abuse and Alcoholism, Bethesda, MD 20892, USA; (B.R.); (W.R.); (K.R.L.)
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4
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Makwana R, Christ C, Marchi E, Harpell R, Lyon GJ. Longitudinal adaptive behavioral outcomes in Ogden syndrome by seizure status and therapeutic intervention. Am J Med Genet A 2024:e63651. [PMID: 38747166 DOI: 10.1002/ajmg.a.63651] [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: 02/21/2024] [Revised: 04/16/2024] [Accepted: 04/27/2024] [Indexed: 05/28/2024]
Abstract
Ogden syndrome, also known as NAA10-related neurodevelopmental syndrome, is a rare genetic condition associated with pathogenic variants in the NAA10 N-terminal acetylation family of proteins. The condition was initially described in 2011 and is characterized by a range of neurologic symptoms, including intellectual disability and seizures, as well as developmental delays, psychiatric symptoms, congenital heart abnormalities, hypotonia, and others. Previously published articles have described the etiology and phenotype of Ogden syndrome, mostly with retrospective analyses; herein, we report prospective data concerning its progress over time. The current study involves a total of 58 distinct participants; of these, 43 caregivers were interviewed using the Vineland-3 and answered a survey regarding therapy and other questions, 10 of whom completed the Vineland-3 but did not answer the survey, and 5 participants who answered the survey but have not yet performed the Vineland-3 due to language constraints. The average age at the time of the most recent assessment was 12.4 years, with individuals ranging in age from 11 months to 40.2 years. Using Vineland-3 scores, we show decline in cognitive function over time in individuals with Ogden syndrome (n = 53). Sub-domain analysis found the decline to be present across all modalities. In addition, we describe the nature of seizures in this condition in greater detail, as well as investigate how already-available non-pharmaceutical therapies impact individuals with NAA10-related neurodevelopmental syndrome. Additional investigation between seizure and non-seizure groups showed no significant difference in adaptive behavior outcomes. A therapy investigation showed speech therapy to be the most commonly used therapy by individuals with NAA10-related neurodevelopmental syndrome, followed by occupational and physical therapy, with more severely affected individuals receiving more types of therapy than their less-severe counterparts. Early intervention analysis was only significantly effective for speech therapy, with analyses of all other therapies being non-significant. Our study portrays the decline in cognitive function over time of individuals within our cohort, independent of seizure status, and therapies being received, and highlights the urgent need for the development of effective treatments for Ogden syndrome.
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Affiliation(s)
- Rikhil Makwana
- Department of Human Genetics, New York State Institute for Basic Research in Developmental Disabilities, New York, New York, USA
| | - Carolina Christ
- Department of Human Genetics, New York State Institute for Basic Research in Developmental Disabilities, New York, New York, USA
| | - Elaine Marchi
- Department of Human Genetics, New York State Institute for Basic Research in Developmental Disabilities, New York, New York, USA
| | - Randie Harpell
- Department of Human Genetics, New York State Institute for Basic Research in Developmental Disabilities, New York, New York, USA
| | - Gholson J Lyon
- Department of Human Genetics, New York State Institute for Basic Research in Developmental Disabilities, New York, New York, USA
- George A. Jervis Clinic, New York State Institute for Basic Research in Developmental Disabilities, New York, New York, USA
- The Graduate Center, The City University of New York, New York, New York, USA
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5
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Demko V, Belova T, Messerer M, Hvidsten TR, Perroud PF, Ako AE, Johansen W, Mayer KFX, Olsen OA, Lang D. Regulation of developmental gatekeeping and cell fate transition by the calpain protease DEK1 in Physcomitrium patens. Commun Biol 2024; 7:261. [PMID: 38438476 PMCID: PMC10912778 DOI: 10.1038/s42003-024-05933-z] [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: 06/09/2023] [Accepted: 02/19/2024] [Indexed: 03/06/2024] Open
Abstract
Calpains are cysteine proteases that control cell fate transitions whose loss of function causes severe, pleiotropic phenotypes in eukaryotes. Although mainly considered as modulatory proteases, human calpain targets are directed to the N-end rule degradation pathway. Several such targets are transcription factors, hinting at a gene-regulatory role. Here, we analyze the gene-regulatory networks of the moss Physcomitrium patens and characterize the regulons that are misregulated in mutants of the calpain DEFECTIVE KERNEL1 (DEK1). Predicted cleavage patterns of the regulatory hierarchies in five DEK1-controlled subnetworks are consistent with a pleiotropic and regulatory role during cell fate transitions targeting multiple functions. Network structure suggests DEK1-gated sequential transitions between cell fates in 2D-to-3D development. Our method combines comprehensive phenotyping, transcriptomics and data science to dissect phenotypic traits, and our model explains the protease function as a switch gatekeeping cell fate transitions potentially also beyond plant development.
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Affiliation(s)
- Viktor Demko
- Department of Plant Sciences, Norwegian University of Life Sciences, P.O. Box 5003, NO-1432, Ås, Norway
- Department of Plant Physiology, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovicova 6, 84104, Bratislava, Slovakia
- Plant Science and Biodiversity Center, Slovak Academy of Sciences, Dubravska cesta 9, 84104, Bratislava, Slovakia
| | - Tatiana Belova
- Department of Plant Sciences, Norwegian University of Life Sciences, P.O. Box 5003, NO-1432, Ås, Norway
- Centre for Molecular Medicine Norway, University of Oslo, Oslo, Norway
| | - Maxim Messerer
- Plant Genome and Systems Biology, Helmholtz Center Munich-Research Center for Environmental Health, 85764, Neuherberg, Germany
| | - Torgeir R Hvidsten
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Pierre-François Perroud
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, 78000, Versailles, France
| | - Ako Eugene Ako
- Department of Biotechnology, Inland Norway University of Applied Sciences, Holsetgata 31, 2318, Hamar, Norway
- School of Animal, Rural and Environmental Sciences, Nottingham Trent University, Brackenhurst Campus, Southwell, Nottinghamshire, NG25 0QF, UK
| | - Wenche Johansen
- Department of Biotechnology, Inland Norway University of Applied Sciences, Holsetgata 31, 2318, Hamar, Norway
| | - Klaus F X Mayer
- Plant Genome and Systems Biology, Helmholtz Center Munich-Research Center for Environmental Health, 85764, Neuherberg, Germany
- School of Life Sciences, Technical University Munich, 85354, Freising, Germany
| | - Odd-Arne Olsen
- Department of Plant Sciences, Norwegian University of Life Sciences, P.O. Box 5003, NO-1432, Ås, Norway
| | - Daniel Lang
- Plant Genome and Systems Biology, Helmholtz Center Munich-Research Center for Environmental Health, 85764, Neuherberg, Germany.
- Bundeswehr Institute of Microbiology, Microbial Genomics and Bioforensics, 80937, Munich, Germany.
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6
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Santhosh Kumar S, Naseri NN, Pather SR, Hallacli E, Ndayisaba A, Buenaventura C, Acosta K, Roof J, Fazelinia H, Spruce LA, Luk K, Khurana V, Rhoades E, Shalem O. Sequential CRISPR screening reveals partial NatB inhibition as a strategy to mitigate alpha-synuclein levels in human neurons. SCIENCE ADVANCES 2024; 10:eadj4767. [PMID: 38335281 PMCID: PMC10857481 DOI: 10.1126/sciadv.adj4767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Accepted: 01/11/2024] [Indexed: 02/12/2024]
Abstract
Alpha-synuclein (αSyn) protein levels correlate with the risk and severity of Parkinson's disease and related neurodegenerative diseases. Lowering αSyn is being actively investigated as a therapeutic modality. Here, we systematically map the regulatory network that controls endogenous αSyn using sequential CRISPR-knockout and -interference screens in an αSyn gene (SNCA)-tagged cell line and induced pluripotent stem cell-derived neurons (iNeurons). We uncover αSyn modifiers at multiple regulatory layers, with amino-terminal acetyltransferase B (NatB) enzymes being the most potent endogenous αSyn modifiers in both cell lines. Amino-terminal acetylation protects the cytosolic αSyn from rapid degradation by the proteasome in a Ube2w-dependent manner. Moreover, we show that pharmacological inhibition of methionyl-aminopeptidase 2, a regulator of NatB complex formation, attenuates endogenous αSyn in iNeurons carrying SNCA triplication. Together, our study reveals several gene networks that control endogenous αSyn, identifies mechanisms mediating the degradation of nonacetylated αSyn, and illustrates potential therapeutic pathways for decreasing αSyn levels in synucleinopathies.
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Affiliation(s)
- Saranya Santhosh Kumar
- Department of Bioengineering, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, PA, USA
- Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Nima N. Naseri
- Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA, USA
| | - Sarshan R. Pather
- Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Erinc Hallacli
- Division of Movement Disorders and Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Alain Ndayisaba
- Division of Movement Disorders and Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Chris Buenaventura
- Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Karen Acosta
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA, USA
| | - Jennifer Roof
- Proteomics Core Facility, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Hossein Fazelinia
- Proteomics Core Facility, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Biomedical and Health Informatics, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Lynn A. Spruce
- Proteomics Core Facility, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Kelvin Luk
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Vikram Khurana
- Division of Movement Disorders and Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Harvard Stem Cell Institute, Cambridge, MA, USA
| | - Elizabeth Rhoades
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA, USA
| | - Ophir Shalem
- Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
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7
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Xu S, Xu X, Wang Z, Wu R. A Systematic Investigation of Proteoforms with N-Terminal Glycine and Their Dynamics Reveals Its Impacts on Protein Stability. Angew Chem Int Ed Engl 2024; 63:e202315286. [PMID: 38117010 PMCID: PMC10981938 DOI: 10.1002/anie.202315286] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 12/18/2023] [Accepted: 12/19/2023] [Indexed: 12/21/2023]
Abstract
The N-termini of proteins can regulate their degradation, and the same protein with different N-termini may have distinct dynamics. Recently, it was found that N-terminal glycine can serve as a degron recognized by two E3 ligases, but N-terminal glycine was also reported to stabilize proteins. Here we developed a chemoenzymatic method for selective enrichment of proteoforms with N-terminal glycine and integrated dual protease cleavage to further improve the enrichment specificity. Over 2000 unique peptides with protein N-terminal glycine were analyzed from >1000 proteins, and most of them are previously unknown, indicating the effectiveness of the current method to capture low-abundance proteoforms with N-terminal glycine. The degradation rates of proteoforms with N-terminal glycine were quantified along with those of proteins from the whole proteome. Bioinformatic analyses reveal that proteoforms with N-terminal glycine with the fastest and slowest degradation rates have different functions and localizations. Membrane proteins with N-terminal glycine and proteins with N-terminal glycine from the N-terminal methionine excision degrade more rapidly. Furthermore, the secondary structures, adjacent amino acid residues, and protease specificities for N-terminal glycine are also vital for protein degradation. The results advance our understanding of the effects of N-terminal glycine on protein properties and functions.
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Affiliation(s)
- Senhan Xu
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Xing Xu
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Zeyu Wang
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Ronghu Wu
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
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8
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Smeir M, Chumala P, Katselis GS, Liu L. Lymphocyte-Specific Protein 1 Regulates Expression and Stability of Endothelial Nitric Oxide Synthase. Biomolecules 2024; 14:111. [PMID: 38254711 PMCID: PMC10813790 DOI: 10.3390/biom14010111] [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: 11/04/2023] [Revised: 12/14/2023] [Accepted: 01/06/2024] [Indexed: 01/24/2024] Open
Abstract
Nitric oxide (NO), synthesized by endothelial nitric oxide synthase (eNOS), plays a critical role in blood pressure regulation. Genome-wide association studies have identified genetic susceptibility loci for hypertension in human lymphocyte-specific protein 1 (LSP1) gene. LSP1 is recognized as modulator of leukocyte extravasation, and endothelial permeability, however, the role of LSP1 in regulation of NO signaling within endothelial cells (ECs) remains unknown. The present study investigated the role of LSP1 in the regulation of eNOS expression and activity utilizing human macrovascular ECs in vitro and LSP1 knockout (KO) mice. In ECs, specific CRISPR-Cas9 genomic editing deleted LSP1 and caused downregulation of eNOS expression. LSP1 gain-of-function through adenovirus-mediated gene transfer was associated with enhanced expression of eNOS. Co-immunoprecipitation and confocal fluorescence microscopy revealed that eNOS and LSP1 formed a protein complex under basal conditions in ECs. Furthermore, LSP1 deficiency in mice promoted significant upregulation and instability of eNOS. Utilizing a mass-spectrometry-based bottom-up proteomics approach, we identified novel truncated forms of eNOS in immunoprecipitates from LSP1 KO aortae. Our experimental data suggest an important role of endothelial LSP1 in regulation of eNOS expression and activity within human ECs and murine vascular tissues.
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Affiliation(s)
- Musstafa Smeir
- Department of Anatomy, Physiology and Pharmacology, College of Medicine, University of Saskatchewan, 107 Wiggins Road, Saskatoon, SK S7N 5E5, Canada;
| | - Paulos Chumala
- Department of Medicine, Canadian Center for Rural and Agricultural Health, University of Saskatchewan, Saskatoon, SK S7N 2Z4, Canada; (P.C.); (G.S.K.)
| | - George S. Katselis
- Department of Medicine, Canadian Center for Rural and Agricultural Health, University of Saskatchewan, Saskatoon, SK S7N 2Z4, Canada; (P.C.); (G.S.K.)
| | - Lixin Liu
- Department of Anatomy, Physiology and Pharmacology, College of Medicine, University of Saskatchewan, 107 Wiggins Road, Saskatoon, SK S7N 5E5, Canada;
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9
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Raghul Kannan S, Tamizhselvi R. N-acetyltransferase and inflammation: Bridging an unexplored niche. Gene 2023; 887:147730. [PMID: 37625560 DOI: 10.1016/j.gene.2023.147730] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 08/07/2023] [Accepted: 08/21/2023] [Indexed: 08/27/2023]
Abstract
Protein N-terminal (Nt) acetylation is an essential post-translational process catalysed by N-acetyltransferases or N-terminal acetyltransferases (NATs). Over the past several decades, several types of NATs (NatA- NatH) have been identified along with their substrates, explaining their significance in eukaryotes. It affects protein stability, protein degradation, protein translocation, and protein-protein interaction. NATs have recently drawn attention as they are associated with the pathogenesis of human diseases. In particular, NAT-induced epigenetic modifications play an important role in the control of mitochondrial function, which may lead to inflammatory diseases. NatC knockdown causes a marked reduction in mitochondrial membrane proteins, impairing their functions, and NatA affects mitophagy via reduced phosphorylation and transcription of the autophagy receptor. However, the NAT-mediated mitochondrial epigenetic mechanisms involved in the inflammatory process remain unexplored. The current review will impart an overview of the biological functions and aberrations of various NAT, which may provide a novel therapeutic strategy for inflammatory disorders.
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Affiliation(s)
- Sampath Raghul Kannan
- School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore 632014, Tamil Nadu, India
| | - Ramasamy Tamizhselvi
- School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore 632014, Tamil Nadu, India.
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10
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Zheng J, Li Y, Liu N, Zhang J, Liu S, Tan H. Multi-omics Data Reveal the Effect of Sodium Butyrate on Gene Expression and Protein Modification in Streptomyces. GENOMICS, PROTEOMICS & BIOINFORMATICS 2023; 21:1149-1162. [PMID: 36115661 PMCID: PMC11082262 DOI: 10.1016/j.gpb.2022.09.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 08/19/2022] [Accepted: 09/02/2022] [Indexed: 06/15/2023]
Abstract
Streptomycetes possess numerous gene clusters and the potential to produce a large amount of natural products. Histone deacetylase (HDAC) inhibitors play an important role in the regulation of histone modifications in fungi, but their roles in prokaryotes remain poorly understood. Here, we investigated the global effects of the HDAC inhibitor, sodium butyrate (SB), on marine-derived Streptomycesolivaceus FXJ 8.021, particularly focusing on the activation of secondary metabolite biosynthesis. The antiSMASH analysis revealed 33 secondary metabolite biosynthetic gene clusters (BGCs) in strain FXJ 8.021, among which the silent lobophorin BGC was activated by SB. Transcriptomic data showed that the expression of genes involved in lobophorin biosynthesis (ge00097-ge00139) and CoA-ester formation (e.g., ge02824), as well as the glycolysis/gluconeogenesis pathway (e.g., ge01661), was significantly up-regulated in the presence of SB. Intracellular CoA-ester analysis confirmed that SB triggered the biosynthesis of CoA-ester, thereby increasing the precursor supply for lobophorin biosynthesis. Further acetylomic analysis revealed that the acetylation levels on 218 sites of 190 proteins were up-regulated and those on 411 sites of 310 proteins were down-regulated. These acetylated proteins were particularly enriched in transcriptional and translational machinery components (e.g., elongation factor GE04399), and their correlations with the proteins involved in lobophorin biosynthesis were established by protein-protein interaction network analysis, suggesting that SB might function via a complex hierarchical regulation to activate the expression of lobophorin BGC. These findings provide solid evidence that acetylated proteins triggered by SB could affect the expression of genes involved in the biosynthesis of primary and secondary metabolites in prokaryotes.
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Affiliation(s)
- Jiazhen Zheng
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yue Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Ning Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jihui Zhang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Shuangjiang Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; State Key Laboratory of Microbial Biotechnology, Shandong University, Qingdao 266237, China.
| | - Huarong Tan
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China.
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11
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Yang J, Lee Y, Hwang CS. The ubiquitin-proteasome system links NADPH metabolism to ferroptosis. Trends Cell Biol 2023; 33:1088-1103. [PMID: 37558595 DOI: 10.1016/j.tcb.2023.07.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 07/07/2023] [Accepted: 07/11/2023] [Indexed: 08/11/2023]
Abstract
Ferroptosis is the type of cell death arising from uncontrolled and excessive lipid peroxidation. NADPH is essential for ferroptosis regulation because it supplies reducing equivalents for antioxidant defense systems and contributes to the generation of reactive oxygen species. Moreover, NADPH level serves as a biomarker for predicting the sensitivity of cells to ferroptosis. The ubiquitin-proteasome system governs the stability of many ferroptosis effectors. Recent research has revealed MARCHF6, the endoplasmic reticulum ubiquitin ligase, as an unprecedented NADPH sensor in the ubiquitin system and a critical regulator of ferroptosis involved in tumorigenesis and fetal development. This review summarizes the current understanding of NADPH metabolism and the ubiquitin-proteasome system in regulating ferroptosis and highlights the emerging importance of MARCHF6 as a vital connector between NADPH metabolism and ferroptosis.
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Affiliation(s)
- Jihye Yang
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Yoontae Lee
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Cheol-Sang Hwang
- Department of Life Sciences, Korea University, Seoul, Republic of Korea.
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12
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Ho KH, Pan KF, Cheng TY, Chien MH, Hua KT. Multiple impacts of Naa10p on cancer progression: Molecular functions and clinical prospects. Biochim Biophys Acta Rev Cancer 2023; 1878:188973. [PMID: 37659460 DOI: 10.1016/j.bbcan.2023.188973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 08/27/2023] [Accepted: 08/28/2023] [Indexed: 09/04/2023]
Abstract
Nα-acetyltransferase 10 protein (Naa10p) is known as the catalytic subunit of N-terminal acetyltransferases A (NatA) complex, associating with Naa15p to acetylate N-termini of the human proteome. Recent investigations have unveiled additional functions for Naa10p, encompassing lysine ε-acetylation and acetyltransferase-independent activities. Its pleiotropic roles have been implicated in diverse physiological and pathological contexts. Emerging evidence has implicated Naa10p in cancer progression, demonstrating dual attributes as an oncogene or a tumor suppressor contingent on the cancer type and acetyltransferase activity context. In this comprehensive review, we present a pan-cancer analysis aimed at elucidating the intricacies underlying Naa10p dysregulation in cancer. Our findings propose the potential involvement of c-Myc as a modulatory factor influencing Naa10p expression. Moreover, we provide a consolidated summary of recent advancements in understanding the intricate molecular underpinnings through which Naa10p contributes to cancer cell proliferation and metastasis. Furthermore, we delve into the multifaceted nature of Naa10p's roles in regulating cancer behaviors, potentially attributed to its interactions with a repertoire of partner proteins. Through an exhaustive exploration of Naa10p's functions, spanning its acetylation activity and acetyltransferase-independent functionalities, this review offers novel insights with implications for targeted therapeutic strategies involving this pivotal protein in the realm of cancer therapeutics.
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Affiliation(s)
- Kuo-Hao Ho
- Graduate Institute of Clinical Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan.
| | - Ke-Fan Pan
- Department of Medical Education and Research, Wan Fang Hospital, Taipei Medical University, Taipei, Taiwan; Division of General Surgery, Department of Surgery, Wan Fang Hospital, Taipei Medical University, Taipei, Taiwan; Division of Colorectal Surgery, Department of Surgery, Wan Fang Hospital, Taipei Medical University, Taipei, Taiwan; Graduate Institute of Toxicology, College of Medicine, National Taiwan University, Taipei, Taiwan.
| | - Tsu-Yao Cheng
- Department of Laboratory Medicine, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei, Taiwan; Division of Gastroenterology, Department of Internal Medicine, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei, Taiwan.
| | - Ming-Hsien Chien
- Graduate Institute of Clinical Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan; TMU Research Center of Cancer Translational Medicine, Taipei Medical University, Taipei, Taiwan; Pulmonary Research Center, Wan Fang Hospital, Taipei Medical University, Taipei, Taiwan; Traditional Herbal Medicine Research Center, Taipei Medical University Hospital, Taipei, Taiwan.
| | - Kuo-Tai Hua
- Graduate Institute of Toxicology, College of Medicine, National Taiwan University, Taipei, Taiwan; Department of Medical Research, China Medical University Hospital, China Medical University, Taichung, Taiwan.
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13
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François CM, Pihl T, Dunoyer de Segonzac M, Hérault C, Hudry B. Metabolic regulation of proteome stability via N-terminal acetylation controls male germline stem cell differentiation and reproduction. Nat Commun 2023; 14:6737. [PMID: 37872135 PMCID: PMC10593830 DOI: 10.1038/s41467-023-42496-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 10/12/2023] [Indexed: 10/25/2023] Open
Abstract
The molecular mechanisms connecting cellular metabolism with differentiation remain poorly understood. Here, we find that metabolic signals contribute to stem cell differentiation and germline homeostasis during Drosophila melanogaster spermatogenesis. We discovered that external citrate, originating outside the gonad, fuels the production of Acetyl-coenzyme A by germline ATP-citrate lyase (dACLY). We show that this pathway is essential during the final spermatogenic stages, where a high Acetyl-coenzyme A level promotes NatB-dependent N-terminal protein acetylation. Using genetic and biochemical experiments, we establish that N-terminal acetylation shields key target proteins, essential for spermatid differentiation, from proteasomal degradation by the ubiquitin ligase dUBR1. Our work uncovers crosstalk between metabolism and proteome stability that is mediated via protein post-translational modification. We propose that this system coordinates the metabolic state of the organism with gamete production. More broadly, modulation of proteome turnover by circulating metabolites may be a conserved regulatory mechanism to control cell functions.
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Affiliation(s)
- Charlotte M François
- Université Côte d'Azur, CNRS, Inserm, Institut de Biologie Valrose, Nice, 06108, France
| | - Thomas Pihl
- Université Côte d'Azur, CNRS, Inserm, Institut de Biologie Valrose, Nice, 06108, France
| | | | - Chloé Hérault
- Université Côte d'Azur, CNRS, Inserm, Institut de Biologie Valrose, Nice, 06108, France
| | - Bruno Hudry
- Université Côte d'Azur, CNRS, Inserm, Institut de Biologie Valrose, Nice, 06108, France.
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14
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Sakato-Antoku M, Balsbaugh JL, King SM. N-Terminal Processing and Modification of Ciliary Dyneins. Cells 2023; 12:2492. [PMID: 37887336 PMCID: PMC10605206 DOI: 10.3390/cells12202492] [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: 09/15/2023] [Revised: 10/17/2023] [Accepted: 10/19/2023] [Indexed: 10/28/2023] Open
Abstract
Axonemal dyneins are highly complex microtubule motors that power ciliary motility. These multi-subunit enzymes are assembled at dedicated sites within the cytoplasm. At least nineteen cytosolic factors are specifically needed to generate dynein holoenzymes and/or for their trafficking to the growing cilium. Many proteins are subject to N-terminal processing and acetylation, which can generate degrons subject to the AcN-end rule, alter N-terminal electrostatics, generate new binding interfaces, and affect subunit stoichiometry through targeted degradation. Here, we have used mass spectrometry of cilia samples and electrophoretically purified dynein heavy chains from Chlamydomonas to define their N-terminal processing; we also detail the N-terminal acetylase complexes present in this organism. We identify four classes of dynein heavy chain based on their processing pathways by two distinct acetylases, one of which is dependent on methionine aminopeptidase activity. In addition, we find that one component of both the outer dynein arm intermediate/light chain subcomplex and the docking complex is processed to yield an unmodified Pro residue, which may provide a setpoint to direct the cytosolic stoichiometry of other dynein complex subunits that contain N-terminal degrons. Thus, we identify and describe an additional level of processing and complexity in the pathways leading to axonemal dynein formation in cytoplasm.
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Affiliation(s)
- Miho Sakato-Antoku
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, 263 Farmington Avenue, Farmington, CT 06030-3305, USA;
| | - Jeremy L. Balsbaugh
- Proteomics and Metabolomics Facility, University of Connecticut, 75 North Eagleville Road, Storrs, CT 06269, USA;
| | - Stephen M. King
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, 263 Farmington Avenue, Farmington, CT 06030-3305, USA;
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15
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Fassad MR, Rumman N, Junger K, Patel MP, Thompson J, Goggin P, Ueffing M, Beyer T, Boldt K, Lucas JS, Mitchison HM. Defective airway intraflagellar transport underlies a combined motile and primary ciliopathy syndrome caused by IFT74 mutations. Hum Mol Genet 2023; 32:3090-3104. [PMID: 37555648 PMCID: PMC10586200 DOI: 10.1093/hmg/ddad132] [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: 06/23/2023] [Revised: 08/01/2023] [Indexed: 08/10/2023] Open
Abstract
Ciliopathies are inherited disorders caused by defective cilia. Mutations affecting motile cilia usually cause the chronic muco-obstructive sinopulmonary disease primary ciliary dyskinesia (PCD) and are associated with laterality defects, while a broad spectrum of early developmental as well as degenerative syndromes arise from mutations affecting signalling of primary (non-motile) cilia. Cilia assembly and functioning requires intraflagellar transport (IFT) of cargos assisted by IFT-B and IFT-A adaptor complexes. Within IFT-B, the N-termini of partner proteins IFT74 and IFT81 govern tubulin transport to build the ciliary microtubular cytoskeleton. We detected a homozygous 3-kb intragenic IFT74 deletion removing the exon 2 initiation codon and 40 N-terminal amino acids in two affected siblings. Both had clinical features of PCD with bronchiectasis, but no laterality defects. They also had retinal dysplasia and abnormal bone growth, with a narrowed thorax and short ribs, shortened long bones and digits, and abnormal skull shape. This resembles short-rib thoracic dysplasia, a skeletal ciliopathy previously linked to IFT defects in primary cilia, not motile cilia. Ciliated nasal epithelial cells collected from affected individuals had reduced numbers of shortened motile cilia with disarranged microtubules, some misorientation of the basal feet, and disrupted cilia structural and IFT protein distributions. No full-length IFT74 was expressed, only truncated forms that were consistent with N-terminal deletion and inframe translation from downstream initiation codons. In affinity purification mass spectrometry, exon 2-deleted IFT74 initiated from the nearest inframe downstream methionine 41 still interacts as part of the IFT-B complex, but only with reduced interaction levels and not with all its usual IFT-B partners. We propose that this is a hypomorphic mutation with some residual protein function retained, which gives rise to a primary skeletal ciliopathy combined with defective motile cilia and PCD.
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Affiliation(s)
- Mahmoud R Fassad
- Genetics and Genomic Medicine Research and Teaching Department, University College London, UCL Great Ormond Street Institute of Child Health, 30 Guilford Street, London WC1N 1EH, United Kingdom
- Department of Human Genetics, Medical Research Institute, Alexandria University, 22 El-Guish Road, El-Shatby, Alexandria 21526, Egypt
| | - Nisreen Rumman
- Department of Pediatrics, Faculty of Medicine, Makassed Hospital and Al-Quds University, East Jerusalem 91220, Palestine
- Section of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, Yale University School of Medicine, 300 Cedar St #441, New Haven, CT 06520, United States
| | - Katrin Junger
- Institute for Ophthalmic Research, Eberhard Karl University of Tübingen, Elfreide-Alhorn-Strasse 5-7, Tübingen 72076, Germany
| | - Mitali P Patel
- Genetics and Genomic Medicine Research and Teaching Department, University College London, UCL Great Ormond Street Institute of Child Health, 30 Guilford Street, London WC1N 1EH, United Kingdom
- MRC Prion Unit at UCL, Institute of Prion Diseases, University College London, 33 Cleveland Street, London W1W 7FF, United Kingdom
| | - James Thompson
- Primary Ciliary Dyskinesia Centre, NIHR Biomedical Research Centre, University Hospital Southampton NHS Foundation Trust, Southampton SO16 6YD, United Kingdom
- School of Clinical and Experimental Sciences, University of Southampton Faculty of Medicine, University Road, Southampton SO17 1BJ, United Kingdom
- Biomedical Imaging Unit, University of Southampton Faculty of Medicine, University Road, Southampton SO17 1BJ, United Kingdom
| | - Patricia Goggin
- Primary Ciliary Dyskinesia Centre, NIHR Biomedical Research Centre, University Hospital Southampton NHS Foundation Trust, Southampton SO16 6YD, United Kingdom
- Biomedical Imaging Unit, University of Southampton Faculty of Medicine, University Road, Southampton SO17 1BJ, United Kingdom
| | - Marius Ueffing
- Institute for Ophthalmic Research, Eberhard Karl University of Tübingen, Elfreide-Alhorn-Strasse 5-7, Tübingen 72076, Germany
| | - Tina Beyer
- Institute for Ophthalmic Research, Eberhard Karl University of Tübingen, Elfreide-Alhorn-Strasse 5-7, Tübingen 72076, Germany
| | - Karsten Boldt
- Institute for Ophthalmic Research, Eberhard Karl University of Tübingen, Elfreide-Alhorn-Strasse 5-7, Tübingen 72076, Germany
| | - Jane S Lucas
- Primary Ciliary Dyskinesia Centre, NIHR Biomedical Research Centre, University Hospital Southampton NHS Foundation Trust, Southampton SO16 6YD, United Kingdom
- School of Clinical and Experimental Sciences, University of Southampton Faculty of Medicine, University Road, Southampton SO17 1BJ, United Kingdom
| | - Hannah M Mitchison
- Genetics and Genomic Medicine Research and Teaching Department, University College London, UCL Great Ormond Street Institute of Child Health, 30 Guilford Street, London WC1N 1EH, United Kingdom
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16
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Nashed S, El Barbry H, Benchouaia M, Dijoux-Maréchal A, Delaveau T, Ruiz-Gutierrez N, Gaulier L, Tribouillard-Tanvier D, Chevreux G, Le Crom S, Palancade B, Devaux F, Laine E, Garcia M. Functional mapping of N-terminal residues in the yeast proteome uncovers novel determinants for mitochondrial protein import. PLoS Genet 2023; 19:e1010848. [PMID: 37585488 PMCID: PMC10482271 DOI: 10.1371/journal.pgen.1010848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 09/06/2023] [Accepted: 06/29/2023] [Indexed: 08/18/2023] Open
Abstract
N-terminal ends of polypeptides are critical for the selective co-translational recruitment of N-terminal modification enzymes. However, it is unknown whether specific N-terminal signatures differentially regulate protein fate according to their cellular functions. In this work, we developed an in-silico approach to detect functional preferences in cellular N-terminomes, and identified in S. cerevisiae more than 200 Gene Ontology terms with specific N-terminal signatures. In particular, we discovered that Mitochondrial Targeting Sequences (MTS) show a strong and specific over-representation at position 2 of hydrophobic residues known to define potential substrates of the N-terminal acetyltransferase NatC. We validated mitochondrial precursors as co-translational targets of NatC by selective purification of translating ribosomes, and found that their N-terminal signature is conserved in Saccharomycotina yeasts. Finally, systematic mutagenesis of the position 2 in a prototypal yeast mitochondrial protein confirmed its critical role in mitochondrial protein import. Our work highlights the hydrophobicity of MTS N-terminal residues and their targeting by NatC as important features for the definition of the mitochondrial proteome, providing a molecular explanation for mitochondrial defects observed in yeast or human NatC-depleted cells. Functional mapping of N-terminal residues thus has the potential to support the discovery of novel mechanisms of protein regulation or targeting.
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Affiliation(s)
- Salomé Nashed
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, UMR 7238, Laboratoire de Biologie Computationnelle et Quantitative, Paris, France
| | - Houssam El Barbry
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, UMR 7238, Laboratoire de Biologie Computationnelle et Quantitative, Paris, France
| | - Médine Benchouaia
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, UMR 7238, Laboratoire de Biologie Computationnelle et Quantitative, Paris, France
| | - Angélie Dijoux-Maréchal
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, UMR 7238, Laboratoire de Biologie Computationnelle et Quantitative, Paris, France
| | - Thierry Delaveau
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, UMR 7238, Laboratoire de Biologie Computationnelle et Quantitative, Paris, France
| | - Nadia Ruiz-Gutierrez
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, UMR 7238, Laboratoire de Biologie Computationnelle et Quantitative, Paris, France
| | - Lucie Gaulier
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, UMR 7238, Laboratoire de Biologie Computationnelle et Quantitative, Paris, France
| | | | | | - Stéphane Le Crom
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, UMR 7238, Laboratoire de Biologie Computationnelle et Quantitative, Paris, France
| | | | - Frédéric Devaux
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, UMR 7238, Laboratoire de Biologie Computationnelle et Quantitative, Paris, France
| | - Elodie Laine
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, UMR 7238, Laboratoire de Biologie Computationnelle et Quantitative, Paris, France
| | - Mathilde Garcia
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, UMR 7238, Laboratoire de Biologie Computationnelle et Quantitative, Paris, France
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17
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Mun SH, Lee CS, Kim HJ, Kim J, Lee H, Yang J, Im SH, Kim JH, Seong JK, Hwang CS. Marchf6 E3 ubiquitin ligase critically regulates endoplasmic reticulum stress, ferroptosis, and metabolic homeostasis in POMC neurons. Cell Rep 2023; 42:112746. [PMID: 37421621 DOI: 10.1016/j.celrep.2023.112746] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 05/18/2023] [Accepted: 06/19/2023] [Indexed: 07/10/2023] Open
Abstract
The metabolic prohormone pro-opiomelanocortin (POMC) is generally translocated into the endoplasmic reticulum (ER) for entry into the secretory pathway. Patients with mutations within the signal peptide (SP) of POMC or its adjoining segment develop metabolic disorders. However, the existence, metabolic fate, and functional outcomes of cytosol-retained POMC remain unclear. Here, we show that SP-uncleaved POMC is produced in the cytosol of POMC neuronal cells, thus inducing ER stress and ferroptotic cell death. Mechanistically, the cytosol-retained POMC sequesters the chaperone Hspa5 and subsequently accelerates degradation of the glutathione peroxidase Gpx4, a core regulator of ferroptosis, via the chaperone-mediated autophagy. We also show that the Marchf6 E3 ubiquitin ligase mediates the degradation of cytosol-retained POMC, thereby preventing ER stress and ferroptosis. Furthermore, POMC-Cre-mediated Marchf6-deficient mice exhibit hyperphagia, reduced energy expenditure, and weight gain. These findings suggest that Marchf6 is a critical regulator of ER stress, ferroptosis, and metabolic homeostasis in POMC neurons.
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Affiliation(s)
- Sang-Hyeon Mun
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, South Korea
| | - Chang-Seok Lee
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, South Korea
| | - Hyun Jin Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, South Korea
| | - Jiye Kim
- Korea Mouse Phenotyping Center, Seoul National University, Seoul 08826, South Korea; Laboratory of Developmental Biology and Genomics, Research Institute for Veterinary Science, and BK21 PLUS Program for Creative Veterinary Science Research, College of Veterinary Medicine, Seoul National University, Seoul 08826, South Korea; Interdisciplinary Program for Bioinformatics, Program for Cancer Biology and BIO-MAX/N-Bio Institute, Seoul National University, Seoul 08826, South Korea
| | - Haena Lee
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, South Korea
| | - Jihye Yang
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, South Korea
| | - Sin-Hyeog Im
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, South Korea; Institute of Convergence Science, Yonsei University, Seoul 03722, South Korea; ImmunoBiome, Inc, Pohang 37666, Republic of Korea
| | - Joung-Hun Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, South Korea; Institute of Convergence Science, Yonsei University, Seoul 03722, South Korea
| | - Je Kyung Seong
- Korea Mouse Phenotyping Center, Seoul National University, Seoul 08826, South Korea; Laboratory of Developmental Biology and Genomics, Research Institute for Veterinary Science, and BK21 PLUS Program for Creative Veterinary Science Research, College of Veterinary Medicine, Seoul National University, Seoul 08826, South Korea; Interdisciplinary Program for Bioinformatics, Program for Cancer Biology and BIO-MAX/N-Bio Institute, Seoul National University, Seoul 08826, South Korea
| | - Cheol-Sang Hwang
- Department of Life Sciences, Korea University, Seoul 02841, South Korea.
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18
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Heo AJ, Kim SB, Kwon YT, Ji CH. The N-degron pathway: From basic science to therapeutic applications. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2023; 1866:194934. [PMID: 36990317 DOI: 10.1016/j.bbagrm.2023.194934] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 03/22/2023] [Accepted: 03/22/2023] [Indexed: 03/30/2023]
Abstract
The N-degron pathway is a degradative system in which single N-terminal (Nt) amino acids regulate the half-lives of proteins and other biological materials. These determinants, called N-degrons, are recognized by N-recognins that link them to the ubiquitin (Ub)-proteasome system (UPS) or autophagy-lysosome system (ALS). In the UPS, the Arg/N-degron pathway targets the Nt-arginine (Nt-Arg) and other N-degrons to assemble Lys48 (K48)-linked Ub chains by UBR box N-recognins for proteasomal proteolysis. In the ALS, Arg/N-degrons are recognized by the N-recognin p62/SQSTSM-1/Sequestosome-1 to induce cis-degradation of substrates and trans-degradation of various cargoes such as protein aggregates and subcellular organelles. This crosstalk between the UPS and ALP involves reprogramming of the Ub code. Eukaryotic cells developed diverse ways to target all 20 principal amino acids for degradation. Here we discuss the components, regulation, and functions of the N-degron pathways, with an emphasis on the basic mechanisms and therapeutic applications of Arg/N-degrons and N-recognins.
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Affiliation(s)
- Ah Jung Heo
- Cellular Degradation Biology Center and Department of Biomedical Sciences, College of Medicine, Seoul National University, Seoul 03080, Republic of Korea
| | - Su Bin Kim
- Cellular Degradation Biology Center and Department of Biomedical Sciences, College of Medicine, Seoul National University, Seoul 03080, Republic of Korea
| | - Yong Tae Kwon
- Cellular Degradation Biology Center and Department of Biomedical Sciences, College of Medicine, Seoul National University, Seoul 03080, Republic of Korea; AUTOTAC Bio Inc., Changkyunggung-ro 254, Jongno-gu, Seoul 03077, Republic of Korea; Ischemic/Hypoxic Disease Institute, College of Medicine, Seoul National University, Seoul 110-799, Republic of Korea; SNU Dementia Research Center, College of Medicine, Seoul National University, Seoul 110-799, Republic of Korea.
| | - Chang Hoon Ji
- Cellular Degradation Biology Center and Department of Biomedical Sciences, College of Medicine, Seoul National University, Seoul 03080, Republic of Korea; AUTOTAC Bio Inc., Changkyunggung-ro 254, Jongno-gu, Seoul 03077, Republic of Korea.
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19
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Elurbide J, Carte B, Guedes J, Aldabe R. NatB Catalytic Subunit Depletion Disrupts DNA Replication Initiation Leading to Senescence in MEFs. Int J Mol Sci 2023; 24:ijms24108724. [PMID: 37240070 DOI: 10.3390/ijms24108724] [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: 04/18/2023] [Revised: 05/09/2023] [Accepted: 05/10/2023] [Indexed: 05/28/2023] Open
Abstract
Alpha-aminoterminal acetyltransferase B (NatB) is a critical enzyme responsible for acetylating the aminoterminal end of proteins, thereby modifying approximately 21% of the proteome. This post-translational modification impacts protein folding, structure, stability, and interactions between proteins which, in turn, play a crucial role in modulating several biological functions. NatB has been widely studied for its role in cytoskeleton function and cell cycle regulation in different organisms, from yeast to human tumor cells. In this study, we aimed to understand the biological importance of this modification by inactivating the catalytic subunit of the NatB enzymatic complex, Naa20, in non-transformed mammal cells. Our findings demonstrate that depletion of NAA20 results in decreased cell cycle progression and DNA replication initiation, ultimately leading to the senescence program. Furthermore, we have identified NatB substrates that play a role in cell cycle progression, and their stability is compromised when NatB is inactivated. These results underscore the significance of N-terminal acetylation by NatB in regulating cell cycle progression and DNA replication.
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Affiliation(s)
- Jasmin Elurbide
- Division of Gene Therapy and Regulation of Gene Expression, Centre for Applied Medical Research CIMA, University of Navarra, 31008 Pamplona, Spain
| | - Beatriz Carte
- Division of Gene Therapy and Regulation of Gene Expression, Centre for Applied Medical Research CIMA, University of Navarra, 31008 Pamplona, Spain
| | - Joana Guedes
- Division of Gene Therapy and Regulation of Gene Expression, Centre for Applied Medical Research CIMA, University of Navarra, 31008 Pamplona, Spain
- Department of Biology, Centre of Molecular and Environmental Biology (CBMA/UM), University of Minho, 4710-057 Braga, Portugal
| | - Rafael Aldabe
- Division of Gene Therapy and Regulation of Gene Expression, Centre for Applied Medical Research CIMA, University of Navarra, 31008 Pamplona, Spain
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20
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Azari M, Bahreini F, Uversky VN, Rezaei N. Current therapeutic approaches and promising perspectives of using bioengineered peptides in fighting chemoresistance in triple-negative breast cancer. Biochem Pharmacol 2023; 210:115459. [PMID: 36813121 DOI: 10.1016/j.bcp.2023.115459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 02/11/2023] [Accepted: 02/14/2023] [Indexed: 02/22/2023]
Abstract
Breast cancer is a collation of malignancies that manifest in the mammary glands at the early stages. Among breast cancer subtypes, triple-negative breast cancer (TNBC) shows the most aggressive behavior, with apparent stemness features. Owing to the lack of response to hormone therapy and specific targeted therapies, chemotherapy remains the first line of the TNBC treatment. However, the acquisition of resistance to chemotherapeutic agents increase therapy failure, and promotes cancer recurrence and distant metastasis. Invasive primary tumors are the birthplace of cancer burden, though metastasis is a key attribute of TNBC-associated morbidity and mortality. Targeting the chemoresistant metastases-initiating cells via specific therapeutic agents with affinity to the upregulated molecular targets is a promising step in the TNBC clinical management. Exploring the capacity of peptides as biocompatible entities with the specificity of action, low immunogenicity, and robust efficacy provides a principle for designing peptide-based drugs capable of increasing the efficacy of current chemotherapy agents for selective targeting of the drug-tolerant TNBC cells. Here, we first focus on the resistance mechanisms that TNBC cells acquire to evade the effect of chemotherapeutic agents. Next, the novel therapeutic approaches employing tumor-targeting peptides to exploit the mechanisms of drug resistance in chemorefractory TNBC are described.
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Affiliation(s)
- Mandana Azari
- School of Chemical Engineering-Biotechnology, College of Engineering, University of Tehran, Iran; Network of Immunity in Infection, Malignancy and Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), Tehran, Iran
| | - Farbod Bahreini
- Network of Immunity in Infection, Malignancy and Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), Tehran, Iran; Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, USA
| | - Nima Rezaei
- Network of Immunity in Infection, Malignancy and Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), Tehran, Iran; Research Center for Immunodeficiencies (RCID), Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran; Department of Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran.
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21
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Rong Y, Jensen SI, Lindorff-Larsen K, Nielsen AT. Folding of heterologous proteins in bacterial cell factories: Cellular mechanisms and engineering strategies. Biotechnol Adv 2023; 63:108079. [PMID: 36528238 DOI: 10.1016/j.biotechadv.2022.108079] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Revised: 11/20/2022] [Accepted: 12/09/2022] [Indexed: 12/23/2022]
Abstract
The expression of correctly folded and functional heterologous proteins is important in many biotechnological production processes, whether it is enzymes, biopharmaceuticals or biosynthetic pathways for production of sustainable chemicals. For industrial applications, bacterial platform organisms, such as E. coli, are still broadly used due to the availability of tools and proven suitability at industrial scale. However, expression of heterologous proteins in these organisms can result in protein aggregation and low amounts of functional protein. This review provides an overview of the cellular mechanisms that can influence protein folding and expression, such as co-translational folding and assembly, chaperone binding, as well as protein quality control, across different model organisms. The knowledge of these mechanisms is then linked to different experimental methods that have been applied in order to improve functional heterologous protein folding, such as codon optimization, fusion tagging, chaperone co-production, as well as strain and protein engineering strategies.
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Affiliation(s)
- Yixin Rong
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, 2800 Kgs. Lyngby, Denmark
| | - Sheila Ingemann Jensen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, 2800 Kgs. Lyngby, Denmark
| | - Kresten Lindorff-Larsen
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, 2200 Copenhagen N, Denmark
| | - Alex Toftgaard Nielsen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, 2800 Kgs. Lyngby, Denmark.
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22
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Heo AJ, Ji CH, Kwon YT. The Cys/N-degron pathway in the ubiquitin-proteasome system and autophagy. Trends Cell Biol 2023; 33:247-259. [PMID: 35945077 DOI: 10.1016/j.tcb.2022.07.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 07/12/2022] [Accepted: 07/13/2022] [Indexed: 10/15/2022]
Abstract
The N-degron pathway is a degradative system in which the N-terminal residues of proteins modulate the half-lives of proteins and other cellular materials. The majority of amino acids in the genetic code have the potential to induce cis or trans degradation in diverse processes, which requires selective recognition between N-degrons and cognate N-recognins. Of particular interest is the Cys/N-degron branch, in which the N-terminal cysteine (Nt-Cys) induces proteolysis via either the ubiquitin (Ub)-proteasome system (UPS) or the autophagy-lysosome pathway (ALP), depending on physiological conditions. Recent studies provided new insights into the central role of Nt-Cys in sensing the fluctuating levels of oxygen and reactive oxygen species (ROS). Here, we discuss the components, regulations, and functions of the Cys/N-degron pathway.
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Affiliation(s)
- Ah Jung Heo
- Cellular Degradation Biology Center and Department of Biomedical Sciences, College of Medicine, Seoul National University, Seoul 03080, Korea
| | - Chang Hoon Ji
- Cellular Degradation Biology Center and Department of Biomedical Sciences, College of Medicine, Seoul National University, Seoul 03080, Korea; AUTOTAC Bio Inc., Changkyunggung-ro 254, Jongno-gu, Seoul 03077, Korea
| | - Yong Tae Kwon
- Cellular Degradation Biology Center and Department of Biomedical Sciences, College of Medicine, Seoul National University, Seoul 03080, Korea; AUTOTAC Bio Inc., Changkyunggung-ro 254, Jongno-gu, Seoul 03077, Korea; Ischemic/Hypoxic Disease Institute, College of Medicine, Seoul National University, Seoul 110-799, Korea.
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23
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Seo DY, Kim D, Nguyen KT, Oh J, Lee JS, Hwang CS. N-Terminally arginylated ubiquitin is attached to histone H2A by RING1B E3 ligase in human cells. Biochem Biophys Res Commun 2023; 666:186-194. [PMID: 36932026 DOI: 10.1016/j.bbrc.2023.02.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 02/09/2023] [Indexed: 02/11/2023]
Abstract
Ubiquitin (Ub) is highly conserved in all eukaryotic organisms and begins at the N-terminus with Met and Gln. Our recent research demonstrates that N-terminally (Nt-) arginylated Ub can be produced in the yeast Saccharomyces cerevisiae. However, the existence of Nt-arginylated Ub in multicellular organisms remains unknown. Here we explore the mechanism for creating Nt-arginylated Ub using human embryonic kidney HEK293 cells that express various Nt-modified Ubs. We found that Gln-starting Q-Ub was converted into Glu-starting E-Ub by NTAQ1 Nt-deamidase and subsequently Nt-arginylated by ATE1 arginyltransferase in HEK293 cells. We also found that the resulting Arg-Glu-starting RE-Ub was mainly deposited on the Lys119 residue of histone H2A. Furthermore, RING1B E3 Ub ligase mediated the attachment of RE-Ub to H2A. These findings reveal a previously unknown type of histone ubiquitylation which greatly increases the combinatorial complexity of histone and ubiquitin codes.
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Affiliation(s)
- Dong-Young Seo
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk, 37673, Republic of Korea
| | - Dasom Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk, 37673, Republic of Korea
| | - Kha The Nguyen
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk, 37673, Republic of Korea
| | - Junsoo Oh
- Department of Molecular Bioscience, College of Biomedical Science, Kangwon National University, Chuncheon, Kangwon, 24341, Republic of Korea
| | - Jung-Shin Lee
- Department of Molecular Bioscience, College of Biomedical Science, Kangwon National University, Chuncheon, Kangwon, 24341, Republic of Korea
| | - Cheol-Sang Hwang
- Department of Life Sciences, Korea University, Seoul, 02841, Republic of Korea.
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Significance of NatB-mediated N-terminal acetylation of auxin biosynthetic enzymes in maintaining auxin homeostasis in Arabidopsis thaliana. Commun Biol 2022; 5:1410. [PMID: 36550195 PMCID: PMC9780221 DOI: 10.1038/s42003-022-04313-9] [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: 11/29/2019] [Accepted: 11/29/2022] [Indexed: 12/24/2022] Open
Abstract
The auxin IAA (Indole-3-acetic acid) plays key roles in regulating plant growth and development, which depends on an intricate homeostasis that is determined by the balance between its biosynthesis, metabolism and transport. YUC flavin monooxygenases catalyze the rate-limiting step of auxin biosynthesis via IPyA (indole pyruvic acid) and are critical targets in regulating auxin homeostasis. Despite of numerous reports on the transcriptional regulation of YUC genes, little is known about those at the post-translational protein level. Here, we show that loss of function of CKRC3/TCU2, the auxiliary subunit (Naa25) of Arabidopsis NatB, and/or of its catalytic subunit (Naa20), NBC, led to auxin-deficiency in plants. Experimental evidences show that CKRC3/TCU2 can interact with NBC to form a NatB complex, catalyzing the N-terminal acetylation (NTA) of YUC proteins for their intracellular stability to maintain normal auxin homeostasis in plants. Hence, our findings provide significantly new insight into the link between protein NTA and auxin biosynthesis in plants.
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Li Y, Zhao Y, Yan X, Ye C, Weirich S, Zhang B, Wang X, Song L, Jiang C, Jeltsch A, Dong C, Mi W. CRL2 ZER1/ZYG11B recognizes small N-terminal residues for degradation. Nat Commun 2022; 13:7636. [PMID: 36496439 PMCID: PMC9741652 DOI: 10.1038/s41467-022-35169-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 11/17/2022] [Indexed: 12/13/2022] Open
Abstract
N-degron pathway plays an important role in the protein quality control and maintenance of cellular protein homeostasis. ZER1 and ZYG11B, the substrate receptors of the Cullin 2-RING E3 ubiquitin ligase (CRL2), recognize N-terminal (Nt) glycine degrons and participate in the Nt-myristoylation quality control through the Gly/N-degron pathway. Here we show that ZER1 and ZYG11B can also recognize small Nt-residues other than glycine. Specifically, ZER1 binds better to Nt-Ser, -Ala, -Thr and -Cys than to -Gly, while ZYG11B prefers Nt-Gly but also has the capacity to recognize Nt-Ser, -Ala and -Cys in vitro. We found that Nt-Ser, -Ala and -Cys undergo Nt-acetylation catalyzed by Nt-acetyltransferase (NAT), thereby shielding them from recognition by ZER1/ZYG11B in cells. Instead, ZER1/ZYG11B readily targets a selection of small Nt-residues lacking Nt-acetylation for degradation in NAT-deficient cells, implicating its role in the Nt-acetylation quality control. Furthermore, we present the crystal structures of ZER1 and ZYG11B bound to various small Nt-residues and uncover the molecular mechanism of non-acetylated substrate recognition by ZER1 and ZYG11B.
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Affiliation(s)
- Yao Li
- grid.265021.20000 0000 9792 1228The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Medical University General Hospital, The Second Hospital of Tianjin Medical University, Department of Biochemistry and Molecular Biology, Tianjin Medical University, Tianjin, 300070 China
| | - Yueling Zhao
- grid.265021.20000 0000 9792 1228The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Medical University General Hospital, Department of Immunology, Tianjin Medical University, Tianjin, 300070 China
| | - Xiaojie Yan
- grid.265021.20000 0000 9792 1228The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Medical University General Hospital, The Second Hospital of Tianjin Medical University, Department of Biochemistry and Molecular Biology, Tianjin Medical University, Tianjin, 300070 China
| | - Chen Ye
- grid.265021.20000 0000 9792 1228The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Medical University General Hospital, Department of Immunology, Tianjin Medical University, Tianjin, 300070 China
| | - Sara Weirich
- grid.5719.a0000 0004 1936 9713Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| | - Bing Zhang
- grid.265021.20000 0000 9792 1228The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Medical University General Hospital, The Second Hospital of Tianjin Medical University, Department of Biochemistry and Molecular Biology, Tianjin Medical University, Tianjin, 300070 China
| | - Xiaolu Wang
- grid.265021.20000 0000 9792 1228Department of Pharmacology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070 China
| | - Lili Song
- grid.265021.20000 0000 9792 1228The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Medical University General Hospital, Department of Immunology, Tianjin Medical University, Tianjin, 300070 China
| | - Chenhao Jiang
- grid.265021.20000 0000 9792 1228The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Medical University General Hospital, Department of Immunology, Tianjin Medical University, Tianjin, 300070 China
| | - Albert Jeltsch
- grid.5719.a0000 0004 1936 9713Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| | - Cheng Dong
- grid.265021.20000 0000 9792 1228The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Medical University General Hospital, The Second Hospital of Tianjin Medical University, Department of Biochemistry and Molecular Biology, Tianjin Medical University, Tianjin, 300070 China
| | - Wenyi Mi
- grid.265021.20000 0000 9792 1228The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Medical University General Hospital, Department of Immunology, Tianjin Medical University, Tianjin, 300070 China
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Integrative transcriptome analysis of SARS-CoV-2 human-infected cells combined with deep learning algorithms identifies two potential cellular targets for the treatment of coronavirus disease. Braz J Microbiol 2022; 54:53-68. [PMID: 36435956 PMCID: PMC9702651 DOI: 10.1007/s42770-022-00875-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 11/14/2022] [Indexed: 11/27/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) quickly spread worldwide, leading coronavirus disease 2019 (COVID-19) to hit pandemic level less than 4 months after the first official cases. Hence, the search for drugs and vaccines that could prevent or treat infections by SARS-CoV-2 began, intending to reduce a possible collapse of health systems. After 2 years, efforts to find therapies to treat COVID-19 continue. However, there is still much to be understood about the virus' pathology. Tools such as transcriptomics have been used to understand the impact of SARS-CoV-2 on different cells isolated from various tissues, leaving datasets in the databases that integrate genes and differentially expressed pathways during SARS-CoV-2 infection. After retrieving transcriptome datasets from different human cells infected with SARS-CoV-2 available in the database, we performed an integrative analysis associated with deep learning algorithms to determine differentially expressed targets mainly after infection. The targets found represented a fructose transporter (GLUT5) and a component of proteasome 26s. These targets were then molecularly modeled, followed by molecular docking that identified potential inhibitors for both structures. Once the inhibition of structures that have the expression increased by the virus can represent a strategy for reducing the viral replication by selecting infected cells, associating these bioinformatics tools, therefore, can be helpful in the screening of molecules being tested for new uses, saving financial resources, time, and making a personalized screening for each infectious disease.
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27
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Metabolic recycling of storage lipids promotes squalene biosynthesis in yeast. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2022; 15:108. [PMID: 36224649 PMCID: PMC9555684 DOI: 10.1186/s13068-022-02208-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 10/04/2022] [Indexed: 12/02/2022]
Abstract
BACKGROUND Metabolic rewiring in microbes is an economical and sustainable strategy for synthesizing valuable natural terpenes. Terpenes are the largest class of nature-derived specialized metabolites, and many have valuable pharmaceutical or biological activity. Squalene, a medicinal terpene, is used as a vaccine adjuvant to improve the efficacy of vaccines, including pandemic coronavirus disease 2019 (COVID-19) vaccines, and plays diverse biological roles as an antioxidant and anticancer agent. However, metabolic rewiring interferes with inherent metabolic pathways, often in a way that impairs the cellular growth and fitness of the microbial host. In particular, as the key starting molecule for producing various compounds including squalene, acetyl-CoA is involved in numerous biological processes with tight regulation to maintain metabolic homeostasis, which limits redirection of metabolic fluxes toward desired products. RESULTS In this study, focusing on the recycling of surplus metabolic energy stored in lipid droplets, we show that the metabolic recycling of the surplus energy to acetyl-CoA can increase squalene production in yeast, concomitant with minimizing the metabolic interferences in inherent pathways. Moreover, by integrating multiple copies of the rate-limiting enzyme and implementing N-degron-dependent protein degradation to downregulate the competing pathway, we systematically rewired the metabolic flux toward squalene, enabling remarkable squalene production (1024.88 mg/L in a shake flask). Ultimately, further optimization of the fed-batch fermentation process enabled remarkable squalene production of 6.53 g/L. CONCLUSIONS Our demonstration of squalene production via engineered yeast suggests that plant- or animal-based supplies of medicinal squalene can potentially be complemented or replaced by industrial fermentation. This approach will also provide a universal strategy for the more stable and sustainable production of high-value terpenes.
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Abstract
Many viruses induce shutoff of host gene expression (host shutoff) as a strategy to take over cellular machinery and evade host immunity. Without host shutoff activity, these viruses generally replicate poorly in vivo, attesting to the importance of this antiviral strategy. In this review, we discuss one particularly advantageous way for viruses to induce host shutoff: triggering widespread host messenger RNA (mRNA) decay. Viruses can trigger increased mRNA destruction either directly, by encoding RNA cleaving or decapping enzymes, or indirectly, by activating cellular RNA degradation pathways. We review what is known about the mechanism of action of several viral RNA degradation factors. We then discuss the consequences of widespread RNA degradation on host gene expression and on the mechanisms of immune evasion, highlighting open questions. Answering these questions is critical to understanding how viral RNA degradation factors regulate host gene expression and how this process helps viruses evade host responses and replicate.
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Affiliation(s)
- Léa Gaucherand
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, and Graduate Program in Molecular Microbiology, Tufts Graduate School of Biomedical Sciences, Tufts University, Boston, Massachusetts, USA;
| | - Marta Maria Gaglia
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, and Graduate Program in Molecular Microbiology, Tufts Graduate School of Biomedical Sciences, Tufts University, Boston, Massachusetts, USA;
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Label-Free Quantitative Proteomics Reveal the Involvement of PRT6 in Arabidopsis thaliana Seed Responsiveness to Ethylene. Int J Mol Sci 2022; 23:ijms23169352. [PMID: 36012613 PMCID: PMC9409418 DOI: 10.3390/ijms23169352] [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: 07/15/2022] [Revised: 08/11/2022] [Accepted: 08/16/2022] [Indexed: 11/17/2022] Open
Abstract
In Arabidopsis thaliana, the breaking of seed dormancy in wild type (Col-0) by ethylene at 100 μL L-1 required at least 30 h application. A mutant of the proteolytic N-degron pathway, lacking the E3 ligase PROTEOLYSIS 6 (PRT6), was investigated for its role in ethylene-triggered changes in proteomes during seed germination. Label-free quantitative proteomics was carried out on dormant wild type Col-0 and prt6 seeds treated with (+) or without (-) ethylene. After 16 h, 1737 proteins were identified, but none was significantly different in protein levels in response to ethylene. After longer ethylene treatment (30 h), 2552 proteins were identified, and 619 Differentially Expressed Proteins (DEPs) had significant differences in protein abundances between ethylene treatments and genotypes. In Col, 587 DEPs were enriched for those involved in signal perception and transduction, reserve mobilization and new material generation, which potentially contributed to seed germination. DEPs up-regulated by ethylene in Col included S-adenosylmethionine synthase 1, methionine adenosyltransferase 3 and ACC oxidase involved in ethylene synthesis and of Pyrabactin Resistance1 acting as an ABA receptor, while DEPs down-regulated by ethylene in Col included aldehyde oxidase 4 involved in ABA synthesis. In contrast, in prt6 seeds, ethylene did not result in strong proteomic changes with only 30 DEPs. Taken together, the present work demonstrates that the proteolytic N-degron pathway is essential for ethylene-mediated reprogramming of seed proteomes during germination.
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The MARCHF6 E3 ubiquitin ligase acts as an NADPH sensor for the regulation of ferroptosis. Nat Cell Biol 2022; 24:1239-1251. [PMID: 35941365 DOI: 10.1038/s41556-022-00973-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 06/29/2022] [Indexed: 01/16/2023]
Abstract
Ferroptosis is a unique form of cell death caused by excessive iron-dependent lipid peroxidation. The level of the anabolic reductant NADPH is a biomarker of ferroptosis sensitivity. However, specific regulators that detect cellular NADPH levels, thereby modulating downstream ferroptosis cascades, are largely unknown. We show here that the transmembrane endoplasmic reticulum MARCHF6 E3 ubiquitin ligase recognizes NADPH through its C-terminal regulatory region. This interaction upregulates the E3 ligase activity of MARCHF6, thus downregulating ferroptosis. We also found that MARCHF6 mediates the degradation of the key ferroptosis effectors ACSL4 and p53. Furthermore, inhibiting ferroptosis rescued the growth of MARCHF6-deficient tumours and peri-natal lethality of Marchf6-/- mice. Together, these findings identify MARCHF6 as a previously unknown NADPH sensor in the ubiquitin system and a crucial regulator of ferroptosis.
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31
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Popov VN, Syromyatnikov MY, Franceschi C, Moskalev AA, Krutovsky KV, Krutovsky KV. Genetic mechanisms of aging in plants: What can we learn from them? Ageing Res Rev 2022; 77:101601. [PMID: 35278719 DOI: 10.1016/j.arr.2022.101601] [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] [Received: 10/12/2021] [Revised: 02/03/2022] [Accepted: 03/02/2022] [Indexed: 12/18/2022]
Abstract
Plants hold all records in longevity. Their aging is a complex process. In the presented review, we analyzed published data on various aspects of plant aging with focus on any inferences that could shed a light on aging in animals and help to fight it in human. Plant aging can be caused by many factors, such as telomere depletion, genomic instability, loss of proteostasis, changes in intercellular interaction, desynchronosis, autophagy misregulation, epigenetic changes and others. Plants have developed a number of mechanisms to increase lifespan. Among these mechanisms are gene duplication ("genetic backup"), the active work of telomerases, abundance of meristematic cells, capacity of maintaining the meristems permanently active and continuous activity of phytohormones. Plant aging usually occurs throughout the whole perennial life, but could be also seasonal senescence. Study of causes for seasonal aging can also help to uncover the mechanisms of plant longevity. The influence of different factors such as microbiome communities, glycation, alternative oxidase activity, mitochondrial dysfunction on plant longevity was also reviewed. Adaptive mechanisms of long-lived plants are considered. Further comparative study of the mechanisms underlying longevity of plants is necessary. This will allow us to reach a potentially new level of understanding of the aging process of plants.
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Ribosomal protein S18 acetyltransferase RimI is responsible for the acetylation of elongation factor Tu. J Biol Chem 2022; 298:101914. [PMID: 35398352 PMCID: PMC9079301 DOI: 10.1016/j.jbc.2022.101914] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 04/02/2022] [Accepted: 04/04/2022] [Indexed: 11/21/2022] Open
Abstract
N-terminal acetylation is widespread in the eukaryotic proteome but in bacteria is restricted to a small number of proteins mainly involved in translation. It was long known that elongation factor Tu (EF-Tu) is N-terminally acetylated, whereas the enzyme responsible for this process was unclear. Here, we report that RimI acetyltransferase, known to modify ribosomal protein S18, is likewise responsible for N-acetylation of the EF-Tu. With the help of inducible tufA expression plasmid, we demonstrated that the acetylation does not alter the stability of EF-Tu. Binding of aminoacyl tRNA to the recombinant EF-Tu in vitro was found to be unaffected by the acetylation. At the same time, with the help of fast kinetics methods, we demonstrate that an acetylated variant of EF-Tu more efficiently accelerates A-site occupation by aminoacyl-tRNA, thus increasing the efficiency of in vitro translation. Finally, we show that a strain devoid of RimI has a reduced growth rate, expanded to an evolutionary timescale, and might potentially promote conservation of the acetylation mechanism of S18 and EF-Tu. This study increased our understanding of the modification of bacterial translation apparatus.
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Nguyen KT, Ju S, Kim SY, Lee CS, Lee C, Hwang CS. N-Terminal Modifications of Ubiquitin via Methionine Excision, Deamination, and Arginylation Expand the Ubiquitin Code. Mol Cells 2022; 45:158-167. [PMID: 35253655 PMCID: PMC8926867 DOI: 10.14348/molcells.2022.2027] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 12/16/2021] [Accepted: 01/12/2022] [Indexed: 11/27/2022] Open
Abstract
Ubiquitin (Ub) is post-translationally modified by Ub itself or Ub-like proteins, phosphorylation, and acetylation, among others, which elicits a variety of Ub topologies and cellular functions. However, N-terminal (Nt) modifications of Ub remain unknown, except the linear head-to-tail ubiquitylation via Nt-Met. Here, using the yeast Saccharomyces cerevisiae and an Nt-arginylated Ub-specific antibody, we found that the detectable level of Ub undergoes Nt-Met excision, Nt-deamination, and Nt-arginylation. The resulting Nt-arginylated Ub and its conjugated proteins are upregulated in the stationary-growth phase or by oxidative stress. We further proved the existence of Nt-arginylated Ub in vivo and identified Nt-arginylated Ub-protein conjugates using stable isotope labeling by amino acids in cell culture (SILAC)-based tandem mass spectrometry. In silico structural modeling of Nt-arginylated Ub predicted that Nt-Arg flexibly protrudes from the surface of the Ub, thereby most likely providing a docking site for the factors that recognize it. Collectively, these results reveal unprecedented Nt-arginylated Ub and the pathway by which it is produced, which greatly expands the known complexity of the Ub code.
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Affiliation(s)
- Kha The Nguyen
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673, Korea
| | - Shinyeong Ju
- Center for Theragnosis, Korea Institute of Science and Technology, Seoul 02792, Korea
| | - Sang-Yoon Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673, Korea
| | - Chang-Seok Lee
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673, Korea
| | - Cheolju Lee
- Center for Theragnosis, Korea Institute of Science and Technology, Seoul 02792, Korea
- Division of Bio-Medical Science & Technology, KIST School, Korea University of Science and Technology, Seoul 02792, Korea
| | - Cheol-Sang Hwang
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673, Korea
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Cirinelli A, Wheelan J, Grieg C, Molina CA. Evidence that the transcriptional repressor ICER is regulated via the N-end rule for ubiquitination. Exp Cell Res 2022; 414:113083. [PMID: 35227662 PMCID: PMC8930515 DOI: 10.1016/j.yexcr.2022.113083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 02/20/2022] [Accepted: 02/22/2022] [Indexed: 11/04/2022]
Abstract
ICER is a transcriptional repressor that is mono- or poly-ubiquitinated. This either causes ICER to be translocated from the nucleus, or degraded via the proteasome, respectively. In order to further studies the proteins involved in ICER regulation mass spectrometry analysis was performed to identify potential candidates. We identified twenty eight ICER-interacting proteins in human melanoma cells, Sk-Mel-24. In this study we focus on two proteins with potential roles in ICER proteasomal degradation in response to the N-end rule for ubiquitination: the N-alpha-acetyltransferase 15 (NAA15) and the E3 ubiquitin-protein ligase UBR4. Using an HA-tag on the N- or C-terminus of ICER (NHAICER or ICERCHA) it was found that the N-terminus of ICER is important for its interaction to UBR4, whereas NARG1 interaction is independent of HA-tag position. Silencing RNA experiments show that both NAA15 and UBR4 up-regulates ICER levels and that ICER's N-terminus is important for this regulation. The N-terminus of ICER was found to have dire consequences on its regulation by ubiquitination and cellular functions. The half-life of NHAICER was found to be about twice as long as ICERCHA. Polyubiquitination of ICER was found to be dependent on its N-terminus and mediated by UBR4. This data strongly suggests that ICER is ubiquitinated as a response to the N-end rule that governs protein degradation rate through recognition of the N-terminal residue of proteins. Furthermore, we found that NHAICER inhibits transcription two times more efficiently than ICERCHA, and causes apoptosis 5 times more efficiently than ICERCHA. As forced expression of ICER has been shown before to block cells in mitosis, our data represent a potentially novel mechanism for apoptosis of cells in mitotic arrest.
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35
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Buttermore ED, Anderson NC, Chen PF, Makhortova NR, Kim KH, Wafa SMA, Dwyer S, Micozzi JM, Winden KD, Zhang B, Han MJ, Kleiman RJ, Brownstein CA, Sahin M, Gonzalez-Heydrich J. 16p13.11 deletion variants associated with neuropsychiatric disorders cause morphological and synaptic changes in induced pluripotent stem cell-derived neurons. Front Psychiatry 2022; 13:924956. [PMID: 36405918 PMCID: PMC9669751 DOI: 10.3389/fpsyt.2022.924956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 10/12/2022] [Indexed: 11/05/2022] Open
Abstract
16p13.11 copy number variants (CNVs) have been associated with autism, schizophrenia, psychosis, intellectual disability, and epilepsy. The majority of 16p13.11 deletions or duplications occur within three well-defined intervals, and despite growing knowledge of the functions of individual genes within these intervals, the molecular mechanisms that underlie commonly observed clinical phenotypes remain largely unknown. Patient-derived, induced pluripotent stem cells (iPSCs) provide a platform for investigating the morphological, electrophysiological, and gene-expression changes that result from 16p13.11 CNVs in human-derived neurons. Patient derived iPSCs with varying sizes of 16p13.11 deletions and familial controls were differentiated into cortical neurons for phenotypic analysis. High-content imaging and morphological analysis of patient-derived neurons demonstrated an increase in neurite branching in patients compared with controls. Whole-transcriptome sequencing revealed expression level changes in neuron development and synaptic-related gene families, suggesting a defect in synapse formation. Subsequent quantification of synapse number demonstrated increased numbers of synapses on neurons derived from early-onset patients compared to controls. The identification of common phenotypes among neurons derived from patients with overlapping 16p13.11 deletions will further assist in ascertaining common pathways and targets that could be utilized for screening drug candidates. These studies can help to improve future treatment options and clinical outcomes for 16p13.11 deletion patients.
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Affiliation(s)
- Elizabeth D Buttermore
- Human Neuron Core, Rosamund Stone Zander Translational Neuroscience Center, Boston Children's Hospital, Boston, MA, United States.,Department of Neurology, Boston Children's Hospital, Boston, MA, United States
| | - Nickesha C Anderson
- Department of Neurology, Boston Children's Hospital, Boston, MA, United States.,Harvard Medical School Teaching Hospital, Boston, MA, United States
| | - Pin-Fang Chen
- Human Neuron Core, Rosamund Stone Zander Translational Neuroscience Center, Boston Children's Hospital, Boston, MA, United States.,Department of Neurology, Boston Children's Hospital, Boston, MA, United States
| | - Nina R Makhortova
- Human Neuron Core, Rosamund Stone Zander Translational Neuroscience Center, Boston Children's Hospital, Boston, MA, United States.,Department of Neurology, Boston Children's Hospital, Boston, MA, United States.,Harvard Medical School Teaching Hospital, Boston, MA, United States
| | - Kristina H Kim
- Human Neuron Core, Rosamund Stone Zander Translational Neuroscience Center, Boston Children's Hospital, Boston, MA, United States.,Department of Neurology, Boston Children's Hospital, Boston, MA, United States
| | - Syed M A Wafa
- Human Neuron Core, Rosamund Stone Zander Translational Neuroscience Center, Boston Children's Hospital, Boston, MA, United States
| | - Sean Dwyer
- Human Neuron Core, Rosamund Stone Zander Translational Neuroscience Center, Boston Children's Hospital, Boston, MA, United States
| | - John M Micozzi
- Human Neuron Core, Rosamund Stone Zander Translational Neuroscience Center, Boston Children's Hospital, Boston, MA, United States
| | - Kellen D Winden
- Department of Neurology, Boston Children's Hospital, Boston, MA, United States.,Harvard Medical School Teaching Hospital, Boston, MA, United States
| | - Bo Zhang
- Department of Neurology, Boston Children's Hospital, Boston, MA, United States.,Harvard Medical School Teaching Hospital, Boston, MA, United States
| | - Min-Joon Han
- Human Neuron Core, Rosamund Stone Zander Translational Neuroscience Center, Boston Children's Hospital, Boston, MA, United States
| | - Robin J Kleiman
- Human Neuron Core, Rosamund Stone Zander Translational Neuroscience Center, Boston Children's Hospital, Boston, MA, United States.,Department of Neurology, Boston Children's Hospital, Boston, MA, United States.,Harvard Medical School Teaching Hospital, Boston, MA, United States
| | - Catherine A Brownstein
- The Manton Center of Orphan Disease Research, Boston Children's Hospital, Boston, MA, United States
| | - Mustafa Sahin
- Human Neuron Core, Rosamund Stone Zander Translational Neuroscience Center, Boston Children's Hospital, Boston, MA, United States.,Department of Neurology, Boston Children's Hospital, Boston, MA, United States.,Harvard Medical School Teaching Hospital, Boston, MA, United States
| | - Joseph Gonzalez-Heydrich
- Department of Psychiatry, Developmental Neuropsychiatry Research Program, Boston Children's Hospital, Boston, MA, United States
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36
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Gallego-Jara J, Ortega Á, Lozano Terol G, Sola Martínez RA, Cánovas Díaz M, de Diego Puente T. Bacterial Sirtuins Overview: An Open Niche to Explore. Front Microbiol 2021; 12:744416. [PMID: 34803965 PMCID: PMC8603916 DOI: 10.3389/fmicb.2021.744416] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 10/04/2021] [Indexed: 11/13/2022] Open
Abstract
Sirtuins are deacetylase enzymes widely distributed in all domains of life. Although for decades they have been related only to histones deacetylation in eukaryotic organisms, today they are considered global regulators in both prokaryotes and eukaryotes. Despite the important role of sirtuins in humans, the knowledge about bacterial sirtuins is still limited. Several proteomics studies have shown that bacterial sirtuins deacetylate a large number of lysines in vivo, although the effect that this deacetylation causes in most of them remains unknown. To date, only the regulation of a few bacterial sirtuin substrates has been characterized, being their metabolic roles widely distributed: carbon and nitrogen metabolism, DNA transcription, protein translation, or virulence. One of the most current topics on acetylation and deacetylation focuses on studying stoichiometry using quantitative LC-MS/MS. The results suggest that prokaryotic sirtuins deacetylate at low stoichiometry sites, although more studies are needed to know if it is a common characteristic of bacterial sirtuins and its biological significance. Unlike eukaryotic organisms, bacteria usually have one or few sirtuins, which have been reported to have closer phylogenetic similarity with the human Sirt5 than with any other human sirtuin. In this work, in addition to carrying out an in-depth review of the role of bacterial sirtuins in their physiology, a phylogenetic study has been performed that reveals the evolutionary differences between sirtuins of different bacterial species and even between homologous sirtuins.
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Affiliation(s)
- Julia Gallego-Jara
- Department of Biochemistry and Molecular Biology (B) and Immunology, Faculty of Chemistry, University of Murcia, Campus de Espinardo, Regional Campus of International Excellence "Campus Mare Nostrum", Murcia, Spain
| | - Álvaro Ortega
- Department of Biochemistry and Molecular Biology (B) and Immunology, Faculty of Chemistry, University of Murcia, Campus de Espinardo, Regional Campus of International Excellence "Campus Mare Nostrum", Murcia, Spain
| | - Gema Lozano Terol
- Department of Biochemistry and Molecular Biology (B) and Immunology, Faculty of Chemistry, University of Murcia, Campus de Espinardo, Regional Campus of International Excellence "Campus Mare Nostrum", Murcia, Spain
| | - Rosa A Sola Martínez
- Department of Biochemistry and Molecular Biology (B) and Immunology, Faculty of Chemistry, University of Murcia, Campus de Espinardo, Regional Campus of International Excellence "Campus Mare Nostrum", Murcia, Spain
| | - Manuel Cánovas Díaz
- Department of Biochemistry and Molecular Biology (B) and Immunology, Faculty of Chemistry, University of Murcia, Campus de Espinardo, Regional Campus of International Excellence "Campus Mare Nostrum", Murcia, Spain
| | - Teresa de Diego Puente
- Department of Biochemistry and Molecular Biology (B) and Immunology, Faculty of Chemistry, University of Murcia, Campus de Espinardo, Regional Campus of International Excellence "Campus Mare Nostrum", Murcia, Spain
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37
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Kats I, Reinbold C, Kschonsak M, Khmelinskii A, Armbruster L, Ruppert T, Knop M. Up-regulation of ubiquitin-proteasome activity upon loss of NatA-dependent N-terminal acetylation. Life Sci Alliance 2021; 5:5/2/e202000730. [PMID: 34764209 PMCID: PMC8605321 DOI: 10.26508/lsa.202000730] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 10/26/2021] [Accepted: 10/27/2021] [Indexed: 11/26/2022] Open
Abstract
Inactivation of N-terminal acetyltransferase A is found to alter Rpn4 as well as E3 ligase abundance, causing up-regulation of Ubiquitin–proteasome activity. In this context, Tom1 is also identified as a novel chain-elongating enzyme of the UFD-pathway. N-terminal acetylation is a prominent protein modification, and inactivation of N-terminal acetyltransferases (NATs) cause protein homeostasis stress. Using multiplexed protein stability profiling with linear ubiquitin fusions as reporters for the activity of the ubiquitin proteasome system, we observed increased ubiquitin proteasome system activity in NatA, but not NatB or NatC mutants. We find several mechanisms contributing to this behavior. First, NatA-mediated acetylation of the N-terminal ubiquitin–independent degron regulates the abundance of Rpn4, the master regulator of the expression of proteasomal genes. Second, the abundance of several E3 ligases involved in degradation of UFD substrates is increased in cells lacking NatA. Finally, we identify the E3 ligase Tom1 as a novel chain-elongating enzyme (E4) involved in the degradation of linear ubiquitin fusions via the formation of branched K11, K29, and K48 ubiquitin chains, independently of the known E4 ligases involved in UFD, leading to enhanced ubiquitination of the UFD substrates.
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Affiliation(s)
- Ilia Kats
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Christian Reinbold
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Marc Kschonsak
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | | | - Laura Armbruster
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Thomas Ruppert
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Michael Knop
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany .,Deutsches Krebsforschungszentrum (DKFZ), DKFZ-ZMBH Alliance, Heidelberg, Germany
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38
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Lammers M. Post-translational Lysine Ac(et)ylation in Bacteria: A Biochemical, Structural, and Synthetic Biological Perspective. Front Microbiol 2021; 12:757179. [PMID: 34721364 PMCID: PMC8556138 DOI: 10.3389/fmicb.2021.757179] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 09/10/2021] [Indexed: 12/21/2022] Open
Abstract
Ac(et)ylation is a post-translational modification present in all domains of life. First identified in mammals in histones to regulate RNA synthesis, today it is known that is regulates fundamental cellular processes also in bacteria: transcription, translation, metabolism, cell motility. Ac(et)ylation can occur at the ε-amino group of lysine side chains or at the α-amino group of a protein. Furthermore small molecules such as polyamines and antibiotics can be acetylated and deacetylated enzymatically at amino groups. While much research focused on N-(ε)-ac(et)ylation of lysine side chains, much less is known about the occurrence, the regulation and the physiological roles on N-(α)-ac(et)ylation of protein amino termini in bacteria. Lysine ac(et)ylation was shown to affect protein function by various mechanisms ranging from quenching of the positive charge, increasing the lysine side chains’ size affecting the protein surface complementarity, increasing the hydrophobicity and by interfering with other post-translational modifications. While N-(ε)-lysine ac(et)ylation was shown to be reversible, dynamically regulated by lysine acetyltransferases and lysine deacetylases, for N-(α)-ac(et)ylation only N-terminal acetyltransferases were identified and so far no deacetylases were discovered neither in bacteria nor in mammals. To this end, N-terminal ac(et)ylation is regarded as being irreversible. Besides enzymatic ac(et)ylation, recent data showed that ac(et)ylation of lysine side chains and of the proteins N-termini can also occur non-enzymatically by the high-energy molecules acetyl-coenzyme A and acetyl-phosphate. Acetyl-phosphate is supposed to be the key molecule that drives non-enzymatic ac(et)ylation in bacteria. Non-enzymatic ac(et)ylation can occur site-specifically with both, the protein primary sequence and the three dimensional structure affecting its efficiency. Ac(et)ylation is tightly controlled by the cellular metabolic state as acetyltransferases use ac(et)yl-CoA as donor molecule for the ac(et)ylation and sirtuin deacetylases use NAD+ as co-substrate for the deac(et)ylation. Moreover, the accumulation of ac(et)yl-CoA and acetyl-phosphate is dependent on the cellular metabolic state. This constitutes a feedback control mechanism as activities of many metabolic enzymes were shown to be regulated by lysine ac(et)ylation. Our knowledge on lysine ac(et)ylation significantly increased in the last decade predominantly due to the huge methodological advances that were made in fields such as mass-spectrometry, structural biology and synthetic biology. This also includes the identification of additional acylations occurring on lysine side chains with supposedly different regulatory potential. This review highlights recent advances in the research field. Our knowledge on enzymatic regulation of lysine ac(et)ylation will be summarized with a special focus on structural and mechanistic characterization of the enzymes, the mechanisms underlying non-enzymatic/chemical ac(et)ylation are explained, recent technological progress in the field are presented and selected examples highlighting the important physiological roles of lysine ac(et)ylation are summarized.
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Affiliation(s)
- Michael Lammers
- Synthetic and Structural Biochemistry, Institute for Biochemistry, University of Greifswald, Greifswald, Germany
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39
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Chen D, Zhu S. Whole-exome sequencing identification of a recurrent CRYBB2 variant in a four-generation Chinese family with congenital nuclear cataracts. Exp Ther Med 2021; 22:1375. [PMID: 34650623 PMCID: PMC8506933 DOI: 10.3892/etm.2021.10810] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 08/19/2021] [Indexed: 12/25/2022] Open
Abstract
Congenital cataracts is the most common cause of visual impairment and blindness in children. Although there have been extensive studies into the pathogenesis of congenital cataracts, the pathogenic mechanism underlying the recurrent variant CRYBB2:c.62T>A(p.I21N) has not been previously reported. Thus, the present study aimed to use whole-exome sequencing (WES) to identify potential genetic variants and investigate how they may have induced the occurrence of cataracts in a four-generation Chinese family with congenital nuclear cataracts. The medical history of this family was recorded and WES was conducted for one proband. Sanger sequencing was used to verify the presence of the putative variant in all participants. PolyPhen-2, SIFT and ProtScale were used to analyze the effect of the identified variants on protein function and hydrophobicity, and Pymol was used to show the structure of the wild-type (Wt) and mutant β-crystallin B2 (CRYBB2) protein. Full-length Wt-CRYBB2 or mutant-CRYBB2 (I21N-CRYBB2) were fused to green fluorescent protein (GFP), and the recombinant plasmids were transfected into HeLa cells. Reverse transcription-quantitative PCR and western blotting were used to detect the expression levels of CRYBB2 mRNA and protein. Immunofluorescence and flow cytometry analyses were used to detect protein localization and apoptosis, respectively. A recurrent variant CRYBB2:c.62T>A(p.I21N) was identified in a four-generation Chinese family with congenital nuclear cataracts. Multiple-sequence alignment of CRYBB2 demonstrated that codon 21 was highly conserved. Pymol revealed that the structure of the I21N-CRYBB2 protein was distinct from that of Wt-CRYBB2. PolyPhen-2 predicted that it had a variant provean score 1.0, suggesting it was 'probably damaging', and SIFT predicted it had a variant provean score of -5.113, indicating it was 'deleterious'. ProtScale indicated that the hydrophobicity of the mutation site was significantly reduced. The protein expression levels of the I21N-CRYBB2 were decreased compared with the Wt-CRYBB2. Immunofluorescence analysis revealed that the variant I21N-CRYBB2 protein tended to accumulate around the nucleus, and flow cytometry analysis indicated that it increased cell apoptosis. Furthermore, I21N-CRYBB2 induced the activation of the unfolded protein response (UPR). In conclusion, a pathogenic variant of CRYBB2:c.62T>A(p.I21N) was identified via WES in a four-generation Chinese family with congenital nuclear cataracts. Through biological analysis, it was found that the variant induced abnormal protein aggregation, activated the UPR and triggered excessive cell apoptosis, which may lead to the occurrence of congenital nuclear cataracts in this family.
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Affiliation(s)
- Doudou Chen
- Eye School of Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan 610075, P.R. China.,Department of Ophthalmology, Ineye Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan 610032, P.R. China.,Key Laboratory of Sichuan Province Ophthalmopathy Prevention & Cure and Visual Function Protection, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan 610032, P.R. China
| | - Siquan Zhu
- Eye School of Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan 610075, P.R. China.,Department of Ophthalmology, Ineye Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan 610032, P.R. China.,Key Laboratory of Sichuan Province Ophthalmopathy Prevention & Cure and Visual Function Protection, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan 610032, P.R. China.,Department of Ophthalmology, Beijing Anzhen Hospital, Capital Medical University, Beijing 100006, P.R. China
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40
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Soini L, Redhead M, Westwood M, Leysen S, Davis J, Ottmann C. Identification of molecular glues of the SLP76/14-3-3 protein-protein interaction. RSC Med Chem 2021; 12:1555-1564. [PMID: 34667951 PMCID: PMC8459327 DOI: 10.1039/d1md00172h] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 07/01/2021] [Indexed: 12/12/2022] Open
Abstract
The stabilisation of protein-protein interactions (PPIs) through molecular glues is a novel and promising approach in drug discovery. In stark contrast to research in protein-protein inhibition the field of stabilisation remains underdeveloped with comparatively few examples of small-molecule stabilisers of PPIs reported to date. At the same time identifying molecular glues has received recent sustained interest, especially in the fields of targeted protein degradation and 14-3-3 PPIs. The hub-protein 14-3-3 has a broad interactome with more than 500 known protein partners which presents a great opportunity for therapeutic intervention. In this study we have developed an HTRF assay suitable for HTS of the 14-3-3/SLP76 PPI and have completed a proof of concept screen against a chemically diverse library of 20 K molecules. The adaptor protein SLP76 has been reported to interact with 14-3-3 proteins downstream of the TCR playing an important role in mediating its own proteasomal degradation. We believe that stabilisation of this PPI could be exploited to potentiate degradation of SLP76 and therefore inhibit TCR signalling. This would represent an interesting alternative to other approaches in the field of targeted protein degradation. Here we disclose 16 novel stabilisers of the 14-3-3/SLP76 PPI across multiple different chemotypes. Based on the early results presented here we would recommend this approach to find molecular glues with broad applicability in the field of 14-3-3 PPIs.
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Affiliation(s)
- Lorenzo Soini
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology Eindhoven The Netherlands .,Department of Chemistry, UCB Celltech Slough UK
| | - Martin Redhead
- Exscientia Ltd, Schrodinger Building, Oxford Science Park Oxford OX44GE UK
| | - Marta Westwood
- Structural Biology, Discovery, Charles River, Chesterford Research Park UK
| | - Seppe Leysen
- Department of Structural Biology and Biophysics, UCB Celltech Slough UK
| | | | - Christian Ottmann
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology Eindhoven The Netherlands
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41
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Collier MP, Moreira KB, Li KH, Chen YC, Itzhak D, Samant R, Leitner A, Burlingame A, Frydman J. Native mass spectrometry analyses of chaperonin complex TRiC/CCT reveal subunit N-terminal processing and re-association patterns. Sci Rep 2021; 11:13084. [PMID: 34158536 PMCID: PMC8219831 DOI: 10.1038/s41598-021-91086-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 05/05/2021] [Indexed: 11/14/2022] Open
Abstract
The eukaryotic chaperonin TRiC/CCT is a large ATP-dependent complex essential for cellular protein folding. Its subunit arrangement into two stacked eight-membered hetero-oligomeric rings is conserved from yeast to man. A recent breakthrough enables production of functional human TRiC (hTRiC) from insect cells. Here, we apply a suite of mass spectrometry techniques to characterize recombinant hTRiC. We find all subunits CCT1-8 are N-terminally processed by combinations of methionine excision and acetylation observed in native human TRiC. Dissociation by organic solvents yields primarily monomeric subunits with a small population of CCT dimers. Notably, some dimers feature non-canonical inter-subunit contacts absent in the initial hTRiC. This indicates individual CCT monomers can promiscuously re-assemble into dimers, and lack the information to assume the specific interface pairings in the holocomplex. CCT5 is consistently the most stable subunit and engages in the greatest number of non-canonical dimer pairings. These findings confirm physiologically relevant post-translational processing and function of recombinant hTRiC and offer quantitative insight into the relative stabilities of TRiC subunits and interfaces, a key step toward reconstructing its assembly mechanism. Our results also highlight the importance of assigning contacts identified by native mass spectrometry after solution dissociation as canonical or non-canonical when investigating multimeric assemblies.
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Affiliation(s)
| | | | - Kathy H Li
- Department of Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Yu-Chan Chen
- Department of Biology, Stanford University, Stanford, CA, USA
| | | | - Rahul Samant
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Alexander Leitner
- Department of Biology, Institute of Molecular Systems Biology, Zurich, Switzerland
| | - Alma Burlingame
- Department of Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Judith Frydman
- Department of Biology, Stanford University, Stanford, CA, USA.
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42
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Kong KYE, Coelho JPL, Feige MJ, Khmelinskii A. Quality control of mislocalized and orphan proteins. Exp Cell Res 2021; 403:112617. [PMID: 33930402 DOI: 10.1016/j.yexcr.2021.112617] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 04/10/2021] [Accepted: 04/18/2021] [Indexed: 12/16/2022]
Abstract
A healthy and functional proteome is essential to cell physiology. However, this is constantly being challenged as most steps of protein metabolism are error-prone and changes in the physico-chemical environment can affect protein structure and function, thereby disrupting proteome homeostasis. Among a variety of potential mistakes, proteins can be targeted to incorrect compartments or subunits of protein complexes may fail to assemble properly with their partners, resulting in the formation of mislocalized and orphan proteins, respectively. Quality control systems are in place to handle these aberrant proteins, and to minimize their detrimental impact on cellular functions. Here, we discuss recent findings on quality control mechanisms handling mislocalized and orphan proteins. We highlight common principles involved in their recognition and summarize how accumulation of these aberrant molecules is associated with aging and disease.
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Affiliation(s)
| | - João P L Coelho
- Department of Chemistry and Institute for Advanced Study, Technical University of Munich, Garching, Germany
| | - Matthias J Feige
- Department of Chemistry and Institute for Advanced Study, Technical University of Munich, Garching, Germany
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43
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Kang JA, Jeon YJ. How Is the Fidelity of Proteins Ensured in Terms of Both Quality and Quantity at the Endoplasmic Reticulum? Mechanistic Insights into E3 Ubiquitin Ligases. Int J Mol Sci 2021; 22:ijms22042078. [PMID: 33669844 PMCID: PMC7923238 DOI: 10.3390/ijms22042078] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 02/16/2021] [Accepted: 02/16/2021] [Indexed: 02/06/2023] Open
Abstract
The endoplasmic reticulum (ER) is an interconnected organelle that plays fundamental roles in the biosynthesis, folding, stabilization, maturation, and trafficking of secretory and transmembrane proteins. It is the largest organelle and critically modulates nearly all aspects of life. Therefore, in the endoplasmic reticulum, an enormous investment of resources, including chaperones and protein folding facilitators, is dedicated to adequate protein maturation and delivery to final destinations. Unfortunately, the folding and assembly of proteins can be quite error-prone, which leads to the generation of misfolded proteins. Notably, protein homeostasis, referred to as proteostasis, is constantly exposed to danger by flows of misfolded proteins and subsequent protein aggregates. To maintain proteostasis, the ER triages and eliminates terminally misfolded proteins by delivering substrates to the ubiquitin–proteasome system (UPS) or to the lysosome, which is termed ER-associated degradation (ERAD) or ER-phagy, respectively. ERAD not only eliminates misfolded or unassembled proteins via protein quality control but also fine-tunes correctly folded proteins via protein quantity control. Intriguingly, the diversity and distinctive nature of E3 ubiquitin ligases determine efficiency, complexity, and specificity of ubiquitination during ERAD. ER-phagy utilizes the core autophagy machinery and eliminates ERAD-resistant misfolded proteins. Here, we conceptually outline not only ubiquitination machinery but also catalytic mechanisms of E3 ubiquitin ligases. Further, we discuss the mechanistic insights into E3 ubiquitin ligases involved in the two guardian pathways in the ER, ERAD and ER-phagy. Finally, we provide the molecular mechanisms by which ERAD and ER-phagy conduct not only protein quality control but also protein quantity control to ensure proteostasis and subsequent organismal homeostasis.
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Affiliation(s)
- Ji An Kang
- Department of Biochemistry, College of Medicine, Chungnam National University, Daejeon 35015, Korea;
- Department of Medical Science, College of Medicine, Chungnam National University, Daejeon 35015, Korea
| | - Young Joo Jeon
- Department of Biochemistry, College of Medicine, Chungnam National University, Daejeon 35015, Korea;
- Department of Medical Science, College of Medicine, Chungnam National University, Daejeon 35015, Korea
- Correspondence:
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44
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Bhagwat P, Amobonye A, Singh S, Pillai S. A comparative analysis of GH18 chitinases and their isoforms from Beauveria bassiana: An in-silico approach. Process Biochem 2021. [DOI: 10.1016/j.procbio.2020.10.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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45
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Abstract
The ubiquitin–proteasome system (UPS) is responsible for the rapid targeting of proteins for degradation at 26S proteasomes and requires the orchestrated action of E1, E2 and E3 enzymes in a well-defined cascade. F-box proteins (FBPs) are substrate-recruiting subunits of Skp1-cullin1-FBP (SCF)-type E3 ubiquitin ligases that determine which proteins are ubiquitinated. To date, around 70 FBPs have been identified in humans and can be subdivided into distinct families, based on the protein-recruiting domains they possess. The FBXL subfamily is defined by the presence of multiple leucine-rich repeat (LRR) protein-binding domains. But how the 22 FBPs of the FBXL family achieve their individual specificities, despite having highly similar structural domains to recruit their substrates, is not clear. Here, we review and explore the FBXL family members in detail highlighting their structural and functional similarities and differences and how they engage their substrates through their LRRs to adopt unique interactomes.
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Affiliation(s)
- Bethany Mason
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP
| | - Heike Laman
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP
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46
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Diskin C, Ryan TAJ, O'Neill LAJ. Modification of Proteins by Metabolites in Immunity. Immunity 2020; 54:19-31. [PMID: 33220233 DOI: 10.1016/j.immuni.2020.09.014] [Citation(s) in RCA: 82] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 07/31/2020] [Accepted: 09/15/2020] [Indexed: 12/14/2022]
Abstract
Immunometabolism has emerged as a key focus for immunologists, with metabolic change in immune cells becoming as important a determinant for specific immune effector responses as discrete signaling pathways. A key output for these changes involves post-translational modification (PTM) of proteins by metabolites. Products of glycolysis and Krebs cycle pathways can mediate these events, as can lipids, amino acids, and polyamines. A rich and diverse set of PTMs in macrophages and T cells has been uncovered, altering phenotype and modulating immunity and inflammation in different contexts. We review the recent findings in this area and speculate whether they could be of use in the effort to develop therapeutics for immune-related diseases.
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Affiliation(s)
- C Diskin
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Ireland
| | - T A J Ryan
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Ireland
| | - L A J O'Neill
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Ireland.
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47
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The Role of Posttranslational Modifications in DNA Repair. BIOMED RESEARCH INTERNATIONAL 2020. [DOI: 10.1155/2020/7493902] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The human body is a complex structure of cells, which are exposed to many types of stress. Cells must utilize various mechanisms to protect their DNA from damage caused by metabolic and external sources to maintain genomic integrity and homeostasis and to prevent the development of cancer. DNA damage inevitably occurs regardless of physiological or abnormal conditions. In response to DNA damage, signaling pathways are activated to repair the damaged DNA or to induce cell apoptosis. During the process, posttranslational modifications (PTMs) can be used to modulate enzymatic activities and regulate protein stability, protein localization, and protein-protein interactions. Thus, PTMs in DNA repair should be studied. In this review, we will focus on the current understanding of the phosphorylation, poly(ADP-ribosyl)ation, ubiquitination, SUMOylation, acetylation, and methylation of six typical PTMs and summarize PTMs of the key proteins in DNA repair, providing important insight into the role of PTMs in the maintenance of genome stability and contributing to reveal new and selective therapeutic approaches to target cancers.
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48
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Scott NA, Sharpe LJ, Brown AJ. The E3 ubiquitin ligase MARCHF6 as a metabolic integrator in cholesterol synthesis and beyond. Biochim Biophys Acta Mol Cell Biol Lipids 2020; 1866:158837. [PMID: 33049405 DOI: 10.1016/j.bbalip.2020.158837] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 09/29/2020] [Accepted: 10/02/2020] [Indexed: 12/19/2022]
Abstract
MARCHF6 is a large multi-pass E3 ubiquitin ligase embedded in the membranes of the endoplasmic reticulum. It participates in endoplasmic reticulum associated degradation, including autoubiquitination, and many of its identified substrates are involved in sterol and lipid metabolism. Post-translationally, MARCHF6 expression is attuned to cholesterol status, with high cholesterol preventing its degradation and hence boosting MARCHF6 levels. By modulating MARCHF6 activity, cholesterol may regulate other aspects of cell metabolism beyond the known repertoire. Whilst we have learnt much about MARCHF6 in the past decade, there are still many more mysteries to be unravelled to fully understand its regulation, substrates, and role in human health and disease.
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Affiliation(s)
- Nicola A Scott
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Laura J Sharpe
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Andrew J Brown
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia.
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49
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Almeida T, Pinto G, Correia B, Gonçalves S, Meijón M, Escandón M. In-depth analysis of the Quercus suber metabolome under drought stress and recovery reveals potential key metabolic players. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 299:110606. [PMID: 32900444 DOI: 10.1016/j.plantsci.2020.110606] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 06/12/2020] [Accepted: 07/16/2020] [Indexed: 05/08/2023]
Abstract
Cork oak (Quercus suber L.) is a species of ecological, social and economic importance in the Mediterranean region. Given its xerophytic adaptability, the study of cork oak's response to drought stress conditions may provide important data in the global scenario of climate change. The mechanisms behind cork oak's adaptation to drought conditions can inform the design and development of tools to better manage this species under the changing climate patterns. Metabolomics is one of the most promising omics layers to capture a snapshot of a particular physiological state and to identify putative biomarkers of stress tolerance. Drastic changes were observed in the leaf metabolome of Q. suber between the different experimental conditions, namely at the beginning of the drought stress treatment, after one month under drought and post rehydration. All experimental treatments were analyzed through sPLS to inspect for global changes and stress and rehydration responses were analyzed independently for specific alterations. This allowed a more in-depth study and a search for biomarkers specific to a given hydric treatment. The metabolome analyses showed changes in both primary and secondary metabolism, but highlighted the role of secondary metabolism. In addition, a compound-specific response was observed in stress and rehydration. Key compounds such as L-phenylalanine and epigallocatechin 3-gallate were identified in relation to early drought response, terpenoid leonuridine and the flavonoid glycoside (-)-epicatechin-3'-O-glucuronide in long-term drought response, and flavone isoscoparine was identified in relation to the recovery process. The results here obtained provide novel insights into the biology of cork oak, highlighting pathways and metabolites potentially involved in the response of this species during drought and recovery that may be essential for its adaptation to long periods of drought. It is expected that this knowledge can encourage further functional studies in order to validate potential biomarkers of drought and recovery that maybe used to support decision-making in cork oak breeding programs.
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Affiliation(s)
- Tânia Almeida
- Centro de Biotecnologia Agrícola e Agro-Alimentar do Alentejo (CEBAL)/Instituto Politécnico de Beja (IPBeja), Rua Pedro Soares, Beja, Portugal; Centre for Research in Ceramics & Composite Materials (CICECO), University of Aveiro, Campus Universitário de Santiago, Aveiro, Portugal; Centre for Environmental and Marine Studies (CESAM) & Department of Biology, University of Aveiro, Aveiro, Portugal
| | - Gloria Pinto
- Centre for Environmental and Marine Studies (CESAM) & Department of Biology, University of Aveiro, Aveiro, Portugal..
| | - Barbara Correia
- Centre for Environmental and Marine Studies (CESAM) & Department of Biology, University of Aveiro, Aveiro, Portugal
| | - Sónia Gonçalves
- Centro de Biotecnologia Agrícola e Agro-Alimentar do Alentejo (CEBAL)/Instituto Politécnico de Beja (IPBeja), Rua Pedro Soares, Beja, Portugal
| | - Mónica Meijón
- Plant Physiology, Department B.O.S., Faculty of Biology, University of Oviedo, Oviedo, Asturias, Spain
| | - Mónica Escandón
- Centre for Environmental and Marine Studies (CESAM) & Department of Biology, University of Aveiro, Aveiro, Portugal..
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50
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Finger Y, Habich M, Gerlich S, Urbanczyk S, van de Logt E, Koch J, Schu L, Lapacz KJ, Ali M, Petrungaro C, Salscheider SL, Pichlo C, Baumann U, Mielenz D, Dengjel J, Brachvogel B, Hofmann K, Riemer J. Proteasomal degradation induced by DPP9-mediated processing competes with mitochondrial protein import. EMBO J 2020; 39:e103889. [PMID: 32815200 PMCID: PMC7527813 DOI: 10.15252/embj.2019103889] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 06/29/2020] [Accepted: 07/03/2020] [Indexed: 12/14/2022] Open
Abstract
Plasticity of the proteome is critical to adapt to varying conditions. Control of mitochondrial protein import contributes to this plasticity. Here, we identified a pathway that regulates mitochondrial protein import by regulated N-terminal processing. We demonstrate that dipeptidyl peptidases 8/9 (DPP8/9) mediate the N-terminal processing of adenylate kinase 2 (AK2) en route to mitochondria. We show that AK2 is a substrate of the mitochondrial disulfide relay, thus lacking an N-terminal mitochondrial targeting sequence and undergoing comparatively slow import. DPP9-mediated processing of AK2 induces its rapid proteasomal degradation and prevents cytosolic accumulation of enzymatically active AK2. Besides AK2, we identify more than 100 mitochondrial proteins with putative DPP8/9 recognition sites and demonstrate that DPP8/9 influence the cellular levels of a number of these proteins. Collectively, we provide in this study a conceptual framework on how regulated cytosolic processing controls levels of mitochondrial proteins as well as their dual localization to mitochondria and other compartments.
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Affiliation(s)
- Yannik Finger
- Institute of Biochemistry, Redox Biochemistry, University of Cologne, Cologne, Germany
| | - Markus Habich
- Institute of Biochemistry, Redox Biochemistry, University of Cologne, Cologne, Germany
| | - Sarah Gerlich
- Institute of Biochemistry, Redox Biochemistry, University of Cologne, Cologne, Germany
| | - Sophia Urbanczyk
- Division of Molecular Immunology, Department of Internal Medicine III, Nikolaus-Fiebiger-Center, University of Erlangen-Nürnberg, Erlangen, Germany
| | - Erik van de Logt
- Institute of Biochemistry, Redox Biochemistry, University of Cologne, Cologne, Germany
| | - Julian Koch
- Institute of Biochemistry, Redox Biochemistry, University of Cologne, Cologne, Germany
| | - Laura Schu
- Institute of Biochemistry, Redox Biochemistry, University of Cologne, Cologne, Germany
| | - Kim Jasmin Lapacz
- Institute of Biochemistry, Redox Biochemistry, University of Cologne, Cologne, Germany
| | - Muna Ali
- Institute of Biochemistry, Redox Biochemistry, University of Cologne, Cologne, Germany
| | - Carmelina Petrungaro
- Institute of Biochemistry, Redox Biochemistry, University of Cologne, Cologne, Germany
| | | | - Christian Pichlo
- Institute of Biochemistry, University of Cologne, Cologne, Germany
| | - Ulrich Baumann
- Institute of Biochemistry, University of Cologne, Cologne, Germany
| | - Dirk Mielenz
- Division of Molecular Immunology, Department of Internal Medicine III, Nikolaus-Fiebiger-Center, University of Erlangen-Nürnberg, Erlangen, Germany
| | - Joern Dengjel
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Bent Brachvogel
- Department of Pediatrics and Adolescent Medicine, Experimental Neonatology, Faculty of Medicine, University of Cologne, Cologne, Germany.,Center for Biochemistry, Faculty of Medicine, University of Cologne, Cologne, Germany
| | - Kay Hofmann
- Institute of Genetics, University of Cologne, Cologne, Germany
| | - Jan Riemer
- Institute of Biochemistry, Redox Biochemistry, University of Cologne, Cologne, Germany.,Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
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