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Velasco‐Carneros L, Bernardo‐Seisdedos G, Maréchal J, Millet O, Moro F, Muga A. Pseudophosphorylation of single residues of the J-domain of DNAJA2 regulates the holding/folding balance of the Hsc70 system. Protein Sci 2024; 33:e5105. [PMID: 39012012 PMCID: PMC11249846 DOI: 10.1002/pro.5105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 06/20/2024] [Accepted: 06/23/2024] [Indexed: 07/17/2024]
Abstract
The Hsp70 system is essential for maintaining protein homeostasis and comprises a central Hsp70 and two accessory proteins that belong to the J-domain protein (JDP) and nucleotide exchange factor families. Posttranslational modifications offer a means to tune the activity of the system. We explore how phosphorylation of specific residues of the J-domain of DNAJA2, a class A JDP, regulates Hsc70 activity using biochemical and structural approaches. Among these residues, we find that pseudophosphorylation of Y10 and S51 enhances the holding/folding balance of the Hsp70 system, reducing cochaperone collaboration with Hsc70 while maintaining the holding capacity. Truly phosphorylated J domains corroborate phosphomimetic variant effects. Notably, distinct mechanisms underlie functional impacts of these DNAJA2 variants. Pseudophosphorylation of Y10 induces partial disordering of the J domain, whereas the S51E substitution weakens essential DNAJA2-Hsc70 interactions without a large structural reorganization of the protein. S51 phosphorylation might be class-specific, as all cytosolic class A human JDPs harbor a phosphorylatable residue at this position.
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Affiliation(s)
- Lorea Velasco‐Carneros
- Instituto Biofisika (UPV/EHU, CSIC)University of Basque CountryLeioaSpain
- Department of Biochemistry and Molecular Biology, Faculty of Science and TechnologyUniversity of the Basque Country (UPV/EHU)LeioaSpain
| | - Ganeko Bernardo‐Seisdedos
- Precision Medicine and Metabolism LabCIC bioGUNEDerioSpain
- Department of Medicine, Faculty of Health SciencesUniversity of DeustoBilbaoSpain
| | - Jean‐Didier Maréchal
- Insilichem, Departament de QuímicaUniversitat Autònoma de Barcelona (UAB)Bellaterra (Barcelona)Spain
| | - Oscar Millet
- Precision Medicine and Metabolism LabCIC bioGUNEDerioSpain
| | - Fernando Moro
- Instituto Biofisika (UPV/EHU, CSIC)University of Basque CountryLeioaSpain
- Department of Biochemistry and Molecular Biology, Faculty of Science and TechnologyUniversity of the Basque Country (UPV/EHU)LeioaSpain
| | - Arturo Muga
- Instituto Biofisika (UPV/EHU, CSIC)University of Basque CountryLeioaSpain
- Department of Biochemistry and Molecular Biology, Faculty of Science and TechnologyUniversity of the Basque Country (UPV/EHU)LeioaSpain
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2
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Baños-Jaime B, Corrales-Guerrero L, Pérez-Mejías G, Rejano-Gordillo CM, Velázquez-Campoy A, Martínez-Cruz LA, Martínez-Chantar ML, De la Rosa MA, Díaz-Moreno I. Phosphorylation at the disordered N-end makes HuR accumulate and dimerize in the cytoplasm. Nucleic Acids Res 2024:gkae564. [PMID: 38966993 DOI: 10.1093/nar/gkae564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 05/30/2024] [Accepted: 07/02/2024] [Indexed: 07/06/2024] Open
Abstract
Human antigen R (HuR) is an RNA binding protein mainly involved in maintaining the stability and controlling the translation of mRNAs, critical for immune response, cell survival, proliferation and apoptosis. Although HuR is a nuclear protein, its mRNA translational-related function occurs at the cytoplasm, where the oligomeric form of HuR is more abundant. However, the regulation of nucleo-cytoplasmic transport of HuR and its connection with protein oligomerization remain unclear. In this work, we describe the phosphorylation of Tyr5 as a new hallmark for HuR activation. Our biophysical, structural and computational assays using phosphorylated and phosphomimetic HuR proteins demonstrate that phosphorylation of Tyr5 at the disordered N-end stretch induces global changes on HuR dynamics and conformation, modifying the solvent accessible surface of the HuR nucleo-cytoplasmic shuttling (HNS) sequence and releasing regions implicated in HuR dimerization. These findings explain the preferential cytoplasmic accumulation of phosphorylated HuR in HeLa cells, aiding to comprehend the mechanisms underlying HuR nucleus-cytoplasm shuttling and its later dimerization, both of which are relevant in HuR-related pathogenesis.
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Affiliation(s)
- Blanca Baños-Jaime
- Institute for Chemical Research (IIQ), Scientific Research Center "Isla de la Cartuja" (cicCartuja), University of Seville - CSIC, Seville 41092, Spain
| | - Laura Corrales-Guerrero
- Institute for Chemical Research (IIQ), Scientific Research Center "Isla de la Cartuja" (cicCartuja), University of Seville - CSIC, Seville 41092, Spain
| | - Gonzalo Pérez-Mejías
- Institute for Chemical Research (IIQ), Scientific Research Center "Isla de la Cartuja" (cicCartuja), University of Seville - CSIC, Seville 41092, Spain
| | - Claudia M Rejano-Gordillo
- Centre for Biomedical Research Network of Hepatic and Digestive Diseases (CIBERehd), Madrid 28029, Spain
- Liver Disease Lab, BRTA CIC bioGUNE, Derio 48160 Bizkaia, Spain
- Department of Biochemistry and Molecular Biology, Faculty of Sciences, University of Extremadura; University Institute of Biosanitary Research of Extremadura (INUBE), Badajoz 06071, Spain
| | - Adrián Velázquez-Campoy
- Institute for Biocomputation and Physic of Complex Systems (BIFI), Joint Unit GBsC-CSIC-BIFI, University of Zaragoza, Zaragoza 50018, Spain
- Departament of Biochemistry and Molecular and Cellular Biology, University of Zaragoza, Zaragoza 50009, Spain
- Institute for Health Research of Aragón (IIS Aragon), Zaragoza 50009, Spain
| | - Luis Alfonso Martínez-Cruz
- Centre for Biomedical Research Network of Hepatic and Digestive Diseases (CIBERehd), Madrid 28029, Spain
- Liver Disease Lab, BRTA CIC bioGUNE, Derio 48160 Bizkaia, Spain
| | - María Luz Martínez-Chantar
- Centre for Biomedical Research Network of Hepatic and Digestive Diseases (CIBERehd), Madrid 28029, Spain
- Liver Disease Lab, BRTA CIC bioGUNE, Derio 48160 Bizkaia, Spain
| | - Miguel A De la Rosa
- Institute for Chemical Research (IIQ), Scientific Research Center "Isla de la Cartuja" (cicCartuja), University of Seville - CSIC, Seville 41092, Spain
| | - Irene Díaz-Moreno
- Institute for Chemical Research (IIQ), Scientific Research Center "Isla de la Cartuja" (cicCartuja), University of Seville - CSIC, Seville 41092, Spain
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3
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Matheny CJ, Qadota H, Bailey AO, Valdebenito-Silva S, Oberhauser AF, Benian GM. The myosin chaperone UNC-45 has an important role in maintaining the structure and function of muscle sarcomeres during adult aging. Mol Biol Cell 2024; 35:ar98. [PMID: 38809582 PMCID: PMC11244168 DOI: 10.1091/mbc.e23-12-0488] [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: 12/18/2023] [Revised: 04/26/2024] [Accepted: 05/21/2024] [Indexed: 05/30/2024] Open
Abstract
C. elegans undergo age-dependent declines in muscle organization and function, similar to human sarcopenia. The chaperone UNC-45 is required to fold myosin heads after translation and is likely used for refolding after thermally- or chemically-induced unfolding. UNC-45's TPR region binds HSP-90 and its UCS domain binds myosin heads. We observe early onset sarcopenia when UNC-45 is reduced at the beginning of adulthood. There is sequential decline of HSP-90, UNC-45, and MHC B myosin. A mutation in age-1 delays sarcopenia and loss of HSP-90, UNC-45, and myosin. UNC-45 undergoes age-dependent phosphorylation, and mass spectrometry reveals phosphorylation of six serines and two threonines, seven of which occur in the UCS domain. Additional expression of UNC-45 results in maintenance of MHC B myosin and suppression of A-band disorganization in old animals. Our results suggest that increased expression or activity of UNC-45 might be a strategy for prevention or treatment of sarcopenia.
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Affiliation(s)
| | - Hiroshi Qadota
- Department of Pathology, Emory University, Atlanta, GA 30322
| | - Aaron O Bailey
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77550
| | | | - Andres F Oberhauser
- Department of Neurobiology, University of Texas Medical Branch, Galveston, TX 77550
| | - Guy M Benian
- Department of Pathology, Emory University, Atlanta, GA 30322
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4
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Rrustemi T, Meyer K, Roske Y, Uyar B, Akalin A, Imami K, Ishihama Y, Daumke O, Selbach M. Pathogenic mutations of human phosphorylation sites affect protein-protein interactions. Nat Commun 2024; 15:3146. [PMID: 38605029 PMCID: PMC11009412 DOI: 10.1038/s41467-024-46794-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 03/11/2024] [Indexed: 04/13/2024] Open
Abstract
Despite their lack of a defined 3D structure, intrinsically disordered regions (IDRs) of proteins play important biological roles. Many IDRs contain short linear motifs (SLiMs) that mediate protein-protein interactions (PPIs), which can be regulated by post-translational modifications like phosphorylation. 20% of pathogenic missense mutations are found in IDRs, and understanding how such mutations affect PPIs is essential for unraveling disease mechanisms. Here, we employ peptide-based interaction proteomics to investigate 36 disease-associated mutations affecting phosphorylation sites. Our results unveil significant differences in interactomes between phosphorylated and non-phosphorylated peptides, often due to disrupted phosphorylation-dependent SLiMs. We focused on a mutation of a serine phosphorylation site in the transcription factor GATAD1, which causes dilated cardiomyopathy. We find that this phosphorylation site mediates interaction with 14-3-3 family proteins. Follow-up experiments reveal the structural basis of this interaction and suggest that 14-3-3 binding affects GATAD1 nucleocytoplasmic transport by masking a nuclear localisation signal. Our results demonstrate that pathogenic mutations of human phosphorylation sites can significantly impact protein-protein interactions, offering insights into potential molecular mechanisms underlying pathogenesis.
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Affiliation(s)
| | - Katrina Meyer
- Max Delbrück Center (MDC), Robert-Rössle-Str. 10, 13125, Berlin, Germany
- Max Planck Institute for Molecular Genetics, Ihnestraße 63, 14195, Berlin, Germany
| | - Yvette Roske
- Max Delbrück Center (MDC), Robert-Rössle-Str. 10, 13125, Berlin, Germany
| | - Bora Uyar
- Max Delbrück Center (MDC), Robert-Rössle-Str. 10, 13125, Berlin, Germany
| | - Altuna Akalin
- Max Delbrück Center (MDC), Robert-Rössle-Str. 10, 13125, Berlin, Germany
| | - Koshi Imami
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, 606-8501, Japan
- RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045, Kanagawa, Japan
| | - Yasushi Ishihama
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, 606-8501, Japan
| | - Oliver Daumke
- Max Delbrück Center (MDC), Robert-Rössle-Str. 10, 13125, Berlin, Germany
- Freie Universität Berlin, Institute of Chemistry and Biochemistry, Takustraße 6, Berlin, Germany
| | - Matthias Selbach
- Max Delbrück Center (MDC), Robert-Rössle-Str. 10, 13125, Berlin, Germany.
- Charité-Universitätsmedizin Berlin, 10117, Berlin, Germany.
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5
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Volkova A, Semenyuk P. Tyrosine phosphorylation of recombinant hirudin increases affinity to thrombin and antithrombotic activity. Proteins 2024; 92:329-342. [PMID: 37860993 DOI: 10.1002/prot.26616] [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: 06/22/2023] [Revised: 09/22/2023] [Accepted: 10/06/2023] [Indexed: 10/21/2023]
Abstract
Thrombin is one of the key enzymes of the blood coagulation system and a promising target for the development of anticoagulants. One of the most specific natural thrombin inhibitors is hirudin, contained in the salivary glands of medicinal leeches. The medicinal use of recombinant hirudin is limited because of the lack of sulfation on Tyr63, resulting in a 10-fold decrease in activity compared to native (sulfated) hirudin. In the present work, a set of hirudin derivatives was tested for affinity to thrombin: phospho-Tyr63, Tyr63(carboxymethyl)Phe, and Tyr63Glu mutants, which mimic Tyr63 sulfation and Gln65Glu mutant and lysine-succinylated hirudin, which enhance the overall negative charge of hirudin, as well as sulfo-hirudin and desulfo-hirudin as references. Using steered molecular dynamics simulations with subsequent umbrella sampling, phospho-hirudin was shown to exhibit the highest affinity to thrombin among all hirudin analogs, including native sulfo-hirudin; succinylated hirudin was also prospective. Phospho-hirudin exhibited the highest antithrombotic activity in in vitro assay in human plasma. Taking into account the modern methods for obtaining phospho-hirudin and succinylated hirudin, they are prospective as anticoagulants in clinical practice.
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Affiliation(s)
- Alina Volkova
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | - Pavel Semenyuk
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
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6
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Kapinos LE, Kalita J, Kassianidou E, Rencurel C, Lim RYH. Mechanism of exportin retention in the cell nucleus. J Cell Biol 2024; 223:e202306094. [PMID: 38241019 PMCID: PMC10798875 DOI: 10.1083/jcb.202306094] [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: 06/22/2023] [Revised: 11/06/2023] [Accepted: 12/07/2023] [Indexed: 01/22/2024] Open
Abstract
Exportin receptors are concentrated in the nucleus to transport essential cargoes out of it. A mislocalization of exportins to the cytoplasm is linked to disease. Hence, it is important to understand how their containment within the nucleus is regulated. Here, we have studied the nuclear efflux of exportin2 (cellular apoptosis susceptibility protein or CAS) that delivers karyopherinα (Kapα or importinα), the cargo adaptor for karyopherinβ1 (Kapβ1 or importinβ1), to the cytoplasm in a Ran guanosine triphosphate (RanGTP)-mediated manner. We show that the N-terminus of CAS attenuates the interaction of RanGTPase activating protein 1 (RanGAP1) with RanGTP to slow GTP hydrolysis, which suppresses CAS nuclear exit at nuclear pore complexes (NPCs). Strikingly, a single phosphomimetic mutation (T18D) at the CAS N-terminus is sufficient to abolish its nuclear retention and coincides with metastatic cellular behavior. Furthermore, downregulating Kapβ1 disrupts CAS nuclear retention, which highlights the balance between their respective functions that is essential for maintaining the Kapα transport cycle. Therefore, NPCs play a functional role in selectively partitioning exportins in the cell nucleus.
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Affiliation(s)
- Larisa E. Kapinos
- Biozentrum and the Swiss Nanoscience Institute, University of Basel Switzerland, Basel, Switzerland
| | - Joanna Kalita
- Biozentrum and the Swiss Nanoscience Institute, University of Basel Switzerland, Basel, Switzerland
| | - Elena Kassianidou
- Biozentrum and the Swiss Nanoscience Institute, University of Basel Switzerland, Basel, Switzerland
| | - Chantal Rencurel
- Biozentrum and the Swiss Nanoscience Institute, University of Basel Switzerland, Basel, Switzerland
| | - Roderick Y. H. Lim
- Biozentrum and the Swiss Nanoscience Institute, University of Basel Switzerland, Basel, Switzerland
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7
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Yu A, Nguyen DH, Nguyen TJ, Wang Z. A novel phosphorylation site involved in dissociating RAF kinase from the scaffolding protein 14-3-3 and disrupting RAF dimerization. J Biol Chem 2023; 299:105188. [PMID: 37625591 PMCID: PMC10520314 DOI: 10.1016/j.jbc.2023.105188] [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: 03/30/2023] [Revised: 08/01/2023] [Accepted: 08/14/2023] [Indexed: 08/27/2023] Open
Abstract
Rapidly accelerated fibrosarcoma (ARAF, BRAF, CRAF) kinase is central to the MAPK pathway (RAS-RAF-MEK-ERK). Inactive RAF kinase is believed to be monomeric, autoinhibited, and cytosolic, while activated RAF is recruited to the membrane via RAS-GTP, leading to the relief of autoinhibition, phosphorylation of key regulatory sites, and dimerization of RAF protomers. Although it is well known that active and inactive BRAF have differential phosphorylation sites that play a crucial role in regulating BRAF, key details are still missing. In this study, we report the characterization of a novel phosphorylation site, BRAFS732 (equivalent in CRAFS624), located in proximity to the C-terminus binding motif for the 14-3-3 scaffolding protein. At the C terminus, 14-3-3 binds to BRAFpS729 (CRAFpS621) and enhances RAF dimerization. We conducted mutational analysis of BRAFS732A/E and CRAFS624A/E and revealed that the phosphomimetic S→E mutant decreases 14-3-3 association and RAF dimerization. In normal cell signaling, dimerized RAF phosphorylates MEK1/2, which is observed in the phospho-deficient S→A mutant. Our results suggest that phosphorylation and dephosphorylation of this site fine-tune the association of 14-3-3 and RAF dimerization, ultimately impacting MEK phosphorylation. We further characterized the BRAF homodimer and BRAF:CRAF heterodimer and identified a correlation between phosphorylation of this site with drug sensitivity. Our work reveals a novel negative regulatory role for phosphorylation of BRAFS732 and CRAFS624 in decreasing 14-3-3 association, dimerization, and MEK phosphorylation. These findings provide insight into the regulation of the MAPK pathway and may have implications for cancers driven by mutations in the pathway.
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Affiliation(s)
- Alison Yu
- Department of Chemistry & Biochemistry, Rowan University, Glassboro, New Jersey, USA
| | - Duc Huy Nguyen
- Department of Chemistry & Biochemistry, Rowan University, Glassboro, New Jersey, USA
| | - Thomas Joseph Nguyen
- Department of Chemistry & Biochemistry, Rowan University, Glassboro, New Jersey, USA
| | - Zhihong Wang
- Department of Chemistry & Biochemistry, Rowan University, Glassboro, New Jersey, USA.
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8
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Lototskaja E, Liblekas L, Piirsoo M, Laaneväli A, Ibragimov R, Piirsoo A. Phosphorylation of E2 Serine Residue 402 Is Required for the Transcription and Replication of the HPV5 Genome. J Virol 2023; 97:e0064323. [PMID: 37272841 PMCID: PMC10308906 DOI: 10.1128/jvi.00643-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Accepted: 05/13/2023] [Indexed: 06/06/2023] Open
Abstract
Cutaneous human papillomavirus type 5 (HPV5) belongs to the supposedly oncogenic β-HPVs associated with specific types of skin and oral cavity cancers. Three viral proteins, namely, helicase E1 and transcription factors E2 and E8^E2, are master regulators of the viral life cycle. HPV5 E2 is a transcriptional activator that also participates in the E1-dependent replication and nuclear retention of the viral genome, whereas E8^E2 counterbalances the activity of E2 and inhibits HPV transcription and replication. In the present study, we demonstrate that the HPV5 E2 protein is extensively phosphorylated by cellular protein kinases, and serine residue 402 (S402) is the highest scoring phosphoacceptor site. This residue is located within a motif conserved among many β-HPVs and in the oncogenic HPV31 α-type. Using the nonphosphorylatable and phosphomimetic mutants, we demonstrate that phosphorylation of the E2 S402 residue is required for the transcription and replication of the HPV5 genome in U2OS cells and human primary keratinocytes. Mechanistically, the E2-S402-phopshodeficient protein is unable to trigger viral gene transcription and has an impaired ability to support E1-dependent replication, but the respective E8^E2-S213 mutant displays no phenotype. However, phosphorylation of the E2 S402 residue has no impact on the E2 stability, subcellular localization, self-assembly, DNA-binding capacity, and affinity to the E1 and BRD4 proteins. Further studies are needed to identify the protein kinase(s) responsible for this phosphorylation. IMPORTANCE Human papillomavirus type 5 (HPV5) may play a role in the development of specific types of cutaneous and head and neck cancers. The persistence of the HPV genome in host cells depends on the activity of its proteins, namely, a helicase E1 and transcription/replication factor E2. The latter also facilitates the attachment of episomal viral genomes to host cell chromosomes. In the present study, we show that the HPV5 E2 protein is extensively phosphorylated by host cell protein kinases, and we identify serine residue 402 as the highest scoring phosphoacceptor site of E2. We demonstrate that the replication of the HPV5 genome may be blocked by a single point mutation that prevents phosphorylation of this serine residue and switches off the transcriptional activity of the E2 protein. The present study contributes to a better understanding of β-HPV5 replication and its regulation by host cell protein kinases.
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Affiliation(s)
| | - Lisett Liblekas
- Institute of Technology, University of Tartu, Tartu, Estonia
| | - Marko Piirsoo
- Institute of Technology, University of Tartu, Tartu, Estonia
| | | | | | - Alla Piirsoo
- Institute of Technology, University of Tartu, Tartu, Estonia
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9
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Matsui H, Ito S, Matsui H, Ito J, Gabdulkhaev R, Hirose M, Yamanaka T, Koyama A, Kato T, Tanaka M, Uemura N, Matsui N, Hirokawa S, Yoshihama M, Shimozawa A, Kubo SI, Iwasaki K, Hasegawa M, Takahashi R, Hirai K, Kakita A, Onodera O. Phosphorylation of α-synuclein at T64 results in distinct oligomers and exerts toxicity in models of Parkinson's disease. Proc Natl Acad Sci U S A 2023; 120:e2214652120. [PMID: 37252975 PMCID: PMC10266017 DOI: 10.1073/pnas.2214652120] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 04/16/2023] [Indexed: 06/01/2023] Open
Abstract
α-Synuclein accumulates in Lewy bodies, and this accumulation is a pathological hallmark of Parkinson's disease (PD). Previous studies have indicated a causal role of α-synuclein in the pathogenesis of PD. However, the molecular and cellular mechanisms of α-synuclein toxicity remain elusive. Here, we describe a novel phosphorylation site of α-synuclein at T64 and the detailed characteristics of this post-translational modification. T64 phosphorylation was enhanced in both PD models and human PD brains. T64D phosphomimetic mutation led to distinct oligomer formation, and the structure of the oligomer was similar to that of α-synuclein oligomer with A53T mutation. Such phosphomimetic mutation induced mitochondrial dysfunction, lysosomal disorder, and cell death in cells and neurodegeneration in vivo, indicating a pathogenic role of α-synuclein phosphorylation at T64 in PD.
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Affiliation(s)
- Hideaki Matsui
- Department of Neuroscience of Disease, Center for Transdisciplinary Research, Niigata University, Niigata951-8585, Japan
- Department of Neuroscience of Disease, Brain Research Institute, Niigata University, Niigata951-8585, Japan
| | - Shinji Ito
- Medical Research Support Center, Graduate School of Medicine, Kyoto University, Kyoto606-8501, Japan
| | - Hideki Matsui
- Neuroscience Drug Discovery Unit, Research, Takeda Pharmaceutical Company Limited, Fujisawa251-8555, Japan
| | - Junko Ito
- Department of Pathology, Brain Research Institute, Niigata University, Niigata951-8585, Japan
| | - Ramil Gabdulkhaev
- Department of Pathology, Brain Research Institute, Niigata University, Niigata951-8585, Japan
| | - Mika Hirose
- Institute for Protein Research, Osaka University, Suita, Osaka565-0871, Japan
| | - Tomoyuki Yamanaka
- Department of Neuroscience of Disease, Brain Research Institute, Niigata University, Niigata951-8585, Japan
| | - Akihide Koyama
- Department of Legal Medicine, Niigata University Graduate School of Medical and Dental Science, Niigata951-8585, Japan
| | - Taisuke Kato
- Department of System Pathology for Neurological Disorders, Brain Science Branch, Brain Research Institute, Niigata University, Niigata951-8585, Japan
| | - Maiko Tanaka
- Neuroscience Drug Discovery Unit, Research, Takeda Pharmaceutical Company Limited, Fujisawa251-8555, Japan
| | - Norihito Uemura
- Department of Neurology, Kyoto University Graduate School of Medicine, Kyoto University, Kyoto606-8507, Japan
| | - Noriko Matsui
- Department of Neuroscience of Disease, Center for Transdisciplinary Research, Niigata University, Niigata951-8585, Japan
- Department of Neuroscience of Disease, Brain Research Institute, Niigata University, Niigata951-8585, Japan
| | - Sachiko Hirokawa
- Department of Neurology, Clinical Neuroscience Branch, Brain Research Institute, Niigata University, Niigata951-8585, Japan
| | - Maki Yoshihama
- Frontier Science Research Center, University of Miyazaki, Miyazaki889-1692, Japan
| | - Aki Shimozawa
- Dementia Research Project, Tokyo Metropolitan Institute of Medical Science, Tokyo156-8506, Japan
| | - Shin-ichiro Kubo
- Neuroscience Drug Discovery Unit, Research, Takeda Pharmaceutical Company Limited, Fujisawa251-8555, Japan
- Department of Neurology, Parkinson's Disease Center, Eisei Hospital, Tokyo193-0942, Japan
| | - Kenji Iwasaki
- Institute for Protein Research, Osaka University, Suita, Osaka565-0871, Japan
- Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance, University of Tsukuba, Tsukuba305-8577, Japan
| | - Masato Hasegawa
- Dementia Research Project, Tokyo Metropolitan Institute of Medical Science, Tokyo156-8506, Japan
| | - Ryosuke Takahashi
- Department of Neurology, Kyoto University Graduate School of Medicine, Kyoto University, Kyoto606-8507, Japan
| | - Keisuke Hirai
- Neuroscience Drug Discovery Unit, Research, Takeda Pharmaceutical Company Limited, Fujisawa251-8555, Japan
| | - Akiyoshi Kakita
- Department of Pathology, Brain Research Institute, Niigata University, Niigata951-8585, Japan
| | - Osamu Onodera
- Department of Neurology, Clinical Neuroscience Branch, Brain Research Institute, Niigata University, Niigata951-8585, Japan
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10
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Hong X, Lv J, Li Z, Xiong Y, Zhang J, Chen HF. Sequence-based machine learning method for predicting the effects of phosphorylation on protein-protein interactions. Int J Biol Macromol 2023; 243:125233. [PMID: 37290543 DOI: 10.1016/j.ijbiomac.2023.125233] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 06/02/2023] [Accepted: 06/03/2023] [Indexed: 06/10/2023]
Abstract
Protein phosphorylation, catalyzed by kinases, is an important biochemical process, which plays an essential role in multiple cell signaling pathways. Meanwhile, protein-protein interactions (PPI) constitute the signaling pathways. Abnormal phosphorylation status on protein can regulate protein functions through PPI to evoke severe diseases, such as Cancer and Alzheimer's disease. Due to the limited experimental evidence and high costs to experimentally identify novel evidence of phosphorylation regulation on PPI, it is necessary to develop a high-accuracy and user-friendly artificial intelligence method to predict phosphorylation effect on PPI. Here, we proposed a novel sequence-based machine learning method named PhosPPI, which achieved better identification performance (Accuracy and AUC) than other competing predictive methods of Betts, HawkDock and FoldX. PhosPPI is now freely available in web server (https://phosppi.sjtu.edu.cn/). This tool can help the user to identify functional phosphorylation sites affecting PPI and explore phosphorylation-associated disease mechanism and drug development.
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Affiliation(s)
- Xiaokun Hong
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jiyang Lv
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Zhengxin Li
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yi Xiong
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jian Zhang
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao-Tong University School of Medicine (SJTU-SM), Shanghai 200025, China.
| | - Hai-Feng Chen
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China.
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11
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Varshney N, Mishra AK. Deep Learning in Phosphoproteomics: Methods and Application in Cancer Drug Discovery. Proteomes 2023; 11:proteomes11020016. [PMID: 37218921 DOI: 10.3390/proteomes11020016] [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: 02/13/2023] [Revised: 04/24/2023] [Accepted: 04/25/2023] [Indexed: 05/24/2023] Open
Abstract
Protein phosphorylation is a key post-translational modification (PTM) that is a central regulatory mechanism of many cellular signaling pathways. Several protein kinases and phosphatases precisely control this biochemical process. Defects in the functions of these proteins have been implicated in many diseases, including cancer. Mass spectrometry (MS)-based analysis of biological samples provides in-depth coverage of phosphoproteome. A large amount of MS data available in public repositories has unveiled big data in the field of phosphoproteomics. To address the challenges associated with handling large data and expanding confidence in phosphorylation site prediction, the development of many computational algorithms and machine learning-based approaches have gained momentum in recent years. Together, the emergence of experimental methods with high resolution and sensitivity and data mining algorithms has provided robust analytical platforms for quantitative proteomics. In this review, we compile a comprehensive collection of bioinformatic resources used for the prediction of phosphorylation sites, and their potential therapeutic applications in the context of cancer.
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Affiliation(s)
- Neha Varshney
- Division of Biological Sciences, Department of Cellular and Molecular Medicine, University of California, San Diego, CA 93093, USA
- Ludwig Institute for Cancer Research, La Jolla, CA 92093, USA
| | - Abhinava K Mishra
- Molecular, Cellular and Developmental Biology Department, University of California, Santa Barbara, CA 93106, USA
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12
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Hauswirth P, Graber P, Buczak K, Mancuso RV, Schenk SH, Nüesch JPF, Huwyler J. Design and Characterization of Mutated Variants of the Oncotoxic Parvoviral Protein NS1. Viruses 2023; 15:209. [PMID: 36680249 PMCID: PMC9866090 DOI: 10.3390/v15010209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Revised: 12/30/2022] [Accepted: 01/08/2023] [Indexed: 01/13/2023] Open
Abstract
Oncotoxic proteins such as the non-structural protein 1 (NS1), a constituent of the rodent parvovirus H1 (H1-PV), offer a novel approach for treatment of tumors that are refractory to other treatments. In the present study, mutated NS1 variants were designed and tested with respect to their oncotoxic potential in human hepatocellular carcinoma cell lines. We introduced single point mutations of previously described important residues of the wild-type NS1 protein and a deletion of 114 base pairs localized within the N-terminal domain of NS1. Cell-viability screening with HepG2 and Hep3B hepatocarcinoma cells transfected with the constructed NS1-mutants led to identification of the single-amino acid NS1-mutant NS1-T585E, which led to a 30% decrease in cell viability as compared to NS1 wildtype. Using proteomics analysis, we could identify new interaction partners and signaling pathways of NS1. We could thus identify new oncotoxic NS1 variants and gain insight into the modes of action of NS1, which is exclusively toxic to human cancer cells. Our in-vitro studies provide mechanistic explanations for the observed oncolytic effects. Expression of NS1 variants had no effect on cell viability in NS1 unresponsive control HepG2 cells or primary mouse hepatocytes. The availability of new NS1 variants in combination with a better understanding of their modes of action offers new possibilities for the design of innovative cancer treatment strategies.
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Affiliation(s)
- Patrick Hauswirth
- Division of Pharmaceutical Technology, Department of Pharmaceutical Sciences, University of Basel, 4056 Basel, Switzerland
| | - Philipp Graber
- Division of Pharmaceutical Technology, Department of Pharmaceutical Sciences, University of Basel, 4056 Basel, Switzerland
| | - Katarzyna Buczak
- Proteomics Core Facility, Biozentrum, University of Basel, 4056 Basel, Switzerland
| | - Riccardo Vincenzo Mancuso
- Division of Clinical Pharmacology & Toxicology, University Hospital of Basel, University of Basel, 4055 Basel, Switzerland
- Division of Molecular Pharmacy, Department of Pharmaceutical Sciences, University of Basel, 4056 Basel, Switzerland
| | - Susanne Heidi Schenk
- Division of Pharmaceutical Technology, Department of Pharmaceutical Sciences, University of Basel, 4056 Basel, Switzerland
| | - Jürg P. F. Nüesch
- Infection, Inflammation and Cancer Program, Division of Tumor Virology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Jörg Huwyler
- Division of Pharmaceutical Technology, Department of Pharmaceutical Sciences, University of Basel, 4056 Basel, Switzerland
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13
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Kuzdere T, Flury V, Schalch T, Iesmantavicius V, Hess D, Bühler M. Differential phosphorylation of Clr4 SUV39H by Cdk1 accompanies a histone H3 methylation switch that is essential for gametogenesis. EMBO Rep 2022; 24:e55928. [PMID: 36408846 PMCID: PMC9827552 DOI: 10.15252/embr.202255928] [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: 08/08/2022] [Revised: 10/18/2022] [Accepted: 10/27/2022] [Indexed: 11/22/2022] Open
Abstract
Methylation of histone H3 at lysine 9 (H3K9) is a hallmark of heterochromatin that plays crucial roles in gene silencing, genome stability, and chromosome segregation. In Schizosaccharomyces pombe, Clr4 mediates both di- and tri-methylation of H3K9. Although H3K9 methylation has been intensely studied in mitotic cells, its role during sexual differentiation remains unclear. Here, we map H3K9 methylation genome-wide during meiosis and show that constitutive heterochromatin temporarily loses H3K9me2 and becomes H3K9me3 when cells commit to meiosis. Cells lacking the ability to tri-methylate H3K9 exhibit meiotic chromosome segregation defects. Finally, the H3K9 methylation switch is accompanied by differential phosphorylation of Clr4 by the cyclin-dependent kinase Cdk1. Our results suggest that a conserved master regulator of the cell cycle controls the specificity of an H3K9 methyltransferase to prevent ectopic H3K9 methylation and to ensure faithful gametogenesis.
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Affiliation(s)
- Tahsin Kuzdere
- Friedrich Miescher Institute for Biomedical ResearchBaselSwitzerland,University of BaselBaselSwitzerland
| | - Valentin Flury
- Friedrich Miescher Institute for Biomedical ResearchBaselSwitzerland,University of BaselBaselSwitzerland
| | - Thomas Schalch
- Department of Molecular and Cell Biology, Leicester Institute of Structural and Chemical BiologyUniversity of LeicesterLeicesterUK
| | | | - Daniel Hess
- Friedrich Miescher Institute for Biomedical ResearchBaselSwitzerland
| | - Marc Bühler
- Friedrich Miescher Institute for Biomedical ResearchBaselSwitzerland,University of BaselBaselSwitzerland
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14
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Phosphorylation disrupts long-distance electron transport in cytochrome c. Nat Commun 2022; 13:7100. [PMID: 36402842 PMCID: PMC9675734 DOI: 10.1038/s41467-022-34809-1] [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: 07/18/2022] [Accepted: 11/08/2022] [Indexed: 11/21/2022] Open
Abstract
It has been recently shown that electron transfer between mitochondrial cytochrome c and the cytochrome c1 subunit of the cytochrome bc1 can proceed at long-distance through the aqueous solution. Cytochrome c is thought to adjust its activity by changing the affinity for its partners via Tyr48 phosphorylation, but it is unknown how it impacts the nanoscopic environment, interaction forces, and long-range electron transfer. Here, we constrain the orientation and separation between cytochrome c1 and cytochrome c or the phosphomimetic Y48pCMF cytochrome c, and deploy an array of single-molecule, bulk, and computational methods to investigate the molecular mechanism of electron transfer regulation by cytochrome c phosphorylation. We demonstrate that phosphorylation impairs long-range electron transfer, shortens the long-distance charge conduit between the partners, strengthens their interaction, and departs it from equilibrium. These results unveil a nanoscopic view of the interaction between redox protein partners in electron transport chains and its mechanisms of regulation.
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15
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Molecular Dynamics Simulations to Decipher the Role of Phosphorylation of SARS-CoV-2 Nonstructural Proteins (nsps) in Viral Replication. Viruses 2022; 14:v14112436. [PMID: 36366534 PMCID: PMC9693435 DOI: 10.3390/v14112436] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 10/19/2022] [Accepted: 10/27/2022] [Indexed: 11/06/2022] Open
Abstract
Protein phosphorylation is a post-translational modification that enables various cellular activities and plays essential roles in protein interactions. Phosphorylation is an important process for the replication of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). To shed more light on the effects of phosphorylation, we used an ensemble of neural networks to predict potential kinases that might phosphorylate SARS-CoV-2 nonstructural proteins (nsps) and molecular dynamics (MD) simulations to investigate the effects of phosphorylation on nsps structure, which could be a potential inhibitory target to attenuate viral replication. Eight target candidate sites were found as top-ranked phosphorylation sites of SARS-CoV-2. During the process of molecular dynamics (MD) simulation, the root-mean-square deviation (RMSD) analysis was used to measure conformational changes in each nsps. Root-mean-square fluctuation (RMSF) was employed to measure the fluctuation in each residue of 36 systems considered, allowing us to evaluate the most flexible regions. These analysis shows that there are significant structural deviations in the residues namely nsp1 THR 72, nsp2 THR 73, nsp3 SER 64, nsp4 SER 81, nsp4 SER 455, nsp5 SER284, nsp6 THR 238, and nsp16 SER 132. The identified list of residues suggests how phosphorylation affects SARS-CoV-2 nsps function and stability. This research also suggests that kinase inhibitors could be a possible component for evaluating drug binding studies, which are crucial in therapeutic discovery research.
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16
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Olloqui-Sariego JL, Pérez-Mejías G, Márquez I, Guerra-Castellano A, Calvente JJ, De la Rosa MA, Andreu R, Díaz-Moreno I. Electric field-induced functional changes in electrode-immobilized mutant species of human cytochrome c. BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 2022; 1863:148570. [PMID: 35643148 DOI: 10.1016/j.bbabio.2022.148570] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 04/21/2022] [Accepted: 05/20/2022] [Indexed: 06/15/2023]
Abstract
Post-translational modifications and naturally occurring mutations of cytochrome c have been recognized as a regulatory mechanism to control its biology. In this work, we investigate the effect of such in vivo chemical modifications of human cytochrome c on its redox properties in the adsorbed state onto an electrode. In particular, tyrosines 48 and 97 have been replaced by the non-canonical amino acid p-carboxymethyl-L-phenylalanine (pCMF), thus mimicking tyrosine phosphorylation. Additionally, tyrosine 48 has been replaced by a histidine producing the natural Y48H pathogenic mutant. Thermodynamics and kinetics of the interfacial electron transfer of wild-type cytochrome c and herein produced variants, adsorbed electrostatically under different local interfacial electric fields, were determined by means of variable temperature cyclic film voltammetry. It is shown that non-native cytochrome c variants immobilized under a low interfacial electric field display redox thermodynamics and kinetics similar to those of wild-type cytochrome c. However, upon increasing the strength of the electric field, the redox thermodynamics and kinetics of the modified proteins markedly differ from those of the wild-type species. The mutations promote stabilization of the oxidized form and a significant increase in the activation enthalpy values that can be ascribed to a subtle distortion of the heme cofactor and/or difference of the amino acid rearrangements rather than to a coarse protein structural change. Overall, these results point to a combined effect of the single point mutations at positions 48 and 97 and the strength of electrostatic binding on the regulatory mechanism of mitochondrial membrane activity, when acting as a redox shuttle protein.
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Affiliation(s)
- José Luis Olloqui-Sariego
- Departamento de Química Física, Universidad de Sevilla, Profesor García González, 1, 41012 Sevilla, Spain
| | - Gonzalo Pérez-Mejías
- Instituto de Investigaciones Químicas, cicCartuja, Universidad de Sevilla, Consejo Superior de Investigaciones Científicas (CSIC), Américo Vespucio 49, 41092 Sevilla, (Spain)
| | - Inmaculada Márquez
- Departamento de Química Física, Universidad de Sevilla, Profesor García González, 1, 41012 Sevilla, Spain; Instituto de Investigaciones Químicas, cicCartuja, Universidad de Sevilla, Consejo Superior de Investigaciones Científicas (CSIC), Américo Vespucio 49, 41092 Sevilla, (Spain)
| | - Alejandra Guerra-Castellano
- Instituto de Investigaciones Químicas, cicCartuja, Universidad de Sevilla, Consejo Superior de Investigaciones Científicas (CSIC), Américo Vespucio 49, 41092 Sevilla, (Spain)
| | - Juan José Calvente
- Departamento de Química Física, Universidad de Sevilla, Profesor García González, 1, 41012 Sevilla, Spain
| | - Miguel A De la Rosa
- Instituto de Investigaciones Químicas, cicCartuja, Universidad de Sevilla, Consejo Superior de Investigaciones Científicas (CSIC), Américo Vespucio 49, 41092 Sevilla, (Spain)
| | - Rafael Andreu
- Departamento de Química Física, Universidad de Sevilla, Profesor García González, 1, 41012 Sevilla, Spain
| | - Irene Díaz-Moreno
- Instituto de Investigaciones Químicas, cicCartuja, Universidad de Sevilla, Consejo Superior de Investigaciones Científicas (CSIC), Américo Vespucio 49, 41092 Sevilla, (Spain).
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17
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Pawara R, Ahmad I, Nayak D, Belamkar S, Surana S, Kundu CN, Patil C, Patel H. Design and synthesis of the novel, selective WZ4002 analogue as EGFR-L858R/T790M tyrosine kinase inhibitors for targeted drug therapy in non-small-cell lung cancer (NSCLC). J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2021.132313] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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18
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Willis SD, Hanley SE, Doyle SJ, Beluch K, Strich R, Cooper KF. Cyclin C-Cdk8 Kinase Phosphorylation of Rim15 Prevents the Aberrant Activation of Stress Response Genes. Front Cell Dev Biol 2022; 10:867257. [PMID: 35433688 PMCID: PMC9008841 DOI: 10.3389/fcell.2022.867257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 02/22/2022] [Indexed: 11/13/2022] Open
Abstract
Cells facing adverse environmental cues respond by inducing signal transduction pathways resulting in transcriptional reprograming. In the budding yeast Saccharomyces cerevisiae, nutrient deprivation stimulates stress response gene (SRG) transcription critical for entry into either quiescence or gametogenesis depending on the cell type. The induction of a subset of SRGs require nuclear translocation of the conserved serine-threonine kinase Rim15. However, Rim15 is also present in unstressed nuclei suggesting that additional activities are required to constrain its activity in the absence of stress. Here we show that Rim15 is directly phosphorylated by cyclin C-Cdk8, the conserved kinase module of the Mediator complex. Several results indicate that Cdk8-dependent phosphorylation prevents Rim15 activation in unstressed cells. First, Cdk8 does not control Rim15 subcellular localization and rim15∆ is epistatic to cdk8∆ with respect to SRG transcription and the execution of starvation programs required for viability. Next, Cdk8 phosphorylates a residue in the conserved PAS domain in vitro. This modification appears important as introducing a phosphomimetic at Cdk8 target residues reduces Rim15 activity. Moreover, the Rim15 phosphomimetic only compromises cell viability in stresses that induce cyclin C destruction as well as entrance into meiosis. Taken together, these findings suggest a model in which Cdk8 phosphorylation contributes to Rim15 repression whilst it cycles through the nucleus. Cyclin C destruction in response to stress inactivates Cdk8 which in turn stimulates Rim15 to maximize SRG transcription and cell survival.
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19
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Kozeleková A, Náplavová A, Brom T, Gašparik N, Šimek J, Houser J, Hritz J. Phosphorylated and Phosphomimicking Variants May Differ—A Case Study of 14-3-3 Protein. Front Chem 2022; 10:835733. [PMID: 35321476 PMCID: PMC8935074 DOI: 10.3389/fchem.2022.835733] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 02/14/2022] [Indexed: 12/12/2022] Open
Abstract
Protein phosphorylation is a critical mechanism that biology uses to govern cellular processes. To study the impact of phosphorylation on protein properties, a fully and specifically phosphorylated sample is required although not always achievable. Commonly, this issue is overcome by installing phosphomimicking mutations at the desired site of phosphorylation. 14-3-3 proteins are regulatory protein hubs that interact with hundreds of phosphorylated proteins and modulate their structure and activity. 14-3-3 protein function relies on its dimeric nature, which is controlled by Ser58 phosphorylation. However, incomplete Ser58 phosphorylation has obstructed the detailed study of its effect so far. In the present study, we describe the full and specific phosphorylation of 14-3-3ζ protein at Ser58 and we compare its characteristics with phosphomimicking mutants that have been used in the past (S58E/D). Our results show that in case of the 14-3-3 proteins, phosphomimicking mutations are not a sufficient replacement for phosphorylation. At physiological concentrations of 14-3-3ζ protein, the dimer-monomer equilibrium of phosphorylated protein is much more shifted towards monomers than that of the phosphomimicking mutants. The oligomeric state also influences protein properties such as thermodynamic stability and hydrophobicity. Moreover, phosphorylation changes the localization of 14-3-3ζ in HeLa and U251 human cancer cells. In summary, our study highlights that phosphomimicking mutations may not faithfully represent the effects of phosphorylation on the protein structure and function and that their use should be justified by comparing to the genuinely phosphorylated counterpart.
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Affiliation(s)
- Aneta Kozeleková
- Central European Institute of Technology, Masaryk University, Brno, Czechia
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czechia
| | | | - Tomáš Brom
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czechia
| | - Norbert Gašparik
- Central European Institute of Technology, Masaryk University, Brno, Czechia
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czechia
| | - Jan Šimek
- Central European Institute of Technology, Masaryk University, Brno, Czechia
| | - Josef Houser
- Central European Institute of Technology, Masaryk University, Brno, Czechia
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czechia
| | - Jozef Hritz
- Central European Institute of Technology, Masaryk University, Brno, Czechia
- Department of Chemistry, Faculty of Science, Masaryk University, Brno, Czechia
- *Correspondence: Jozef Hritz,
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20
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Lateef OM, Akintubosun MO, Olaoba OT, Samson SO, Adamczyk M. Making Sense of "Nonsense" and More: Challenges and Opportunities in the Genetic Code Expansion, in the World of tRNA Modifications. Int J Mol Sci 2022; 23:938. [PMID: 35055121 PMCID: PMC8779196 DOI: 10.3390/ijms23020938] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 01/10/2022] [Accepted: 01/12/2022] [Indexed: 01/09/2023] Open
Abstract
The evolutional development of the RNA translation process that leads to protein synthesis based on naturally occurring amino acids has its continuation via synthetic biology, the so-called rational bioengineering. Genetic code expansion (GCE) explores beyond the natural translational processes to further enhance the structural properties and augment the functionality of a wide range of proteins. Prokaryotic and eukaryotic ribosomal machinery have been proven to accept engineered tRNAs from orthogonal organisms to efficiently incorporate noncanonical amino acids (ncAAs) with rationally designed side chains. These side chains can be reactive or functional groups, which can be extensively utilized in biochemical, biophysical, and cellular studies. Genetic code extension offers the contingency of introducing more than one ncAA into protein through frameshift suppression, multi-site-specific incorporation of ncAAs, thereby increasing the vast number of possible applications. However, different mediating factors reduce the yield and efficiency of ncAA incorporation into synthetic proteins. In this review, we comment on the recent advancements in genetic code expansion to signify the relevance of systems biology in improving ncAA incorporation efficiency. We discuss the emerging impact of tRNA modifications and metabolism in protein design. We also provide examples of the latest successful accomplishments in synthetic protein therapeutics and show how codon expansion has been employed in various scientific and biotechnological applications.
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Affiliation(s)
- Olubodun Michael Lateef
- Faculty of Chemistry, Warsaw University of Technology, 00-664 Warsaw, Poland; (O.M.L.); (M.O.A.); (S.O.S.)
| | | | - Olamide Tosin Olaoba
- Laboratory of Functional and Structural Biochemistry, Federal University of Sao Carlos, Sao Carlos 13565-905, SP, Brazil;
| | - Sunday Ocholi Samson
- Faculty of Chemistry, Warsaw University of Technology, 00-664 Warsaw, Poland; (O.M.L.); (M.O.A.); (S.O.S.)
| | - Malgorzata Adamczyk
- Faculty of Chemistry, Warsaw University of Technology, 00-664 Warsaw, Poland; (O.M.L.); (M.O.A.); (S.O.S.)
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21
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Li X, Wang C, Peng T, Chai Z, Ni D, Liu Y, Zhang J, Chen T, Lu S. Atomic-scale insights into allosteric inhibition and evolutional rescue mechanism of Streptococcus thermophilus Cas9 by the anti-CRISPR protein AcrIIA6. Comput Struct Biotechnol J 2021; 19:6108-6124. [PMID: 34900128 PMCID: PMC8632846 DOI: 10.1016/j.csbj.2021.11.010] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 11/10/2021] [Accepted: 11/11/2021] [Indexed: 12/26/2022] Open
Abstract
CRISPR-Cas systems are prokaryotic adaptive immunity against invading phages and plasmids. Phages have evolved diverse protein inhibitors of CRISPR-Cas systems, called anti-CRISPR (Acr) proteins, to neutralize this CRISPR machinery. In response, bacteria have co-evolved Cas variants to escape phage's anti-CRISPR strategies, called anti-anti-CRISPR systems. Here we explore the anti-CRISPR allosteric inhibition and anti-anti-CRISPR rescue mechanisms between Streptococcus thermophilus Cas9 (St1Cas9) and the anti-CRISPR protein AcrIIA6 at the atomic level, by generating mutants of key residues in St1Cas9. Extensive unbiased molecular dynamics simulations show that the functional motions of St1Cas9 in the presence of AcrIIA6 differ substantially from those of St1Cas9 alone. AcrIIA6 binding triggers a shift of St1Cas9 conformational ensemble towards a less catalytically competent state; this state significantly compromises protospacer adjacent motif (PAM) recognition and nuclease activity by altering interdependently conformational dynamics and allosteric signals among nuclease domains, PAM-interacting (PI) regions, and AcrIIA6 binding motifs. Via in vitro DNA cleavage assays, we further elucidate the rescue mechanism of efficiently escaping AcrIIA6 inhibition harboring St1Cas9 triple mutations (G993K/K1008M/K1010E) in the PI domain and identify the evolutionary landscape of such mutational escape within species. Our results provide mechanistic insights into Acr proteins as natural brakes for the CRISPR-Cas systems and a promising potential for the design of allosteric Acr peptidomimetics.
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Affiliation(s)
- Xinyi Li
- Department of Cardiology, Changzheng Hospital, Naval Medical University, Shanghai 200003, China
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China
| | - Chengxiang Wang
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China
| | - Ting Peng
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China
| | - Zongtao Chai
- Department of Hepatic Surgery VI, Eastern Hepatobiliary Surgery Hospital, Naval Medical University, Shanghai 200438, China
| | - Duan Ni
- The Charles Perkins Centre, University of Sydney, Sydney, NSW 2006, Australia
| | - Yaqin Liu
- Medicinal Chemistry and Bioinformatics Centre, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China
| | - Jian Zhang
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China
- Medicinal Chemistry and Bioinformatics Centre, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China
| | - Ting Chen
- Department of Cardiology, Changzheng Hospital, Naval Medical University, Shanghai 200003, China
| | - Shaoyong Lu
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China
- Medicinal Chemistry and Bioinformatics Centre, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China
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22
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Structural Insights into Protein Regulation by Phosphorylation and Substrate Recognition of Protein Kinases/Phosphatases. Life (Basel) 2021; 11:life11090957. [PMID: 34575106 PMCID: PMC8467178 DOI: 10.3390/life11090957] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Revised: 09/05/2021] [Accepted: 09/10/2021] [Indexed: 12/30/2022] Open
Abstract
Protein phosphorylation is one of the most widely observed and important post-translational modification (PTM) processes. Protein phosphorylation is regulated by protein kinases, each of which covalently attaches a phosphate group to an amino acid side chain on a serine (Ser), threonine (Thr), or tyrosine (Tyr) residue of a protein, and by protein phosphatases, each of which, conversely, removes a phosphate group from a phosphoprotein. These reversible enzyme activities provide a regulatory mechanism by activating or deactivating many diverse functions of proteins in various cellular processes. In this review, their structures and substrate recognition are described and summarized, focusing on Ser/Thr protein kinases and protein Ser/Thr phosphatases, and the regulation of protein structures by phosphorylation. The studies reviewed here and the resulting information could contribute to further structural, biochemical, and combined studies on the mechanisms of protein phosphorylation and to drug discovery approaches targeting protein kinases or protein phosphatases.
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González‐Arzola K, Guerra‐Castellano A, Rivero‐Rodríguez F, Casado‐Combreras MÁ, Pérez‐Mejías G, Díaz‐Quintana A, Díaz‐Moreno I, De la Rosa MA. Mitochondrial cytochrome c shot towards histone chaperone condensates in the nucleus. FEBS Open Bio 2021; 11:2418-2440. [PMID: 33938164 PMCID: PMC8409293 DOI: 10.1002/2211-5463.13176] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 04/26/2021] [Indexed: 12/15/2022] Open
Abstract
Despite mitochondria being key for the control of cell homeostasis and fate, their role in DNA damage response is usually just regarded as an apoptotic trigger. However, growing evidence points to mitochondrial factors modulating nuclear functions. Remarkably, after DNA damage, cytochrome c (Cc) interacts in the cell nucleus with a variety of well-known histone chaperones, whose activity is competitively inhibited by the haem protein. As nuclear Cc inhibits the nucleosome assembly/disassembly activity of histone chaperones, it might indeed affect chromatin dynamics and histone deposition on DNA. Several histone chaperones actually interact with Cc Lys residues through their acidic regions, which are also involved in heterotypic interactions leading to liquid-liquid phase transitions responsible for the assembly of nuclear condensates, including heterochromatin. This relies on dynamic histone-DNA interactions that can be modulated by acetylation of specific histone Lys residues. Thus, Cc may have a major regulatory role in DNA repair by fine-tuning nucleosome assembly activity and likely nuclear condensate formation.
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Affiliation(s)
- Katiuska González‐Arzola
- Institute for Chemical Research (IIQ)Scientific Research Centre Isla de la Cartuja (cicCartuja)University of Seville – CSICSpain
| | - Alejandra Guerra‐Castellano
- Institute for Chemical Research (IIQ)Scientific Research Centre Isla de la Cartuja (cicCartuja)University of Seville – CSICSpain
| | - Francisco Rivero‐Rodríguez
- Institute for Chemical Research (IIQ)Scientific Research Centre Isla de la Cartuja (cicCartuja)University of Seville – CSICSpain
| | - Miguel Á. Casado‐Combreras
- Institute for Chemical Research (IIQ)Scientific Research Centre Isla de la Cartuja (cicCartuja)University of Seville – CSICSpain
| | - Gonzalo Pérez‐Mejías
- Institute for Chemical Research (IIQ)Scientific Research Centre Isla de la Cartuja (cicCartuja)University of Seville – CSICSpain
| | - Antonio Díaz‐Quintana
- Institute for Chemical Research (IIQ)Scientific Research Centre Isla de la Cartuja (cicCartuja)University of Seville – CSICSpain
| | - Irene Díaz‐Moreno
- Institute for Chemical Research (IIQ)Scientific Research Centre Isla de la Cartuja (cicCartuja)University of Seville – CSICSpain
| | - Miguel A. De la Rosa
- Institute for Chemical Research (IIQ)Scientific Research Centre Isla de la Cartuja (cicCartuja)University of Seville – CSICSpain
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24
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Novel, selective acrylamide linked quinazolines for the treatment of double mutant EGFR-L858R/T790M Non-Small-Cell lung cancer (NSCLC). Bioorg Chem 2021; 115:105234. [PMID: 34399322 DOI: 10.1016/j.bioorg.2021.105234] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 06/21/2021] [Accepted: 07/29/2021] [Indexed: 01/02/2023]
Abstract
T790M mutation is the most common mechanism of acquired resistance to first-generation epidermal growth factor receptor tyrosine kinase inhibitors (EGFR-TKIs). To overcome this resistance, 4-anilinoquinazoline-based irreversible inhibitors afatinib, dacomitinib has been developed. However, the clinical application of these irreversible inhibitors is limited due to its narrow selectivity against L858R/T790M mutant EGFR. In an attempt to develop potent and selective EGFR T790M inhibitors, we have designed and synthesized two series of novel acrylamide linked quinazolines. Among them, compounds 2i (IC50 0.171 µM) and 11h (IC50 0.159 µM) were identified as potent compounds, which displayed selective and potent anti-proliferative activity on gefitinib-resistant cell line NCI-H1975 as compared to the gefitinib and WZ4002 in cellular assay. Furthermore, a molecular dynamic simulation of 11h was carried out to assess the stability to form a complex with the L858R/T790M EGFR Kinase domain, which demonstrated that complex was stable for the 100 ns and form strong crucial covalent binding contacts with the thiol group of Cys797 residue. Finally, satisfactory in silico pharmacokinetics properties of 2i, 11h and 11i compounds were predicted. The synthesized compounds were also evaluated for in vitro cytotoxic activity/hepatotoxicity against HepG2 cell line through MTT assay. The results revealed that compounds exhibited lower cytotoxicity to HepG2 cells.
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25
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Escobar EE, Venkat Ramani MK, Zhang Y, Brodbelt JS. Evaluating Spatiotemporal Dynamics of Phosphorylation of RNA Polymerase II Carboxy-Terminal Domain by Ultraviolet Photodissociation Mass Spectrometry. J Am Chem Soc 2021; 143:8488-8498. [PMID: 34053220 DOI: 10.1021/jacs.1c03321] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The critical role of site-specific phosphorylation in eukaryotic transcription has motivated efforts to decipher the complex phosphorylation patterns exhibited by the carboxyl-terminal domain (CTD) of RNA polymerase II. Phosphorylation remains a challenging post-translational modification to characterize by mass spectrometry owing to the labile phosphate ester linkage and low stoichiometric prevalence, two features that complicate analysis by high-throughput MS/MS methods. Identifying phosphorylation sites represents one significant hurdle in decrypting the CTD phosphorylation, a problem exaggerated by a large number of potential phosphorylation sites. An even greater obstacle is decoding the dynamic phosphorylation pattern along the length of the periodic CTD sequence. Ultraviolet photodissociation (UVPD) is a high-energy ion activation method that provides ample backbone cleavages of peptides while preserving labile post-translational modifications that facilitate their confident localization. Herein, we report a quantitative parallel reaction monitoring (PRM) method developed to monitor spatiotemporal changes in site-specific Ser5 phosphorylation of the CTD by cyclin-dependent kinase 7 (CDK7) using UVPD for sequence identification, phosphosite localization, and differentiation of phosphopeptide isomers. We capitalize on the series of phospho-retaining fragment ions produced by UVPD to create unique transition lists that are pivotal for distinguishing the array of phosphopeptides generated from the CTD.
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26
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Abstract
Organophosphorus compounds play a vital role as nucleic acids, nucleotide coenzymes, metabolic intermediates and are involved in many biochemical processes. They are part of DNA, RNA, ATP and a number of important biological elements of living organisms. Synthetic compounds of this class have found practical application as agrochemicals, pharmaceuticals, bioregulators, and othrs. In recent years, a large number of phosphorus compounds containing P-O, P-N, P-C bonds have been isolated from natural sources. Many of them have shown interesting biological properties and have become the objects of intensive scientific research. Most of these compounds contain asymmetric centers, the absolute configurations of which have a significant effect on the biological properties of the products of their transformations. This area of research on natural phosphorus compounds is still little-studied, that prompted us to analyze and discuss it in our review. Moreover natural organophosphorus compounds represent interesting models for the development of new biologically active compounds, and a number of promising drugs and agrochemicals have already been obtained on their basis. The review also discusses the history of the development of ideas about the role of organophosphorus compounds and stereochemistry in the origin of life on Earth, starting from the prebiotic period, that allows us in a new way to consider this most important problem of fundamental science.
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Velázquez-Cruz A, Baños-Jaime B, Díaz-Quintana A, De la Rosa MA, Díaz-Moreno I. Post-translational Control of RNA-Binding Proteins and Disease-Related Dysregulation. Front Mol Biosci 2021; 8:658852. [PMID: 33987205 PMCID: PMC8111222 DOI: 10.3389/fmolb.2021.658852] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 03/22/2021] [Indexed: 12/20/2022] Open
Abstract
Cell signaling mechanisms modulate gene expression in response to internal and external stimuli. Cellular adaptation requires a precise and coordinated regulation of the transcription and translation processes. The post-transcriptional control of mRNA metabolism is mediated by the so-called RNA-binding proteins (RBPs), which assemble with specific transcripts forming messenger ribonucleoprotein particles of highly dynamic composition. RBPs constitute a class of trans-acting regulatory proteins with affinity for certain consensus elements present in mRNA molecules. However, these regulators are subjected to post-translational modifications (PTMs) that constantly adjust their activity to maintain cell homeostasis. PTMs can dramatically change the subcellular localization, the binding affinity for RNA and protein partners, and the turnover rate of RBPs. Moreover, the ability of many RBPs to undergo phase transition and/or their recruitment to previously formed membrane-less organelles, such as stress granules, is also regulated by specific PTMs. Interestingly, the dysregulation of PTMs in RBPs has been associated with the pathophysiology of many different diseases. Abnormal PTM patterns can lead to the distortion of the physiological role of RBPs due to mislocalization, loss or gain of function, and/or accelerated or disrupted degradation. This Mini Review offers a broad overview of the post-translational regulation of selected RBPs and the involvement of their dysregulation in neurodegenerative disorders, cancer and other pathologies.
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Affiliation(s)
- Alejandro Velázquez-Cruz
- Instituto de Investigaciones Químicas, Centro de Investigaciones Científicas Isla de la Cartuja, Universidad de Sevilla, Consejo Superior de Investigaciones Científicas, Seville, Spain
| | - Blanca Baños-Jaime
- Instituto de Investigaciones Químicas, Centro de Investigaciones Científicas Isla de la Cartuja, Universidad de Sevilla, Consejo Superior de Investigaciones Científicas, Seville, Spain
| | - Antonio Díaz-Quintana
- Instituto de Investigaciones Químicas, Centro de Investigaciones Científicas Isla de la Cartuja, Universidad de Sevilla, Consejo Superior de Investigaciones Científicas, Seville, Spain
| | - Miguel A De la Rosa
- Instituto de Investigaciones Químicas, Centro de Investigaciones Científicas Isla de la Cartuja, Universidad de Sevilla, Consejo Superior de Investigaciones Científicas, Seville, Spain
| | - Irene Díaz-Moreno
- Instituto de Investigaciones Químicas, Centro de Investigaciones Científicas Isla de la Cartuja, Universidad de Sevilla, Consejo Superior de Investigaciones Científicas, Seville, Spain
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28
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Guerra-Castellano A, Márquez I, Pérez-Mejías G, Díaz-Quintana A, De la Rosa MA, Díaz-Moreno I. Post-Translational Modifications of Cytochrome c in Cell Life and Disease. Int J Mol Sci 2020; 21:E8483. [PMID: 33187249 PMCID: PMC7697256 DOI: 10.3390/ijms21228483] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 11/05/2020] [Accepted: 11/07/2020] [Indexed: 02/07/2023] Open
Abstract
Mitochondria are the powerhouses of the cell, whilst their malfunction is related to several human pathologies, including neurodegenerative diseases, cardiovascular diseases, and various types of cancer. In mitochondrial metabolism, cytochrome c is a small soluble heme protein that acts as an essential redox carrier in the respiratory electron transport chain. However, cytochrome c is likewise an essential protein in the cytoplasm acting as an activator of programmed cell death. Such a dual role of cytochrome c in cell life and death is indeed fine-regulated by a wide variety of protein post-translational modifications. In this work, we show how these modifications can alter cytochrome c structure and functionality, thus emerging as a control mechanism of cell metabolism but also as a key element in development and prevention of pathologies.
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Affiliation(s)
| | | | | | | | | | - Irene Díaz-Moreno
- Instituto de Investigaciones Químicas (IIQ), Centro de Investigaciones Científicas Isla de la Cartuja (cicCartuja), Universidad de Sevilla, Consejo Superior de Investigaciones Científicas (CSIC), Avda. Américo Vespucio 49, 41092 Sevilla, Spain; (A.G.-C.); (I.M.); (G.P.-M.); (A.D.-Q.); (M.A.D.l.R.)
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