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Balasco Serrão VH, Minari K, Pereira HD, Thiemann OH. Bacterial selenocysteine synthase structure revealed by single-particle cryoEM. Curr Res Struct Biol 2024; 7:100143. [PMID: 38681238 PMCID: PMC11047290 DOI: 10.1016/j.crstbi.2024.100143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 03/31/2024] [Accepted: 04/09/2024] [Indexed: 05/01/2024] Open
Abstract
The 21st amino acid, selenocysteine (Sec), is synthesized on its dedicated transfer RNA (tRNASec). In bacteria, Sec is synthesized from Ser-tRNA[Ser]Sec by Selenocysteine Synthase (SelA), which is a pivotal enzyme in the biosynthesis of Sec. The structural characterization of bacterial SelA is of paramount importance to decipher its catalytic mechanism and its role in the regulation of the Sec-synthesis pathway. Here, we present a comprehensive single-particle cryo-electron microscopy (SPA cryoEM) structure of the bacterial SelA with an overall resolution of 2.69 Å. Using recombinant Escherichia coli SelA, we purified and prepared samples for single-particle cryoEM. The structural insights from SelA, combined with previous in vivo and in vitro knowledge, underscore the indispensable role of decamerization in SelA's function. Moreover, our structural analysis corroborates previous results that show that SelA adopts a pentamer of dimers configuration, and the active site architecture, substrate binding pocket, and key K295 catalytic residue are identified and described in detail. The differences in protein architecture and substrate coordination between the bacterial enzyme and its counterparts offer compelling structural evidence supporting the independent molecular evolution of the bacterial and archaea/eukarya Ser-Sec biosynthesis present in the natural world.
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Affiliation(s)
- Vitor Hugo Balasco Serrão
- Biomolecular Cryoelectron Microscopy Facility, University of California - Santa Cruz, Santa Cruz, CA, 95064, United States
- Department of Chemistry and Biochemistry, University of California - Santa Cruz, Santa Cruz, CA, 95064, United States
| | - Karine Minari
- Biomolecular Engineering Department, Jack Baskin School of Engineering, University of California - Santa Cruz, Santa Cruz, CA, 95064, United States
| | - Humberto D'Muniz Pereira
- Physics Institute of Sao Carlos, University of Sao Paulo, Trabalhador Sao Carlense Av., 400, São Carlos, SP, CEP 13566-590, Brazil
| | - Otavio Henrique Thiemann
- Physics Institute of Sao Carlos, University of Sao Paulo, Trabalhador Sao Carlense Av., 400, São Carlos, SP, CEP 13566-590, Brazil
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2
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Oguntuyo KY, Haas GD, Azarm KD, Stevens CS, Brambilla L, Kowdle SS, Avanzato VA, Pryce R, Freiberg AN, Bowden TA, Lee B. Structure-guided mutagenesis of Henipavirus receptor-binding proteins reveals molecular determinants of receptor usage and antibody-binding epitopes. J Virol 2024; 98:e0183823. [PMID: 38426726 PMCID: PMC10949843 DOI: 10.1128/jvi.01838-23] [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: 11/30/2023] [Accepted: 02/05/2024] [Indexed: 03/02/2024] Open
Abstract
Nipah virus (NiV) is a highly lethal, zoonotic Henipavirus (HNV) that causes respiratory and neurological signs and symptoms in humans. Similar to other paramyxoviruses, HNVs mediate entry into host cells through the concerted actions of two surface glycoproteins: a receptor-binding protein (RBP) that mediates attachment and a fusion glycoprotein (F) that triggers fusion in an RBP-dependent manner. NiV uses ephrin-B2 (EFNB2) and ephrin-B3 (EFNB3) as entry receptors. Ghana virus (GhV), a novel HNV identified in a Ghanaian bat, uses EFNB2 but not EFNB3. In this study, we employ a structure-informed approach to identify receptor-interfacing residues and systematically introduce GhV-RBP residues into a NiV-RBP backbone to uncover the molecular determinants of EFNB3 usage. We reveal two regions that severely impair EFNB3 binding by NiV-RBP and EFNB3-mediated entry by NiV pseudotyped viral particles. Further analyses uncovered two-point mutations (NiVN557SGhV and NiVY581TGhV) pivotal for this phenotype. Moreover, we identify NiV interaction with Y120 of EFNB3 as important for the usage of this receptor. Beyond these EFNB3-related findings, we reveal two domains that restrict GhV binding of EFNB2, confirm the HNV-head as an immunodominant target for polyclonal and monoclonal antibodies, and describe putative epitopes for GhV- and NiV-specific monoclonal antibodies. Cumulatively, the work presented here generates useful reagents and tools that shed insight to residues important for NiV usage of EFNB3, reveal regions critical for GhV binding of EFNB2, and describe putative HNV antibody-binding epitopes. IMPORTANCE Hendra virus and Nipah virus (NiV) are lethal, zoonotic Henipaviruses (HNVs) that cause respiratory and neurological clinical features in humans. Since their initial outbreaks in the 1990s, several novel HNVs have been discovered worldwide, including Ghana virus. Additionally, there is serological evidence of zoonotic transmission, lending way to concerns about future outbreaks. HNV infection of cells is mediated by the receptor-binding protein (RBP) and the Fusion protein (F). The work presented here identifies NiV RBP amino acids important for the usage of ephrin-B3 (EFNB3), a receptor highly expressed in neurons and predicted to be important for neurological clinical features caused by NiV. This study also characterizes epitopes recognized by antibodies against divergent HNV RBPs. Together, this sheds insight to amino acids critical for HNV receptor usage and antibody binding, which is valuable for future studies investigating determinants of viral pathogenesis and developing antibody therapies.
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Affiliation(s)
| | - Griffin D. Haas
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Kristopher D. Azarm
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Christian S. Stevens
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Luca Brambilla
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Shreyas S. Kowdle
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Victoria A. Avanzato
- Division of Structural Biology, Wellcome Center for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Rhys Pryce
- Division of Structural Biology, Wellcome Center for Human Genetics, University of Oxford, Oxford, United Kingdom
| | | | - Thomas A. Bowden
- Division of Structural Biology, Wellcome Center for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Benhur Lee
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
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3
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Hua X, Yao J, Liu X, Liu Q, Deng Y, Li S, Valdivia CR, Wang F, Pozzolini M, Shou Z, Valdivia HH, Xiao L. Comparison of the structure-function of five newly members of the calcin family. Int J Biol Macromol 2024; 260:129424. [PMID: 38219929 DOI: 10.1016/j.ijbiomac.2024.129424] [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: 08/30/2023] [Revised: 01/03/2024] [Accepted: 01/09/2024] [Indexed: 01/16/2024]
Abstract
Calcins are a group of scorpion toxin peptides specifically binding to ryanodine receptors (RyRs) with high affinity, and have the ability to activate and stabilize RyR in a long-lasting subconductance state. Five newly calcins synthesized compounds exhibit typical structural characteristics of a specific family through chemical synthesis and virtual analysis. As the calcins from the same species, Petersiicalcin1 and Petersiicalcin2, Jendekicalcin2 and Jendekicalcin3, have only one residue difference. Both Petersiicalcin1 and Petersiicalcin2 exhibited different affinities in stimulating [3H]ryanodine binding, but the residue mutation resulted in a 2.7 folds difference. Other calcins also exhibited a stimulatory effect on [3H]ryanodine binding to RyR1, however, their affinities were significantly lower than that of Petersiiicalcin1 and Petersiiicalcin2. The channel domain of RyR1 was found to be capable of binding with the basic residues of these calcins, which also exhibited interactions with the S6 helices on RyR1. Dynamic simulations were conducted for Petersiicalcin1 and Petersiicalcin2, which demonstrated their ability to form a highly stable conformation and resulting in an asymmetric tetramer structure of RyR1. The discovery of five newly calcins further enriches the diversity of the natural calcin family, which provides more native peptides for the structure-function analysis between calcin and RyRs.
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Affiliation(s)
- Xiaoyu Hua
- Department of Occupational and Environmental Health, Faculty of Naval Medicine, Naval Medical University (Second Military Medical University), Shanghai 200433, China
| | - Jinchi Yao
- Department of Occupational and Environmental Health, Faculty of Naval Medicine, Naval Medical University (Second Military Medical University), Shanghai 200433, China; School of Life Sciences, Liaoning Normal University, Dalian 116081, China
| | - Xinyan Liu
- Department of Traditional Chinese Medicine Surgery, the First Affiliated Hospital of the Navy Medical University, Shanghai, 200433, China
| | - Qing Liu
- College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Shanxi, Taigu 030801, China
| | - Yuchen Deng
- Department of Dermatology, Second Affiliated Hospital of Naval Medical University, Shanghai 200003, China
| | - Songhua Li
- Department of Cardiology, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Carmen R Valdivia
- Department of Medicine and Cardiovascular Research Center, University of Wisconsin-Madison School of Medicine and Public Health, Madison, WI, USA.
| | - Fei Wang
- Department of Occupational and Environmental Health, Faculty of Naval Medicine, Naval Medical University (Second Military Medical University), Shanghai 200433, China
| | - Marina Pozzolini
- Department of Earth, Environment and Life Sciences (DISTAV), University of Genova, Via Pastore 3, 16132 Genova, Italy.
| | - Zhaoyong Shou
- Faculty of Health Service, Nacal Medical University (Second Military Medical University), Shanghai 200433, China.
| | - Héctor H Valdivia
- Department of Medicine and Cardiovascular Research Center, University of Wisconsin-Madison School of Medicine and Public Health, Madison, WI, USA.
| | - Liang Xiao
- Department of Occupational and Environmental Health, Faculty of Naval Medicine, Naval Medical University (Second Military Medical University), Shanghai 200433, China.
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4
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Oguntuyo KY, Haas GD, Azarm KD, Stevens CS, Brambilla L, Kowdle S, Avanzato VA, Pryce R, Freiberg AN, Bowden TA, Lee B. Structure guided mutagenesis of Henipavirus Receptor Binding Proteins reveals molecular determinants of receptor usage and antibody binding epitopes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.22.568281. [PMID: 38045373 PMCID: PMC10690272 DOI: 10.1101/2023.11.22.568281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
Nipah virus (NiV) is a highly lethal, zoonotic henipavirus (HNV) that causes respiratory and neurological signs and symptoms in humans. Similar to other paramyxoviruses, HNVs mediate entry into host cells through the concerted actions of two surface glycoproteins: a receptor binding protein (RBP) that mediates attachment and a fusion glycoprotein (F) that triggers fusion in an RBP-dependent manner. NiV uses ephrin-B2 (EFNB2) and ephrin-B3 (EFNB3) as entry receptors. Ghana virus (GhV), a novel HNV identified in a Ghanaian bat, use EFNB2 but not EFNB3. In this study, we employ a structure-informed approach to identify receptor interfacing residues and systematically introduce GhV-RBP residues into a NiV-RBP backbone to uncover the molecular determinants of EFNB3 usage. We reveal two regions that severely impair EFNB3 binding by NiV-RBP and EFNB3-mediated entry by NiV pseudotyped viral particles. Further analyses uncovered two point mutations (NiVN557SGhV and NiVY581TGhV) pivotal for this phenotype. Moreover, we identify NiV interaction with Y120 of EFNB3 as important for usage of this receptor. Beyond these EFNB3-related findings, we reveal two domains that restrict GhV binding of EFNB2, identify the HNV-head as an immunodominant target for polyclonal and monoclonal antibodies, and describe putative epitopes for GhV and NiV-specific monoclonal antibodies. Cumulatively, the work presented here generates useful reagents and tools that shed insight to residues important for NiV usage of EFNB3, reveals regions critical for GhV binding of EFNB2, and describes putative HNV antibody binding epitopes.
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Affiliation(s)
- K Y Oguntuyo
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - G D Haas
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - K D Azarm
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - C S Stevens
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - L Brambilla
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - S Kowdle
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - V A Avanzato
- Division of Structural Biology, Wellcome Center for Human Genetics, University of Oxford, OX3 7BN Oxford, United Kingdom
| | - R Pryce
- Division of Structural Biology, Wellcome Center for Human Genetics, University of Oxford, OX3 7BN Oxford, United Kingdom
| | - A N Freiberg
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA
| | - T A Bowden
- Division of Structural Biology, Wellcome Center for Human Genetics, University of Oxford, OX3 7BN Oxford, United Kingdom
| | - B Lee
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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5
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Mukherjee P, Bagchi A, Banerjee A, Roy H, Bhattacharya A, Biswas A, Chatterji U. PDE4 inhibitor eliminates breast cancer stem cells via noncanonical activation of mTOR. J Cell Biochem 2022; 123:1980-1996. [PMID: 36063486 DOI: 10.1002/jcb.30325] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 05/25/2022] [Accepted: 08/17/2022] [Indexed: 12/24/2022]
Abstract
Ineffective cancer treatment is implicated in metastasis, recurrence, resistance to chemotherapy and radiotherapy, and evasion of immune surveillance. All these failures occur due to the persistence of cancer stem cells (CSCs) even after rigorous therapy, thereby rendering them as essential targets for cancer management. Contrary to the quiescent nature of CSCs, a gene profiler array disclosed that phosphatidylinositol-3-kinase (PI3K), which is known to be crucial for cell proliferation, differentiation, and survival, was significantly upregulated in CSCs. Since PI3K is modulated by cyclic adenosine 3',5' monophosphate (cAMP), analyses of cAMP regulation revealed that breast CSCs expressed increased levels of phosphodiesterase 4 (PDE4) in contrast to normal stem cells. In accordance, the effects of rolipram, a PDE4 inhibitor, were evaluated on PI3K regulators and signaling. The efficacy of rolipram was compared with paclitaxel, an anticancer drug that is ineffective in obliterating breast CSCs. Analyses of downstream signaling components revealed a switch between cell survival and death, in response to rolipram, specifically of the CSCs. Rolipram-mediated downregulation of PDE4A levels in breast CSCs led to an increase in cAMP levels and protein kinase A (PKA) expression. Subsequently, PKA-mediated upregulation of phosphatase and tensin homolog antagonized the PI3K/AKT/mTOR pathway and led to cell cycle arrest. Interestingly, direct yet noncanonical activation of mTOR by PKA, circumventing the influence of PI3K and AKT, temporally shifted the fate of CSCs toward apoptosis. Rolipram in combination with paclitaxel indicated synergistic consequences, which effectively obliterated CSCs within a tumor, thereby suggesting combinatorial therapy as a sustainable and effective strategy to abrogate breast CSCs for better patient prognosis.
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Affiliation(s)
- Pritha Mukherjee
- Cancer Research Laboratory, Department of Zoology, University of Calcutta, Kolkata, India
| | - Arka Bagchi
- Molecular Cell Biology Laboratory, Department of Zoology, University of Kalyani, Kalyani, India
| | - Ananya Banerjee
- Cancer Research Laboratory, Department of Zoology, University of Calcutta, Kolkata, India
| | - Himansu Roy
- Department of Surgery, Calcutta Medical College, Kolkata, India
| | | | - Arunima Biswas
- Molecular Cell Biology Laboratory, Department of Zoology, University of Kalyani, Kalyani, India
| | - Urmi Chatterji
- Cancer Research Laboratory, Department of Zoology, University of Calcutta, Kolkata, India.,Centre for Research in Nanoscience and Nanotechnology, University of Calcutta, Kolkata, India
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6
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Albutti A. Proteome-Wide and Protein-Specific Multi-Epitope Vaccine Constructs Against the Rift Valley Fever Virus Outbreak Using Integrated Omics Approaches. Front Microbiol 2022; 13:921683. [PMID: 35711778 PMCID: PMC9195176 DOI: 10.3389/fmicb.2022.921683] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Accepted: 05/02/2022] [Indexed: 11/13/2022] Open
Abstract
Rift Valley fever (RVF) is a viral disease caused by a member of the Bunyavirales family causing severe infections in humans. The RVF virus is an enveloped, negative-sense, single-stranded RNA virus that can infect both animals and humans. The symptoms associated with these infections span from minor (fever and headaches) to severe (meningoencephalitis and hemorrhagic fever syndrome) symptoms. Despite the outbreaks of the RVF virus being reported in different parts of the world, no effective therapy is available. Herein, the development of an efficient vaccine is critical for the control of infections associated with the RVF virus. Moreover, computational vaccine approaches are helpful in the design of specific, safe, and stable peptide-based designs when compared to the conventional methods of vaccine development. In this study, the whole proteome of the virus, comprising four proteins (NP, L, GP, and NSP), was screened to find putative vaccine epitope sequences (T cell, B cell, and HTL) specific for each protein. These shortlisted epitopes were then combined with flexible linkers to design protein-specific and proteome-wide immunogenic multi-epitope-based vaccine constructs. The results revealed that these multi-epitope vaccine constructs (MEVCs) are strongly antigenic and non-allergenic in nature. The efficacy of these constructs was further validated by docking with immune receptors, which revealed strong binding interactions with human TLR8. Using the MD simulation approach, the binding stability and residual flexibility of the best vaccine construct (proteome-wide) were confirmed, which revealed stable dynamic and favorable features. Furthermore, in-silico cloning and immune simulation analysis confirmed the expression and production of immune factors, that is, IgM, IgG, and IL-6, against the proposed vaccine designs. Additionally, 3D models of all the MEVC constructs have been developed and evaluated for potential immunization against the RVF virus. Finally, the proteome-wide vaccine candidate (MEVC-PW-RVFV) with the highest immune reinforcement potential provides new insights into the development of future vaccines against the emerging RVF virus.
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Affiliation(s)
- Aqel Albutti
- Department of Medical Biotechnology, College of Applied Medical Sciences, Qassim University, Buraydah, Saudi Arabia
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7
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Neuwald AF, Yang H, Tracy Nixon B. SPARC: Structural properties associated with residue constraints. Comput Struct Biotechnol J 2022; 20:1702-1715. [PMID: 35495120 PMCID: PMC9020082 DOI: 10.1016/j.csbj.2022.04.005] [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: 11/23/2021] [Revised: 03/22/2022] [Accepted: 04/05/2022] [Indexed: 11/17/2022] Open
Abstract
SPARC facilitates the generation of plausible hypotheses regarding underlying biochemical mechanisms by structurally characterizing protein sequence constraints. Such constraints appear as residues co-conserved in functionally related subgroups, as subtle pairwise correlations (i.e., direct couplings), and as correlations among these sequence features or with structural features. SPARC performs three types of analyses. First, based on pairwise sequence correlations, it estimates the biological relevance of alternative conformations and of homomeric contacts, as illustrated here for death domains. Second, it estimates the statistical significance of the correspondence between directly coupled residue pairs and interactions at heterodimeric interfaces. Third, given molecular dynamics simulated structures, it characterizes interactions among constrained residues or between such residues and ligands that: (a) are stably maintained during the simulation; (b) undergo correlated formation and/or disruption of interactions with other constrained residues; or (c) switch between alternative interactions. We illustrate this for two homohexameric complexes: the bacterial enhancer binding protein (bEBP) NtrC1, which activates transcription by remodeling RNA polymerase (RNAP) containing σ54, and for DnaB helicase, which opens DNA at the bacterial replication fork. Based on the NtrC1 analysis, we hypothesize possible mechanisms for inhibiting ATP hydrolysis until ADP is released from an adjacent subunit and for coupling ATP hydrolysis to restructuring of σ54 binding loops. Based on the DnaB analysis, we hypothesize that DnaB 'grabs' ssDNA by flipping every fourth base and inserting it into cavities between subunits and that flipping of a DnaB-specific glutamine residue triggers ATP hydrolysis.
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Affiliation(s)
- Andrew F. Neuwald
- Institute for Genome Sciences and Department of Biochemistry & Molecular Biology, University of Maryland School of Medicine, 670 W. Baltimore Steet, Baltimore, MD 21201, USA,Corresponding author.
| | - Hui Yang
- Department of Biology. Penn State University, 304A Frear South Building, University Park, PA 16802
| | - B. Tracy Nixon
- Department of Biochemistry and Molecular Biology, 335 Frear South Building, University Park, PA 16802, USA
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Structural characterization of an L-fuculose-1-phosphate aldolase from Klebsiella pneumoniae. Biochem Biophys Res Commun 2022; 607:15-19. [PMID: 35366538 DOI: 10.1016/j.bbrc.2022.03.127] [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: 03/14/2022] [Accepted: 03/23/2022] [Indexed: 11/23/2022]
Abstract
Fuculose phosphate aldolases play an important role in glycolysis and gluconeogenesis pathways. L-fuculose 1-phosphate aldolase catalyzes the reversible cleavage of L-fuculose 1-phosphate to DHAP and L-lactaldehyde. Class II aldolases found in bacteria are linked to pathogenesis of human pathogens, and have potential applications in the biosynthesis of carbohydrates and other chiral compounds. Here we report the structure of a putative L-fuculose 1-phosphate aldolase (KpFucA) from the nosocomial pathogen Klebsiella pneumoniae to 1.85 Å resolution. The enzyme crystallizes in space group P422 with one monomer per asymmetric unit. Analytical ultracentrifugation analysis confirms that KpFucA is a tetramer in solution. A magnesium ion cofactor and sulfate ion were identified in the active pocket. Enzyme activity assays confirmed that KpFcuA has a strong preference for L-fuculose 1-phosphate as a substrate, but can also catalyze the cleavage of fructose-1,6-bisphosphate and glucose-6-phosphate. This work should provide a starting point for further investigation of the role of KpFucA in K. pneumoniae pathogenesis or in industrial applications.
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Luo W, Li J, Li Z, Lin T, Zhang L, Yang W, Mai Y, Liu R, Chen M, Dai C, Yang H, Lu J, Li H, Guan G, Huang M, Liu P, Li Z. HO-1 nuclear accumulation and interaction with NPM1 protect against stress-induced endothelial senescence independent of its enzymatic activity. Cell Death Dis 2021; 12:738. [PMID: 34312365 PMCID: PMC8313700 DOI: 10.1038/s41419-021-04035-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 07/13/2021] [Accepted: 07/14/2021] [Indexed: 02/07/2023]
Abstract
Heme oxygenase-1 (HO-1) has attracted accumulating attention for its antioxidant enzymatic activity. However, the exact regulatory role of its non-enzymatic activity in the cardiovascular system remains unaddressed. Here, we show that HO-1 was accumulated in the nuclei of stress-induced senescent endothelial cells, and conferred protection against endothelial senescence independent of its enzymatic activity. Overexpression of ΔHO-1, a truncated HO-1 without transmembrane segment (TMS), inhibited H2O2-induced endothelial senescence. Overexpression of ΔHO-1H25A, the catalytically inactive form of ΔHO-1, also exhibited anti-senescent effect. In addition, infection of recombinant adenovirus encoding ΔHO-1 with three nuclear localization sequences (NLS), alleviated endothelial senescence induced by knockdown of endogenous HO-1 by CRISPR/Cas9. Moreover, repression of HO-1 nuclear translocation by silencing of signal peptide peptidase (SPP), which is responsible for enzymatic cleavage of the TMS of HO-1, exacerbated endothelial senescence. Mechanistically, nuclear HO-1 interacted with NPM1 N-terminal portion, prevented NPM1 translocation from nucleolus to nucleoplasm, thus disrupted NPM1/p53/MDM2 interactions and inhibited p53 activation by NPM1, finally resisted endothelial senescence. This study provides a novel understanding of HO-1 as a promising therapeutic strategy for vascular senescence-related cardiovascular diseases.
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Affiliation(s)
- Wenwei Luo
- Department of Pharmacology and Toxicology, School of Pharmaceutical Sciences, National and Local United Engineering Lab of Druggability and New Drugs Evaluation, Guangdong Engineering Laboratory of Druggability and New Drug Evaluation, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou, China
| | - Jingyan Li
- Department of Pharmacology and Toxicology, School of Pharmaceutical Sciences, National and Local United Engineering Lab of Druggability and New Drugs Evaluation, Guangdong Engineering Laboratory of Druggability and New Drug Evaluation, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou, China
- International Institute for Translational Chinese Medicine, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Ziqing Li
- Department of Pharmacology and Toxicology, School of Pharmaceutical Sciences, National and Local United Engineering Lab of Druggability and New Drugs Evaluation, Guangdong Engineering Laboratory of Druggability and New Drug Evaluation, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou, China
| | - Tong Lin
- Department of Pharmacology and Toxicology, School of Pharmaceutical Sciences, National and Local United Engineering Lab of Druggability and New Drugs Evaluation, Guangdong Engineering Laboratory of Druggability and New Drug Evaluation, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou, China
| | - Lili Zhang
- Department of Pharmacology and Toxicology, School of Pharmaceutical Sciences, National and Local United Engineering Lab of Druggability and New Drugs Evaluation, Guangdong Engineering Laboratory of Druggability and New Drug Evaluation, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou, China
| | - Wanqi Yang
- Department of Pharmacology and Toxicology, School of Pharmaceutical Sciences, National and Local United Engineering Lab of Druggability and New Drugs Evaluation, Guangdong Engineering Laboratory of Druggability and New Drug Evaluation, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou, China
| | - Yanqi Mai
- Department of Pharmacology and Toxicology, School of Pharmaceutical Sciences, National and Local United Engineering Lab of Druggability and New Drugs Evaluation, Guangdong Engineering Laboratory of Druggability and New Drug Evaluation, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou, China
| | - Ruiming Liu
- Department of Vascular and Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Meiting Chen
- Emergency Department, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Chunmei Dai
- Department of Pharmacology and Toxicology, School of Pharmaceutical Sciences, National and Local United Engineering Lab of Druggability and New Drugs Evaluation, Guangdong Engineering Laboratory of Druggability and New Drug Evaluation, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou, China
| | - Hanwei Yang
- Department of Pharmacology and Toxicology, School of Pharmaceutical Sciences, National and Local United Engineering Lab of Druggability and New Drugs Evaluation, Guangdong Engineering Laboratory of Druggability and New Drug Evaluation, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou, China
| | - Jing Lu
- Department of Pharmacology and Toxicology, School of Pharmaceutical Sciences, National and Local United Engineering Lab of Druggability and New Drugs Evaluation, Guangdong Engineering Laboratory of Druggability and New Drug Evaluation, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou, China
| | - Hong Li
- Department of Biochemistry and Molecular Biology, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Guimei Guan
- Department of Obstetrics and Gynecology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Min Huang
- Institute of Clinical Pharmacology and Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
| | - Peiqing Liu
- Department of Pharmacology and Toxicology, School of Pharmaceutical Sciences, National and Local United Engineering Lab of Druggability and New Drugs Evaluation, Guangdong Engineering Laboratory of Druggability and New Drug Evaluation, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou, China.
| | - Zhuoming Li
- Department of Pharmacology and Toxicology, School of Pharmaceutical Sciences, National and Local United Engineering Lab of Druggability and New Drugs Evaluation, Guangdong Engineering Laboratory of Druggability and New Drug Evaluation, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou, China.
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10
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Multilevel proteomics reveals host perturbations by SARS-CoV-2 and SARS-CoV. Nature 2021; 594:246-252. [PMID: 33845483 DOI: 10.1038/s41586-021-03493-4] [Citation(s) in RCA: 380] [Impact Index Per Article: 126.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 03/25/2021] [Indexed: 02/06/2023]
Abstract
The emergence and global spread of SARS-CoV-2 has resulted in the urgent need for an in-depth understanding of molecular functions of viral proteins and their interactions with the host proteome. Several individual omics studies have extended our knowledge of COVID-19 pathophysiology1-10. Integration of such datasets to obtain a holistic view of virus-host interactions and to define the pathogenic properties of SARS-CoV-2 is limited by the heterogeneity of the experimental systems. Here we report a concurrent multi-omics study of SARS-CoV-2 and SARS-CoV. Using state-of-the-art proteomics, we profiled the interactomes of both viruses, as well as their influence on the transcriptome, proteome, ubiquitinome and phosphoproteome of a lung-derived human cell line. Projecting these data onto the global network of cellular interactions revealed crosstalk between the perturbations taking place upon infection with SARS-CoV-2 and SARS-CoV at different levels and enabled identification of distinct and common molecular mechanisms of these closely related coronaviruses. The TGF-β pathway, known for its involvement in tissue fibrosis, was specifically dysregulated by SARS-CoV-2 ORF8 and autophagy was specifically dysregulated by SARS-CoV-2 ORF3. The extensive dataset (available at https://covinet.innatelab.org ) highlights many hotspots that could be targeted by existing drugs and may be used to guide rational design of virus- and host-directed therapies, which we exemplify by identifying inhibitors of kinases and matrix metalloproteases with potent antiviral effects against SARS-CoV-2.
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11
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Liang Y, Li W, Liang H, Lou X, Liu R, Zhang Q, Bartlam M. Structural characterization and Kemp eliminase activity of the Mycobacterium smegmatis Ketosteroid Isomerase. Biochem Biophys Res Commun 2021; 560:159-164. [PMID: 33992958 DOI: 10.1016/j.bbrc.2021.05.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 05/04/2021] [Indexed: 11/26/2022]
Abstract
The Kemp elimination reaction, involving the ring-opening of benzoxazole and its derivatives under the action of natural enzymes or chemical catalysts, has been of interest to researchers since its discovery. Because this reaction does not exist in all currently known metabolic pathways, the computational design of Kemp eliminases has provided valuable insights into principles of enzymatic catalysis. However, it was discovered that the naturally occurring promiscuous enzymes ydbC, xapA and ketosteroid isomerase also can catalyze Kemp elimination. Here, we report the crystal structure of ketosteroid isomerase (KSI) from Mycobacterium smegmatis MC2 155. MsKSI crystallizes in the P212121 space group with two molecules in an asymmetric unit, and ultracentrifugation data confirms that it forms a stable dimer in solution, consistent with the 1.9 Å-resolution structure. Our assays confirm that MsKSI accelerates the Kemp elimination of 5-nitrobenzoxazole (5NBI) with an optimal pH of 5.5. A 2.35 Å resolution crystal structure of the MsKSI-5NBI complex reveals that the substrate 5NBI is bound in the active pocket of the enzyme composed of hydrophobic residues. In addition, the Glu127 residue is proposed to play an important role as a general base in proton transfer and breaking weak O-N bonds to open the five-membered ring. This work provides a starting point for exploring the artificial modification of MsKSI using the natural enzyme as the backbone.
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Affiliation(s)
- Yakun Liang
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Protein Science and College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Weiping Li
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Protein Science and College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Han Liang
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Protein Science and College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Xiaorui Lou
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Protein Science and College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Ruihua Liu
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Protein Science and College of Life Sciences, Nankai University, Tianjin, 300071, China.
| | - Qionglin Zhang
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Protein Science and College of Life Sciences, Nankai University, Tianjin, 300071, China.
| | - Mark Bartlam
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Protein Science and College of Life Sciences, Nankai University, Tianjin, 300071, China
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12
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Jia H, Chen Y, Chen Y, Liu R, Zhang Q, Bartlam M. Structural characterization of a 2-aminoethylphosphonate:pyruvate aminotransferase from Pseudomonas aeruginosa PAO1. Biochem Biophys Res Commun 2021; 552:114-119. [PMID: 33743347 DOI: 10.1016/j.bbrc.2021.03.046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 03/09/2021] [Indexed: 11/26/2022]
Abstract
2-aminoethylphosphonate:pyruvate aminotransferase (AEPT) is a pyridoxal 5'-phosphate (PLP)-dependent enzyme that mediates the first step in the AEP degradation pathway. It catalyzes the transamination of 2-aminoethylphosphonate (AEP) with pyruvate to phosphonoacetaldehyde and l-alanine respectively. Although the enzyme is widely present in microorganisms, there are few reports on the structure and function of AEPT to date. Here we report the crystal structure of AEPT from Pseudomonas aeruginosa PAO1 (PaAEPT) to 2.35 Å resolution in the absence of the PLP cofactor. PaAEPT crystallizes in space group P21212 with one monomer per asymmetric unit. Analytical ultracentrifugation analysis shows that PaAEPT forms a stable dimer in solution. Our work provides a valuable starting point for further functional and mechanistic studies of the AEP degradation pathway.
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Affiliation(s)
- Haizhu Jia
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Protein Science and College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Yuan Chen
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Protein Science and College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Yujing Chen
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Protein Science and College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Ruihua Liu
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Protein Science and College of Life Sciences, Nankai University, Tianjin, 300071, China.
| | - Qionglin Zhang
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Protein Science and College of Life Sciences, Nankai University, Tianjin, 300071, China.
| | - Mark Bartlam
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Protein Science and College of Life Sciences, Nankai University, Tianjin, 300071, China
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13
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Crystal structure of cis-aconitate decarboxylase reveals the impact of naturally occurring human mutations on itaconate synthesis. Proc Natl Acad Sci U S A 2019; 116:20644-20654. [PMID: 31548418 PMCID: PMC6789909 DOI: 10.1073/pnas.1908770116] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
cis-Aconitate decarboxylase (CAD, also known as ACOD1 or Irg1) converts cis-aconitate to itaconate and plays central roles in linking innate immunity with metabolism and in the biotechnological production of itaconic acid by Aspergillus terreus We have elucidated the crystal structures of human and murine CADs and compared their enzymological properties to CAD from A. terreus Recombinant CAD is fully active in vitro without a cofactor. Murine CAD has the highest catalytic activity, whereas Aspergillus CAD is best adapted to a more acidic pH. CAD is not homologous to any known decarboxylase and appears to have evolved from prokaryotic enzymes that bind negatively charged substrates. CADs are homodimers, the active center is located in the interface between 2 distinct subdomains, and structural modeling revealed conservation in zebrafish and Aspergillus We identified 8 active-site residues critical for CAD function and rare naturally occurring human mutations in the active site that abolished CAD activity, as well as a variant (Asn152Ser) that increased CAD activity and is common (allele frequency 20%) in African ethnicity. These results open the way for 1) assessing the potential impact of human CAD variants on disease risk at the population level, 2) developing therapeutic interventions to modify CAD activity, and 3) improving CAD efficiency for biotechnological production of itaconic acid.
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14
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Arturo EC, Gupta K, Hansen MR, Borne E, Jaffe EK. Biophysical characterization of full-length human phenylalanine hydroxylase provides a deeper understanding of its quaternary structure equilibrium. J Biol Chem 2019; 294:10131-10145. [PMID: 31076506 PMCID: PMC6664189 DOI: 10.1074/jbc.ra119.008294] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 05/09/2019] [Indexed: 11/06/2022] Open
Abstract
Dysfunction of human phenylalanine hydroxylase (hPAH, EC 1.14.16.1) is the primary cause of phenylketonuria, the most common inborn error of amino acid metabolism. The dynamic domain rearrangements of this multimeric protein have thwarted structural study of the full-length form for decades, until now. In this study, a tractable C29S variant of hPAH (C29S) yielded a 3.06 Å resolution crystal structure of the tetrameric resting-state conformation. We used size-exclusion chromatography in line with small-angle X-ray scattering (SEC-SAXS) to analyze the full-length hPAH solution structure both in the presence and absence of Phe, which serves as both substrate and allosteric activators. Allosteric Phe binding favors accumulation of an activated PAH tetramer conformation, which is biophysically distinct in solution. Protein characterization with enzyme kinetics and intrinsic fluorescence revealed that the C29S variant and hPAH are otherwise equivalent in their response to Phe, further supported by their behavior on various chromatography resins and by analytical ultracentrifugation. Modeling of resting-state and activated forms of C29S against SAXS data with available structural data created and evaluated several new models for the transition between the architecturally distinct conformations of PAH and highlighted unique intra- and inter-subunit interactions. Three best-fitting alternative models all placed the allosteric Phe-binding module 8-10 Å farther from the tetramer center than do all previous models. The structural insights into allosteric activation of hPAH reported here may help inform ongoing efforts to treat phenylketonuria with novel therapeutic approaches.
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Affiliation(s)
- Emilia C Arturo
- From the Molecular Therapeutics Program, Fox Chase Cancer Center, Temple University Health Systems, Philadelphia, Pennsylvania 19111
- the Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, Pennsylvania 19102, and
| | - Kushol Gupta
- the Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Michael R Hansen
- From the Molecular Therapeutics Program, Fox Chase Cancer Center, Temple University Health Systems, Philadelphia, Pennsylvania 19111
| | - Elias Borne
- From the Molecular Therapeutics Program, Fox Chase Cancer Center, Temple University Health Systems, Philadelphia, Pennsylvania 19111
| | - Eileen K Jaffe
- From the Molecular Therapeutics Program, Fox Chase Cancer Center, Temple University Health Systems, Philadelphia, Pennsylvania 19111,
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15
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Rajendran P, Johnson G, Li L, Chen YS, Dashwood M, Nguyen N, Ulusan A, Ertem F, Zhang M, Li J, Sun D, Huang Y, Wang S, Leung HC, Lieberman D, Beaver L, Ho E, Bedford M, Chang K, Vilar E, Dashwood R. Acetylation of CCAR2 Establishes a BET/BRD9 Acetyl Switch in Response to Combined Deacetylase and Bromodomain Inhibition. Cancer Res 2019; 79:918-927. [PMID: 30643017 DOI: 10.1158/0008-5472.can-18-2003] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 10/19/2018] [Accepted: 01/09/2019] [Indexed: 12/15/2022]
Abstract
There continues to be interest in targeting epigenetic "readers, writers, and erasers" for the treatment of cancer and other pathologies. However, a mechanistic understanding is frequently lacking for the synergy observed when combining deacetylase and bromodomain inhibitors. Here we identify cell cycle and apoptosis regulator 2 (CCAR2) as an early target for acetylation in colon cancer cells treated with sulforaphane. N-terminal acetylation of CCAR2 diminished its interactions with histone deacetylase 3 and β-catenin, interfering with Wnt coactivator functions of CCAR2, including in cells harboring genetically encoded CCAR2 acetylation. Protein domain arrays and pull-down assays identified acetyl "reader" proteins that recognized CCAR2 acetylation sites, including BRD9 and members of the bromodomain and extraterminal domain (BET) family. Treatment with the BET inhibitor JQ1 synergized with sulforaphane in colon cancer cells and suppressed tumor development effectively in a preclinical model of colorectal cancer. Studies with sulforaphane+JQ1 in combination implicated a BET/BRD9 acetyl switch and a shift in the pool of acetyl "reader" proteins in favor of BRD9-regulated target genes. SIGNIFICANCE: These results highlight the competition that exists among the "readers" of acetylated histone and nonhistone proteins and provide a mechanistic basis for potential new therapeutic avenues involving epigenetic combination treatments.
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Affiliation(s)
- Praveen Rajendran
- Center for Epigenetics & Disease Prevention, Texas A&M College of Medicine, Houston, Texas.
| | - Gavin Johnson
- Center for Epigenetics & Disease Prevention, Texas A&M College of Medicine, Houston, Texas
| | - Li Li
- Center for Epigenetics & Disease Prevention, Texas A&M College of Medicine, Houston, Texas
| | - Ying-Shiuan Chen
- Center for Epigenetics & Disease Prevention, Texas A&M College of Medicine, Houston, Texas
| | - Mohaiza Dashwood
- Center for Epigenetics & Disease Prevention, Texas A&M College of Medicine, Houston, Texas
| | - Nhung Nguyen
- Center for Epigenetics & Disease Prevention, Texas A&M College of Medicine, Houston, Texas
| | - Ahmet Ulusan
- Center for Epigenetics & Disease Prevention, Texas A&M College of Medicine, Houston, Texas
| | - Furkan Ertem
- Center for Epigenetics & Disease Prevention, Texas A&M College of Medicine, Houston, Texas
| | - Mutian Zhang
- Center for Epigenetics & Disease Prevention, Texas A&M College of Medicine, Houston, Texas
| | - Jia Li
- Center for Epigenetics & Disease Prevention, Texas A&M College of Medicine, Houston, Texas
| | - Deqiang Sun
- Center for Epigenetics & Disease Prevention, Texas A&M College of Medicine, Houston, Texas
| | - Yun Huang
- Center for Epigenetics & Disease Prevention, Texas A&M College of Medicine, Houston, Texas
| | - Shan Wang
- Center for Epigenetics & Disease Prevention, Texas A&M College of Medicine, Houston, Texas
| | - Hon-Chiu Leung
- Mass Spectrometry-Proteomics Core, Baylor College of Medicine, Houston, Texas
| | - David Lieberman
- Division of Gastroenterology and Hepatology, Oregon Health & Science University, Portland, Oregon
| | - Laura Beaver
- College of Public Health and Human Sciences, Oregon State University, Corvallis, Oregon
| | - Emily Ho
- College of Public Health and Human Sciences, Oregon State University, Corvallis, Oregon
| | - Mark Bedford
- The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Kyle Chang
- The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Eduardo Vilar
- The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Roderick Dashwood
- Center for Epigenetics & Disease Prevention, Texas A&M College of Medicine, Houston, Texas. .,The University of Texas MD Anderson Cancer Center, Houston, Texas
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16
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Tosi T, Hoshiga F, Millership C, Singh R, Eldrid C, Patin D, Mengin-Lecreulx D, Thalassinos K, Freemont P, Gründling A. Inhibition of the Staphylococcus aureus c-di-AMP cyclase DacA by direct interaction with the phosphoglucosamine mutase GlmM. PLoS Pathog 2019; 15:e1007537. [PMID: 30668586 PMCID: PMC6368335 DOI: 10.1371/journal.ppat.1007537] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 02/08/2019] [Accepted: 12/18/2018] [Indexed: 02/05/2023] Open
Abstract
c-di-AMP is an important second messenger molecule that plays a pivotal role in regulating fundamental cellular processes, including osmotic and cell wall homeostasis in many Gram-positive organisms. In the opportunistic human pathogen Staphylococcus aureus, c-di-AMP is produced by the membrane-anchored DacA enzyme. Inactivation of this enzyme leads to a growth arrest under standard laboratory growth conditions and a re-sensitization of methicillin-resistant S. aureus (MRSA) strains to ß-lactam antibiotics. The gene coding for DacA is part of the conserved three-gene dacA/ybbR/glmM operon that also encodes the proposed DacA regulator YbbR and the essential phosphoglucosamine mutase GlmM, which is required for the production of glucosamine-1-phosphate, an early intermediate of peptidoglycan synthesis. These three proteins are thought to form a complex in vivo and, in this manner, help to fine-tune the cellular c-di-AMP levels. To further characterize this important regulatory complex, we conducted a comprehensive structural and functional analysis of the S. aureus DacA and GlmM enzymes by determining the structures of the S. aureus GlmM enzyme and the catalytic domain of DacA. Both proteins were found to be dimers in solution as well as in the crystal structures. Further site-directed mutagenesis, structural and enzymatic studies showed that multiple DacA dimers need to interact for enzymatic activity. We also show that DacA and GlmM form a stable complex in vitro and that S. aureus GlmM, but not Escherichia coli or Pseudomonas aeruginosa GlmM, acts as a strong inhibitor of DacA function without the requirement of any additional cellular factor. Based on Small Angle X-ray Scattering (SAXS) data, a model of the complex revealed that GlmM likely inhibits DacA by masking the active site of the cyclase and preventing higher oligomer formation. Together these results provide an important mechanistic insight into how c-di-AMP production can be regulated in the cell.
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Affiliation(s)
- Tommaso Tosi
- Section of Microbiology and MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, United Kingdom
| | - Fumiya Hoshiga
- Section of Microbiology and MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, United Kingdom
| | - Charlotte Millership
- Section of Microbiology and MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, United Kingdom
| | - Rahul Singh
- Section of Microbiology and MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, United Kingdom
| | - Charles Eldrid
- Institute of Structural and Molecular Biology, Birkbeck College, University of London, Malet Street, London, United Kingdom
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London, United Kingdom
| | - Delphine Patin
- Institute for Integrative Biology of the Cell, CEA, CNRS, Univ Paris-Sud and Université Paris-Saclay, Gif-sur-Yvette, France
| | - Dominique Mengin-Lecreulx
- Institute for Integrative Biology of the Cell, CEA, CNRS, Univ Paris-Sud and Université Paris-Saclay, Gif-sur-Yvette, France
| | - Konstantinos Thalassinos
- Institute of Structural and Molecular Biology, Birkbeck College, University of London, Malet Street, London, United Kingdom
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London, United Kingdom
| | - Paul Freemont
- Section of Structural Biology, Department of Medicine, Imperial College London, London, United Kingdom
| | - Angelika Gründling
- Section of Microbiology and MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, United Kingdom
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17
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Zhang J, Zhang B, Zhao Y, Yang X, Huang M, Cui P, Zhang W, Li J, Zhang Y. Snapshots of catalysis: Structure of covalently bound substrate trapped in Mycobacterium tuberculosis thiazole synthase (ThiG). Biochem Biophys Res Commun 2018; 497:214-219. [PMID: 29428731 DOI: 10.1016/j.bbrc.2018.02.056] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 02/06/2018] [Indexed: 10/18/2022]
Abstract
Increasing drug resistance in Mycobacterium tuberculosis (Mtb) has necessitated the design of new anti-mycobacterial drugs with novel targets. Thiazole synthase (ThiG) is an essential enzyme and a potential drug target in Mtb that catalyzes the formation of the thiazole moiety of thiamin-pyrophosphate from 1-deoxy-d-xylulose-5-phosphate (DXP), dehydroglycine and ThiS-thiocarboxylate. To uncover the catalysis mechanism and design potent and selective anti-mycobacterial compounds targeting ThiG, we determined the crystal structure of MtbThiG at 1.5 Å resolution, for the first time, snapshotting a covalently bound substrate trapped in the catalytic pocket. The structure showed a (β/α)8 barrel overall fold as well as the dimer form of MtbThiG existing in solution. In the central pocket, Lys98 is the key residue forming a protonated carbinolamine intermediate, a functional Schiff base precursor, with DXP. The carbinolamine is further stabilized by active site residues mainly through hydrogen bonds. This work revealed that a protonated carbinolamine is initially formed and then it is dehydrated to the imine form of Schiff base during the early catalysis steps. Our research will provide useful information for understanding the ThiG function and lay the basis for future drug design by targeting this essential protein.
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Affiliation(s)
- Jia Zhang
- Key Laboratory of Medical Molecular Virology, Institute of Medical Microbiology, Department of Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, 200040, China
| | - Bing Zhang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, 201210, China; National Center for Protein Science Shanghai, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 201210, China
| | - Yao Zhao
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, 201210, China; National Center for Protein Science Shanghai, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 201210, China
| | - Xiuna Yang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, 201210, China; National Center for Protein Science Shanghai, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 201210, China
| | - Min Huang
- National Center for Protein Science Shanghai, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 201210, China
| | - Peng Cui
- Key Laboratory of Medical Molecular Virology, Institute of Medical Microbiology, Department of Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, 200040, China
| | - Wenhong Zhang
- Key Laboratory of Medical Molecular Virology, Institute of Medical Microbiology, Department of Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, 200040, China
| | - Jun Li
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, 201210, China; National Center for Protein Science Shanghai, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 201210, China.
| | - Ying Zhang
- Key Laboratory of Medical Molecular Virology, Institute of Medical Microbiology, Department of Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, 200040, China; Department of Molecular Microbiology and Immunology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, 21205, USA.
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18
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Bourdin B, Briot J, Tétreault MP, Sauvé R, Parent L. Negatively charged residues in the first extracellular loop of the L-type Ca V1.2 channel anchor the interaction with the Ca Vα2δ1 auxiliary subunit. J Biol Chem 2017; 292:17236-17249. [PMID: 28864774 PMCID: PMC5655503 DOI: 10.1074/jbc.m117.806893] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Revised: 08/18/2017] [Indexed: 12/20/2022] Open
Abstract
Voltage-gated L-type CaV1.2 channels in cardiomyocytes exist as heteromeric complexes. Co-expression of CaVα2δ1 with CaVβ/CaVα1 proteins reconstitutes the functional properties of native L-type currents, but the interacting domains at the CaV1.2/CaVα2δ1 interface are unknown. Here, a homology-based model of CaV1.2 identified protein interfaces between the extracellular domain of CaVα2δ1 and the extracellular loops of the CaVα1 protein in repeats I (IS1S2 and IS5S6), II (IIS5S6), and III (IIIS5S6). Insertion of a 9-residue hemagglutinin epitope in IS1S2, but not in IS5S6 or in IIS5S6, prevented the co-immunoprecipitation of CaV1.2 with CaVα2δ1. IS1S2 contains a cluster of three conserved negatively charged residues Glu-179, Asp-180, and Asp-181 that could contribute to non-bonded interactions with CaVα2δ1. Substitutions of CaV1.2 Asp-181 impaired the co-immunoprecipitation of CaVβ/CaV1.2 with CaVα2δ1 and the CaVα2δ1-dependent shift in voltage-dependent activation gating. In contrast, single substitutions in CaV1.2 in neighboring positions in the same loop (179, 180, and 182–184) did not significantly alter the functional up-regulation of CaV1.2 whole-cell currents. However, a negatively charged residue at position 180 was necessary to convey the CaVα2δ1-mediated shift in the activation gating. We also found a more modest contribution from the positively charged Arg-1119 in the extracellular pore region in repeat III of CaV1.2. We conclude that CaV1.2 Asp-181 anchors the physical interaction that facilitates the CaVα2δ1-mediated functional modulation of CaV1.2 currents. By stabilizing the first extracellular loop of CaV1.2, CaVα2δ1 may up-regulate currents by promoting conformations of the voltage sensor that are associated with the channel's open state.
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Affiliation(s)
- Benoîte Bourdin
- Centre de Recherche de l'Institut de Cardiologie de Montréal, Université de Montréal, Montréal, Québec H3C 3J7, Canada
| | - Julie Briot
- Centre de Recherche de l'Institut de Cardiologie de Montréal, Université de Montréal, Montréal, Québec H3C 3J7, Canada.,From the Département de Pharmacologie et Physiologie, Faculté de Médecine, and
| | - Marie-Philippe Tétreault
- Centre de Recherche de l'Institut de Cardiologie de Montréal, Université de Montréal, Montréal, Québec H3C 3J7, Canada
| | - Rémy Sauvé
- From the Département de Pharmacologie et Physiologie, Faculté de Médecine, and
| | - Lucie Parent
- Centre de Recherche de l'Institut de Cardiologie de Montréal, Université de Montréal, Montréal, Québec H3C 3J7, Canada .,From the Département de Pharmacologie et Physiologie, Faculté de Médecine, and
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