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Budhraja A, Pandey S, Kannan S, Verma CS, Venkatraman P. The polybasic insert, the RBD of the SARS-CoV-2 spike protein, and the feline coronavirus - evolved or yet to evolve. Biochem Biophys Rep 2021; 25:100907. [PMID: 33521335 PMCID: PMC7833556 DOI: 10.1016/j.bbrep.2021.100907] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 01/05/2021] [Accepted: 01/05/2021] [Indexed: 11/20/2022] Open
Abstract
Recent research on the SARS-CoV-2 pandemic has exploded around the furin-cleavable polybasic insert PRRAR↓S, found within the spike protein. The insert and the receptor-binding domain, (RBD), are vital clues in the Sherlock Holmes-like investigation into the origin of the virus and in its zoonotic crossover. Based on comparative analysis of the whole genome and the sequence features of the insert and the RBD domain, the bat and the pangolin have been proposed as very likely intermediary hosts. In this study, using the various databases, in-house developed tools, sequence comparisons, structure-guided docking, and molecular dynamics simulations, we cautiously present a fresh, theoretical perspective on the SARS-CoV-2 virus activation and its intermediary host. They are a) the SARS-CoV-2 has not yet acquired a fully optimal furin binding site or this seemingly less optimal sequence, PRRARS, has been selected for survival; b) in structural models of furin complexed with peptides, PRRAR↓S binds less well and with distinct differences as compared to the all basic RRKRR↓S; c) these differences may be exploited for the design of virus-specific inhibitors; d) the novel polybasic insert of SARS-CoV-2 may be promiscuous enough to be cleaved by multiple enzymes of the human airway epithelium and tissues which may explain its unexpected broad tropism; e) the RBD domain of the feline coronavirus spike protein carries residues that are responsible for high-affinity binding of the SARS-CoV-2 to the ACE 2 receptor; f) en route zoonotic transfer, the virus may have passed through the domestic cat whose very human-like ACE2 receptor and furin may have played some role in optimizing the traits required for zoonotic transfer. Polybasic insert of the SARS-CoV-2 spike protein is rare among several hundred proteins with a motif ‘RRARS’. SARS CoV-2 shares furin-like site and RBD interface residues including hotspot sites, with some of the lethal form of Feline coronavirus spike protein and those from the healthy cats. Polybasic sequence PRRARS binds less well to furin in structural models. SARS-CoV-2 may have passed through the domestic cat during zoonotic transfer.
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Affiliation(s)
- Anshul Budhraja
- School of Biotechnology and Bioinformatics, D.Y. Patil University, Sector 15, Plot No 50, CBD Belapur, Navi Mumbai, Maharashtra, 400614, India
- Protein Interactome Lab for Structural and Functional Biology, Advanced Centre for Treatment, Research and Education in Cancer, Sector 22, Kharghar, Navi Mumbai, Maharashtra, 410210, India
- Homi Bhabha National Institute, 2nd Floor, BARC Training School Complex, Anushaktinagar, Mumbai, Maharashtra, 400094, India
| | - Sakshi Pandey
- School of Biotechnology and Bioinformatics, D.Y. Patil University, Sector 15, Plot No 50, CBD Belapur, Navi Mumbai, Maharashtra, 400614, India
- Protein Interactome Lab for Structural and Functional Biology, Advanced Centre for Treatment, Research and Education in Cancer, Sector 22, Kharghar, Navi Mumbai, Maharashtra, 410210, India
- Homi Bhabha National Institute, 2nd Floor, BARC Training School Complex, Anushaktinagar, Mumbai, Maharashtra, 400094, India
| | - Srinivasaraghavan Kannan
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, 138671, Singapore
| | - Chandra S. Verma
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, 138671, Singapore
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, 117543, Singapore
| | - Prasanna Venkatraman
- Protein Interactome Lab for Structural and Functional Biology, Advanced Centre for Treatment, Research and Education in Cancer, Sector 22, Kharghar, Navi Mumbai, Maharashtra, 410210, India
- Homi Bhabha National Institute, 2nd Floor, BARC Training School Complex, Anushaktinagar, Mumbai, Maharashtra, 400094, India
- Corresponding author. Protein Interactome Lab for Structural and Functional Biology, Advanced Centre for Treatment, Research and Education in Cancer, Sector 22, Kharghar, Navi Mumbai, Maharashtra, 410210, India.
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Rolas L, Boussif A, Weiss E, Lettéron P, Haddad O, El-Benna J, Rautou PE, Moreau R, Périanin A. NADPH oxidase depletion in neutrophils from patients with cirrhosis and restoration via toll-like receptor 7/8 activation. Gut 2018; 67:1505-1516. [PMID: 28601846 DOI: 10.1136/gutjnl-2016-313443] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Revised: 04/27/2017] [Accepted: 05/01/2017] [Indexed: 12/20/2022]
Abstract
OBJECTIVE Cirrhosis downregulates phagocyte oxidant production via their antibacterial superoxide-generating system, NADPH oxidase (NOX2) and increases patients' susceptibility to infection and mortality rate. To explore novel biochemical parameters that explain susceptibility to infections, we investigated the expression of NOX2 and partners in neutrophils of patients with severe alcoholic cirrhosis and have provided a novel approach to restore superoxide production capacity in patients' neutrophils and blood. DESIGN Neutrophils were isolated from patients with decompensated alcoholic cirrhosis. NOX2 activity was assessed after stimulation of purified neutrophils or whole blood with the bacterial-derived peptide fMet-Leu-Phe. The expression of NOX2 and partners was studied by western blot analysis, flow cytometry and reverse transcription-PCR. RESULTS The impaired superoxide production by patients' neutrophils was associated with a severe deficient expression of the NADPH oxidase catalytic core flavocytochrome-b558 (gp91 phox /NOX2 and p22 phox ), its cytosolic partner p47 phox but not p67 phox . NOX2 expression decreased rapidly by protein degradation involving elastase released during degranulation of healthy neutrophils stimulated with fMet-Leu-Phe, or highly present in patients' plasma. Interestingly, the deficient superoxide production was reversed by treatment of patients' neutrophils and whole blood with toll-like receptor 7/8 (TLR7/8) agonists. This treatment stimulated a rapid NOX2 transcription and translation through a process involving mammalian target of rapamycin (mTOR) whose expression was also deficient in patients' neutrophils. NOX2 expression was also increased by the TLR4 agonist lipopolysaccharide but with only a modest improvement of reactive oxygen species production. CONCLUSION Impairment of neutrophil oxidants production in alcoholic cirrhosis is associated with NOX2 degradation and deficient mTOR-dependent translational machinery. The NOX2 depletion can be reversed via TRL7/8 activation and might be used to restore antimicrobial responses of immunocompromised patients.
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Affiliation(s)
- Loïc Rolas
- INSERM UMRS-1149, Faculté de Médecine Xavier Bichat, Paris, France.,CNRS ERL-8252, Centre de Recherche sur l'Inflammation, Paris, France.,Université Paris Diderot, Sorbonne Paris Cité, Laboratoire d'Excellence INFLAMEX, Paris, France
| | - Abdelali Boussif
- INSERM UMRS-1149, Faculté de Médecine Xavier Bichat, Paris, France.,CNRS ERL-8252, Centre de Recherche sur l'Inflammation, Paris, France.,Université Paris Diderot, Sorbonne Paris Cité, Laboratoire d'Excellence INFLAMEX, Paris, France.,Département de Biochimie, Université de Batna, Faculté de Biologie, Batna, Algérie
| | - Emmanuel Weiss
- INSERM UMRS-1149, Faculté de Médecine Xavier Bichat, Paris, France.,CNRS ERL-8252, Centre de Recherche sur l'Inflammation, Paris, France.,Université Paris Diderot, Sorbonne Paris Cité, Laboratoire d'Excellence INFLAMEX, Paris, France.,Département d'Anesthésie Réanimation, Hôpital Beaujon, APHP, Clichy, France
| | - Philippe Lettéron
- INSERM UMRS-1149, Faculté de Médecine Xavier Bichat, Paris, France.,CNRS ERL-8252, Centre de Recherche sur l'Inflammation, Paris, France.,Université Paris Diderot, Sorbonne Paris Cité, Laboratoire d'Excellence INFLAMEX, Paris, France
| | - Oualid Haddad
- UFR SMBH, Université Paris 13, Sorbonne Paris Cité, Bobigny, France
| | - Jamel El-Benna
- INSERM UMRS-1149, Faculté de Médecine Xavier Bichat, Paris, France.,CNRS ERL-8252, Centre de Recherche sur l'Inflammation, Paris, France.,Université Paris Diderot, Sorbonne Paris Cité, Laboratoire d'Excellence INFLAMEX, Paris, France
| | - Pierre-Emmanuel Rautou
- Département Hospitalo-Universitaire (DHU) Unity, Service d'Hépatologie, Hôpital Beaujon, APHP, Clichy, France.,INSERM U970, Paris Cardiovascular Research Center-PARCC, Paris, France
| | - Richard Moreau
- INSERM UMRS-1149, Faculté de Médecine Xavier Bichat, Paris, France.,CNRS ERL-8252, Centre de Recherche sur l'Inflammation, Paris, France.,Université Paris Diderot, Sorbonne Paris Cité, Laboratoire d'Excellence INFLAMEX, Paris, France.,Département Hospitalo-Universitaire (DHU) Unity, Service d'Hépatologie, Hôpital Beaujon, APHP, Clichy, France
| | - Axel Périanin
- INSERM UMRS-1149, Faculté de Médecine Xavier Bichat, Paris, France.,CNRS ERL-8252, Centre de Recherche sur l'Inflammation, Paris, France.,Université Paris Diderot, Sorbonne Paris Cité, Laboratoire d'Excellence INFLAMEX, Paris, France
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Somavarapu AK, Balakrishnan S, Gautam AKS, Palmer DS, Venkatraman P. Structural interrogation of phosphoproteome identified by mass spectrometry reveals allowed and disallowed regions of phosphoconformation. BMC STRUCTURAL BIOLOGY 2014; 14:9. [PMID: 24618394 PMCID: PMC4007652 DOI: 10.1186/1472-6807-14-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2013] [Accepted: 03/04/2014] [Indexed: 12/22/2022]
Abstract
Background High-throughput mass spectrometric (HT-MS) study is the method of choice for monitoring global changes in proteome. Data derived from these studies are meant for further validation and experimentation to discover novel biological insights. Here we evaluate use of relative solvent accessible surface area (rSASA) and DEPTH as indices to assess experimentally determined phosphorylation events deposited in PhosphoSitePlus. Results Based on accessibility, we map these identifications on allowed (accessible) or disallowed (inaccessible) regions of phosphoconformation. Surprisingly a striking number of HT-MS/MS derived events (1461/5947 sites or 24.6%) are present in the disallowed region of conformation. By considering protein dynamics, autophosphorylation events and/or the sequence specificity of kinases, 13.8% of these phosphosites can be moved to the allowed region of conformation. We also demonstrate that rSASA values can be used to increase the confidence of identification of phosphorylation sites within an ambiguous MS dataset. Conclusion While MS is a stand-alone technique for the identification of vast majority of phosphorylation events, identifications within disallowed region of conformation will benefit from techniques that independently probe for phosphorylation and protein dynamics. Our studies also imply that trapping alternate protein conformations may be a viable alternative to the design of inhibitors against mutation prone drug resistance kinases.
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Affiliation(s)
| | | | | | | | - Prasanna Venkatraman
- Protein Interactome Lab for Structural and Functional Biology, Advanced Center for Treatment Research and Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai, Maharashtra 410210, India.
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Nanaware PP, Ramteke MP, Somavarapu AK, Venkatraman P. Discovery of multiple interacting partners of gankyrin, a proteasomal chaperone and an oncoprotein--evidence for a common hot spot site at the interface and its functional relevance. Proteins 2014; 82:1283-300. [PMID: 24338975 DOI: 10.1002/prot.24494] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2013] [Revised: 11/20/2013] [Accepted: 12/09/2013] [Indexed: 12/27/2022]
Abstract
Gankyrin, a non-ATPase component of the proteasome and a chaperone of proteasome assembly, is also an oncoprotein. Gankyrin regulates a variety of oncogenic signaling pathways in cancer cells and accelerates degradation of tumor suppressor proteins p53 and Rb. Therefore gankyrin may be a unique hub integrating signaling networks with the degradation pathway. To identify new interactions that may be crucial in consolidating its role as an oncogenic hub, crystal structure of gankyrin-proteasome ATPase complex was used to predict novel interacting partners. EEVD, a four amino acid linear sequence seems a hot spot site at this interface. By searching for EEVD in exposed regions of human proteins in PDB database, we predicted 34 novel interactions. Eight proteins were tested and seven of them were found to interact with gankyrin. Affinity of four interactions is high enough for endogenous detection. Others require gankyrin overexpression in HEK 293 cells or occur endogenously in breast cancer cell line- MDA-MB-435, reflecting lower affinity or presence of a deregulated network. Mutagenesis and peptide inhibition confirm that EEVD is the common hot spot site at these interfaces and therefore a potential polypharmacological drug target. In MDA-MB-231 cells in which the endogenous CLIC1 is silenced, trans-expression of Wt protein (CLIC1_EEVD) and not the hot spot site mutant (CLIC1_AAVA) resulted in significant rescue of the migratory potential. Our approach can be extended to identify novel functionally relevant protein-protein interactions, in expansion of oncogenic networks and in identifying potential therapeutic targets.
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Affiliation(s)
- Padma P Nanaware
- Advanced Centre for Treatment, Research and Education in Cancer, Navi Mumbai, India
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Dhamne H, Chande AG, Mukhopadhyaya R. Lentiviral vector platform for improved erythropoietin expression concomitant with shRNA mediated host cell elastase down regulation. Plasmid 2014; 71:1-7. [DOI: 10.1016/j.plasmid.2013.11.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2013] [Revised: 11/27/2013] [Accepted: 11/30/2013] [Indexed: 01/28/2023]
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From prediction to experimental validation: desmoglein 2 is a functionally relevant substrate of matriptase in epithelial cells and their reciprocal relationship is important for cell adhesion. Biochem J 2012; 447:61-70. [PMID: 22783993 DOI: 10.1042/bj20111432] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Accurate identification of substrates of a protease is critical in defining its physiological functions. We previously predicted that Dsg-2 (desmoglein-2), a desmosomal protein, is a candidate substrate of the transmembrane serine protease matriptase. The present study is an experimental validation of this prediction. As demanded by our published method PNSAS [Prediction of Natural Substrates from Artificial Substrate of Proteases; Venkatraman, Balakrishnan, Rao, Hooda and Pol (2009) PLoS ONE 4, e5700], this enzyme-substrate pair shares a common subcellular distribution and the predicted cleavage site is accessible to the protease. Matriptase knock-down cells showed enhanced immunoreactive Dsg-2 at the cell surface and formed larger cell clusters. When matriptase was mobilized from intracellular storage deposits to the cell surface there was a decrease in the band intensity of Dsg-2 in the plasma membrane fractions with a concomitant accumulation of a cleaved product in the conditioned medium. The exogenous addition of pure active recombinant matriptase decreased the surface levels of immunoreactive Dsg-2, whereas the levels of CD44 and E-cadherin were unaltered. Dsg-2 with a mutation at the predicted cleavage site is resistant to cleavage by matriptase. Thus Dsg-2 seems to be a functionally relevant physiological substrate of matriptase. Since breakdown of cell-cell contact is the first major event in invasion, this reciprocal relationship is likely to have a profound role in cancers of epithelial origin. Our algorithm has the potential to become an integral tool for discovering new protease-substrate pairs.
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Singh Gautam AK, Balakrishnan S, Venkatraman P. Direct ubiquitin independent recognition and degradation of a folded protein by the eukaryotic proteasomes-origin of intrinsic degradation signals. PLoS One 2012; 7:e34864. [PMID: 22506054 PMCID: PMC3323579 DOI: 10.1371/journal.pone.0034864] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2011] [Accepted: 03/08/2012] [Indexed: 11/18/2022] Open
Abstract
Eukaryotic 26S proteasomes are structurally organized to recognize, unfold and degrade globular proteins. However, all existing model substrates of the 26S proteasome in addition to ubiquitin or adaptor proteins require unstructured regions in the form of fusion tags for efficient degradation. We report for the first time that purified 26S proteasome can directly recognize and degrade apomyoglobin, a globular protein, in the absence of ubiquitin, extrinsic degradation tags or adaptor proteins. Despite a high affinity interaction, absence of a ligand and presence of only helices/loops that follow the degradation signal, apomyoglobin is degraded slowly by the proteasome. A short floppy F-helix exposed upon ligand removal and in conformational equilibrium with a disordered structure is mandatory for recognition and initiation of degradation. Holomyoglobin, in which the helix is buried, is neither recognized nor degraded. Exposure of the floppy F-helix seems to sensitize the proteasome and primes the substrate for degradation. Using peptide panning and competition experiments we speculate that initial encounters through the floppy helix and additional strong interactions with N-terminal helices anchors apomyoglobin to the proteasome. Stabilizing helical structure in the floppy F-helix slows down degradation. Destabilization of adjacent helices accelerates degradation. Unfolding seems to follow the mechanism of helix unraveling rather than global unfolding. Our findings while confirming the requirement for unstructured regions in degradation offers the following new insights: a) origin and identification of an intrinsic degradation signal in the substrate, b) identification of sequences in the native substrate that are likely to be responsible for direct interactions with the proteasome, and c) identification of critical rate limiting steps like exposure of the intrinsic degron and destabilization of an unfolding intermediate that are presumably catalyzed by the ATPases. Apomyoglobin emerges as a new model substrate to further explore the role of ATPases and protein structure in proteasomal degradation.
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Affiliation(s)
| | | | - Prasanna Venkatraman
- Advanced Centre for Treatment, Research and Education in Cancer, Kharghar, Navi Mumbai, India
- * E-mail:
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Song J, Tan H, Boyd SE, Shen H, Mahmood K, Webb GI, Akutsu T, Whisstock JC, Pike RN. Bioinformatic approaches for predicting substrates of proteases. J Bioinform Comput Biol 2011; 9:149-78. [PMID: 21328711 DOI: 10.1142/s0219720011005288] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2010] [Revised: 10/08/2010] [Accepted: 10/09/2010] [Indexed: 11/18/2022]
Abstract
Proteases have central roles in "life and death" processes due to their important ability to catalytically hydrolyze protein substrates, usually altering the function and/or activity of the target in the process. Knowledge of the substrate specificity of a protease should, in theory, dramatically improve the ability to predict target protein substrates. However, experimental identification and characterization of protease substrates is often difficult and time-consuming. Thus solving the "substrate identification" problem is fundamental to both understanding protease biology and the development of therapeutics that target specific protease-regulated pathways. In this context, bioinformatic prediction of protease substrates may provide useful and experimentally testable information about novel potential cleavage sites in candidate substrates. In this article, we provide an overview of recent advances in developing bioinformatic approaches for predicting protease substrate cleavage sites and identifying novel putative substrates. We discuss the advantages and drawbacks of the current methods and detail how more accurate models can be built by deriving multiple sequence and structural features of substrates. We also provide some suggestions about how future studies might further improve the accuracy of protease substrate specificity prediction.
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Affiliation(s)
- Jiangning Song
- Department of Biochemistry and Molecular Biology, Monash University, Victoria 3800, Australia.
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