scholarly journals Immunoinformatics approach for multi-epitope vaccine design against structural proteins and ORF1a polyproteins of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2)

Author(s):  
Khalid Mohamed Adam

Abstract Background The lack of effective treatment and a protective vaccine against the highly infectious SARS-CoV-2 has aggravated the already catastrophic global health issue. Here, in an attempt to design an efficient vaccine, a vigorous immunoinformatics approach was followed to predict the most suitable viral proteins epitopes for building that vaccine. Methods The amino acid sequences of four structural proteins (S, M, N, E) along with one potentially antigenic accessory protein (ORF1a) of SARS-CoV-2 were inspected for the most appropriate epitopes to be used for building the vaccine construct. Several immunoinformatics tools were used to assess the antigenicity, immunogenicity, allergenicity, toxigenicity, interferon-gamma inducing capacity, and the physicochemical properties of the product. Results The final candidate vaccine construct consisted of 468 amino acids, encompassing 30 epitopes. All the vaccine properties and its ability to trigger the humoral and cell-mediated immune response were validated computationally. Molecular modeling, docking to TLR3, simulation, and molecular dynamics were also carried out. Finally, a molecular clone using pET28: :mAID expression plasmid vector was prepared. Conclusion The overall results of the study suggest that the final multi-epitope chimeric construct is a potential candidate for an efficient protective vaccine against SARS-CoV-2.

Author(s):  
Khalid Mohamed Adam

Abstract Background The lack of effective treatment against the highly infectious SARS-CoV-2 has aggravated the already catastrophic global health issue. Here, in an attempt to design an efficient vaccine, a thorough immunoinformatics approach was followed to predict the most suitable viral proteins epitopes for building that vaccine. Methods The amino acid sequences of four structural proteins (S, M, N, E) along with one potentially antigenic accessory protein (ORF1a) of SARS-CoV-2 were inspected for the most appropriate epitopes to be used for building the vaccine construct. Several immunoinformatics tools were used to assess the antigenicity (VaxiJen server), immunogenicity (IEDB immunogenicity tool), allergenicity (AlgPred), toxigenicity (ToxinPred server), interferon-gamma inducing capacity (IFNepitope server), and the physicochemical properties of the construct (ProtParam tool). Results The final candidate vaccine construct consisted of 468 amino acids, encompassing 29 epitopes. The CTL epitopes that passed the antigenicity, allergenicity, toxigenicity and immunogenicity assessment were four epitopes from S protein, one from M protein, two from N protein, 12 from the ORF1a polyprotein and none from E protein. While the HTL epitopes that passed the antigenicity, allergenicity, toxigenicity and INF-$$\gamma$$ γ were one from S protein, three from M protein, six from the ORF1a polyprotein and none from N and E proteins. All the vaccine properties and its ability to trigger the humoral and cell-mediated immune response were validated computationally. Molecular modeling, docking to TLR3, simulation, and molecular dynamics were also carried out. Finally, a molecular clone using pET28::mAID expression plasmid vector was prepared. Conclusion The overall results of the study suggest that the final multi-epitope chimeric construct is a potential candidate for an efficient protective vaccine against SARS-CoV-2.


Microbiology ◽  
2005 ◽  
Vol 151 (12) ◽  
pp. 4093-4102 ◽  
Author(s):  
Saija Kiljunen ◽  
Kristo Hakala ◽  
Elise Pinta ◽  
Suvi Huttunen ◽  
Patrycja Pluta ◽  
...  

Bacteriophage ϕR1-37 was isolated based on its ability to infect strain YeO3-R1, a virulence-plasmid-cured O antigen-negative derivative of Yersinia enterocolitica serotype O : 3. In this study, the phage receptor was found to be a structure in the outer core hexasaccharide of Y. enterocolitica O : 3 LPS. The phage receptor was present in the outer core of strains of many other Y. enterocolitica serotypes, but also in some Yersinia intermedia strains. Surprisingly, the receptor structure resided in the O antigen of Yersinia pseudotuberculosis O : 9. Electron microscopy demonstrated that ϕR1-37 particles have an icosahedral head of 88 nm, a short neck of 10 nm, a long contractile tail of 236 nm, and tail fibres of at least 86 nm. This implies that the phage belongs to the order Caudovirales and the family Myoviridae in the ICTV (International Committee for Taxonomy of Viruses) classification. ϕR1-37 was found to have a lytic life cycle, with eclipse and latent periods of 40 and 50 min, respectively, and a burst size of ∼80 p.f.u. per infected cell. Restriction digestions and PFGE showed that the ϕR1-37 genome was dsDNA and ∼270 kb in size. Enzymically hydrolysed DNA was subjected to HPLC-MS/MS analysis, which demonstrated that the ϕR1-37 genome is composed of DNA in which thymidine (T) is >99 % replaced by deoxyuridine (dU). The only organisms known to have similar DNA are the Bacillus subtilis-specific bacteriophages PBS1 and PBS2. N-terminal amino acid sequences of four major structural proteins did not show any similarity to (viral) protein sequences in databases, indicating that close relatives of ϕR1-37 have not yet been characterized. Genes for two of the structural proteins, p24 and p46, were identified from the partially sequenced ϕR1-37 genome.


2008 ◽  
Vol 89 (6) ◽  
pp. 1442-1445 ◽  
Author(s):  
Marion Poenisch ◽  
Peter Staeheli ◽  
Urs Schneider

The Borna disease virus (BDV) proteins X and P are translated from a bicistronic viral mRNA. Here, it was shown that the rescue of recombinant BDV from cDNA was enhanced approximately eightfold if reconstitution of the viral polymerase complex was performed with an expression vector encoding X and P rather than P alone. The results provide evidence that appropriate amounts of X reduce the previously reported high sensitivity of the BDV polymerase to imbalances between the viral proteins N and P. These data indicate that X buffers an unfavourable excess of P, thereby stimulating the assembly of functional BDV polymerase complexes.


2020 ◽  
Vol 10 (2) ◽  
pp. 305-314
Author(s):  
I. N. Zhilinskaya

A comparative analysis on search for amino acid sequences in viral proteins causing respiratory infections (or respiratory infections syndrome) homologous to amino acid sequences from some human immune proteins was performed. The following viruses were used for comparative computer analysis: coronavirus (SARS-CoV), serotype C subgroup adenovirus C (adenoid 71 strain), measles virus (ICHINOSE-BA strain), rubella (Therien strain) and respiratory syncytial (B1 strain) virus. The search for homologous sequences in viral and human immune proteins was carried out by computer comparison of 12 amino acid fragments, which were assigned as homologous at identity in ≥ 8 positions. The data obtained showed that viral proteins contained homologous motifs in several host immune proteins involved in regulating both the inflammatory response and immune response. Mechanistically, all viruses studied were characterized by sequences homologous to host immune proteins such as complement system proteins, integrins, apoptosis inhibitory proteins, interleukins, and toll-like receptors. Such cellular proteins are actively involved in regulating host inflammatory process and immune response formation. Upon that, a set of host immune proteins, to which homologous fragments were found in viral proteins, was individual for each virus. Interestingly, the largest amount of homologous fragments (up to 20) was mainly concentrated in viral proteins with polymerase and protease activity suggesting that these proteins apart to their major role were involved in production of viral nucleic acids and might participate in regulating host immune system. Envelope, internal and non-structural viral proteins, homologous fragments were detected in much smaller quantities (from 1 to 4). In addition, two fragments homologous to various motifs of the same cellular protein were detected in some viral proteins. Thus, the data obtained further support our understanding that signs of immune system disorders in viral infections can result from multi-layered processes associated with modulation of host innate and adaptive immune system, and open up new approaches to study interaction of viruses with host immune system and identify new functions of viral proteins.


Blood ◽  
2011 ◽  
Vol 118 (21) ◽  
pp. 2167-2167
Author(s):  
Junichi Tsukada ◽  
Takehiro Higashi ◽  
Atsushi Iwashige ◽  
Takefumi Katsuragi ◽  
Naho Nomura ◽  
...  

Abstract Abstract 2167 The human leukemia virus type 1 (HTLV-1) gene expression is regulated by the viral proteins and various cellular transcription factors. HTLV-1 genome encodes not only structural proteins, but also non-structural proteins such as Tax, a transcriptional activator for STAT5 p12I, and HTLV-1 bZIP factor (HBZ) encoded by the minus strand of the viral genome. The functional analysis of the viral proteins such as Tax has shed light on the pathogenesis of adult T cell leukemia/lymphoma (ATL). Expression of Tax is enhanced by T-cell activation stimuli such as phorbol ester (PMA), phytohemagglutinin (PHA) or sodium butyrate in chronically HTLV-1-infected CD4+T-cells. Transgenic mouse studies with Tax expression under the control of the granzyme B promoter or the proximal Lck promoter showed that disease progression is associated with infiltration of activated T- and inflammatory cells, and dysregulated inflammatory cytokine production. More recently, a transgenic mouse model with Tax expression regulated by the LTR (LTR-Tax) showed that LTR-Tax CD4 positive T-cells are hyper-proliferative and hyper-responsive to immune stimulation and strongly produce Th1-, Th2- and Th17-associated cytokines. In addition, HTLV-1 infection causes inflammatory disease of the central nerve system, HTLV-1-associated myelopathy/tropical spastic paraparesis (HAM/TSP) as well as ATL. Aberrant cytokine gene expression is the hallmark of HTLV-1-associated diseases. HTLV-1 infection is widely distributed among mammalian cells. We previously demonstrated that Tax transactivates the promoter of human proIL-1β gene (IL1B) gene through association with two transcription factors, NF-IL6 (C/EBPβ) and Spi-1 (PU.1) in monocytes. Tax synergized with lipopolysaccharide (LPS) to induce IL1B promoter activity. Spi-1 is an Ets family protein restricted in expression to monocytes/myelocytes, B cells, mast cells and erythrocyte stem cells, while NF-IL6 is widely expressed. LPS, a component of the gram-negative bacterial cell wall involved in the activation of monocytes, binds to TLR4, leading to activation of TRAF6, IRAK and MyD88. We now extend these studies to elucidate roles of LPS and Tax on HTLV-1 LTR promoter regulation in monocytes. When HTLV-1 LTR reporter was transfected into THP-1 monocytic cells, LPS dose-dependently induced HTLV-1 LTR. The mid-LTR of the HTLV-1 gene possesses three potential Ets binding elements centered on a GGAA motif (PuB1, pets and PuB2). Elf-1 has been shown to be the predominant protein binding to the HTLV-1 Ets sites in Jurkat and peripheral blood T-cells. In the present study, mutation of the Ets sites, especially pets and PuB2 caused significant inhibition of LPS-induced LTR activity in THP-1 cells. EMSA studies using THP-1 nuclear extracts showed binding of Spi-1 to the HTLV-1 Ets sites in THP-1 cells. Anti-Spi-1 Ab, but not anti-Elf-1 Ab or anti-ets-1 Ab supershifted the complex generated by THP-1 nuclear extract and HTLV-1 LTR Ets site. However, when migration pattern of the complex was compared with recombinant Spi-1 in vitro translated in a reticulocyte lysate system, the THP-1 complex migrated slower than recombinant Spi-1 protein. In this regard, anti-IRF-8 Ab further recognized the slow complex. Several reports recently showed that IRF-8 functions as a heterodimeric complex with spi-1 for expression of relevant genes. On the other hand, when Tax expression vector was cotransfected into THP-1 cells along with HTLV-1 LTR reporter, Tax synergized with LPS to activate LTR. Spi-1 protein has three independent transcriptional activation domains (TAD); a TBP binding region, a Q domain, and a PEST region. GST pull-down studies using GST-Tax and 35S-labeled recombinant Spi-1 revealed that mutant Spi-1 lacking the TADs still retains the ability to interact with Tax. In contrast to THP-1 cells, Jurkat T-cells showed only a marginal increase in IL1B promoter activity following Tax expression. Mutations of the Spi-1 binding site in the IL1B promoter did not affect Tax-induced activity in Jurkat cells. Any factors did not bind to the IL1B Spi-1 site in Jurkat cells. Thus, our data suggest that LPS cooperates with Tax to activate the viral and various cellular genes in HTLV-1-infected monocytes. Spi-1 is a key player in the monocyte-specific gene regulation in HTLV-1 infection. Disclosures: No relevant conflicts of interest to declare.


2004 ◽  
Vol 78 (24) ◽  
pp. 14043-14047 ◽  
Author(s):  
Yee-Joo Tan ◽  
Burtram C. Fielding ◽  
Phuay-Yee Goh ◽  
Shuo Shen ◽  
Timothy H. P. Tan ◽  
...  

ABSTRACT Besides genes that are homologous to proteins found in other coronaviruses, the severe acute respiratory syndrome coronavirus genome also contains nine other potential open reading frames. Previously, we have characterized the expression and cellular localization of two of these “accessory” viral proteins, 3a (previously termed U274) and 7a (previously termed U122). In this study, we further examined whether they can induce apoptosis, which has been observed clinically. We showed that the overexpression of 7a, but not of 3a or the viral structural proteins, nucleocapsid, membrane, and envelope, induces apoptosis. 7a induces apoptosis via a caspase-dependent pathway and in cell lines derived from different organs, including lung, kidney, and liver.


2020 ◽  
Author(s):  
Manabu Murakami ◽  
Agnieszka M. Murakami ◽  
Kazuyoshi Hirota ◽  
Shirou Itagaki

AbstractWe introduce an efficient subcloning and expression plasmid system with two different modes (prokaryotic for expression in Escherichia coli with lac promoter and mammalian modes with cytomegalovirus promoter). The efficient subcloning (DNA insertion) is based upon a DNA topoisomerase II toxin-originated gene for effective selection with isopropyl-β-D-thiogalactoside (IPTG) induction. The new pgMAXs system is manageable size (4452 bp) and has also various types of protein tags (flag, myc, poly-histidine, Human influenza hemagglutinin, strep, and v5) for expression analysis. With pgMAXs system, various types of fluorescent proteins were subcloned and prtein expressions were confirmed. We also tried to identify epitope amino acid sequences for anti-calcium channel β2 antibody, by constructing epitope-library with DNaseI-partial digestion and subcloning into EcoRV site in pgMAXs. The new pgMAXs plasmid system enables highly efficient subcloning, simple expression in E. coli and that it has a simple deletion step of rare 8-nucleotide rare-cutter blunt-end enzymes for mammalian expression plasmid construction. Taken together, the pgMAXs system simplifies prokaryotic and mammalian gene expression analyses.


PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e5873 ◽  
Author(s):  
Qibin Wu ◽  
Shiwu Gao ◽  
Yong-Bao Pan ◽  
Yachun Su ◽  
Michael P. Grisham ◽  
...  

Glyoxalase I belongs to the glyoxalase system that detoxifies methylglyoxal (MG), a cytotoxic by-product produced mainly from triose phosphates. The concentration of MG increases rapidly under stress conditions. In this study, a novel glyoxalase I gene, designated as SoGloI was identified from sugarcane. SoGloI had a size of 1,091 bp with one open reading frame (ORF) of 885 bp encoding a protein of 294 amino acids. SoGloI was predicted as a Ni2+-dependent GLOI protein with two typical glyoxalase domains at positions 28–149 and 159–283, respectively. SoGloI was cloned into an expression plasmid vector, and the Trx-His-S-tag SoGloI protein produced in Escherichia coli was about 51 kDa. The recombinant E. coli cells expressing SoGloI compared to the control grew faster and tolerated higher concentrations of NaCl, CuCl2, CdCl2, or ZnSO4. SoGloI ubiquitously expressed in various sugarcane tissues. The expression was up-regulated under the treatments of NaCl, CuCl2, CdCl2, ZnSO4 and abscisic acid (ABA), or under simulated biotic stress conditions upon exposure to salicylic acid (SA) and methyl jasmonate (MeJA). SoGloI activity steadily increased when sugarcane was subjected to NaCl, CuCl2, CdCl2, or ZnSO4 treatments. Sub-cellular observations indicated that the SoGloI protein was located in both cytosol and nucleus. These results suggest that the SoGloI gene may play an important role in sugarcane’s response to various biotic and abiotic stresses.


2007 ◽  
Vol 81 (12) ◽  
pp. 6709-6717 ◽  
Author(s):  
Xuhua Tang ◽  
Jinlu Wu ◽  
J. Sivaraman ◽  
Choy Leong Hew

ABSTRACT White spot syndrome virus (WSSV) is a virulent pathogen known to infect various crustaceans. It has bacilliform morphology with a tail-like appendage at one end. The envelope consists of four major proteins. Envelope structural proteins play a crucial role in viral infection and are believed to be the first molecules to interact with the host. Here, we report the localization and crystal structure of major envelope proteins VP26 and VP28 from WSSV at resolutions of 2.2 and 2.0 Å, respectively. These two proteins alone account for approximately 60% of the envelope, and their structures represent the first two structural envelope proteins of WSSV. Structural comparisons among VP26, VP28, and other viral proteins reveal an evolutionary relationship between WSSV envelope proteins and structural proteins from other viruses. Both proteins adopt β-barrel architecture with a protruding N-terminal region. We have investigated the localization of VP26 and VP28 using immunoelectron microscopy. This study suggests that VP26 and VP28 are located on the outer surface of the virus and are observed as a surface protrusion in the WSSV envelope, and this is the first convincing observation for VP26. Based on our studies combined with the literature, we speculate that the predicted N-terminal transmembrane region of VP26 and VP28 may anchor on the viral envelope membrane, making the core β-barrel protrude outside the envelope, possibly to interact with the host receptor or to fuse with the host cell membrane for effective transfer of the viral infection. Furthermore, it is tempting to extend this host interaction mode to other structural viral proteins of similar structures. Our finding has the potential to extend further toward drug and vaccine development against WSSV.


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