scholarly journals Analysis of the Amino Acid Sequence Variation of the 67–72p Protein and the Structural Pili Proteins of Corynebacterium diphtheriae for their Suitability as Potential Vaccine Antigens

2019 ◽  
Vol 68 (2) ◽  
pp. 233-246
Author(s):  
KLAUDIA BRODZIK ◽  
KATARZYNA KRYSZTOPA-GRZYBOWSKA ◽  
MACIEJ POLAK ◽  
JAKUB LACH ◽  
DOMINIK STRAPAGIEL ◽  
...  
Keyword(s):  
Amino Acid ◽  
Vaccine Development ◽  
Corynebacterium Diphtheriae ◽  
Amino Acid Sequences ◽  
Host Cells ◽  
Structural Proteins ◽  
Bioinformatics Analyses ◽  
Conserved Regions ◽  
Vaccine Antigens ◽  
Potential Vaccine

The aim of this study was to identify the potential vaccine antigens in Corynebacterium diphtheriae strains by in silico analysis of the amino acid variation in the 67–72p surface protein that is involved in the colonization and induction of epithelial cell apoptosis in the early stages of infection. The analysis of pili structural proteins involved in bacterial adherence to host cells and related to various types of infections was also performed. A polymerase chain reaction (PCR) was carried out to amplify the genes encoding the 67–72p protein and three pili structural proteins (SpaC, SpaI, SapD) and the products obtained were sequenced. The nucleotide sequences of the particular genes were translated into amino acid sequences, which were then matched among all the tested strains using bioinformatics tools. In the last step, the affinity of the tested proteins to major histocompatibility complex (MHC) classes I and II, and linear B-cell epitopes was analyzed. The variations in the nucleotide sequence of the 67–72p protein and pili structural proteins among C. diphtheriae strains isolated from various infections were noted. A transposition of the insertion sequence within the gene encoding the SpaC pili structural proteins was also detected. In addition, the bioinformatics analyses enabled the identification of epitopes for B-cells and T-cells in the conserved regions of the proteins, thus, demonstrating that these proteins could be used as antigens in the potential vaccine development. The results identified the most conserved regions in all tested proteins that are exposed on the surface of C. diphtheriae cells.

scholarly journals Immunoinformatic Analysis to Identify Proteins to Be Used as Potential Targets to Control Bovine Anaplasmosis

2020 ◽  
Vol 2020 ◽  
pp. 1-8
Author(s):  
Sergio D. Rodríguez-Camarillo ◽  
Rosa E. Quiroz-Castañeda ◽  
Hugo Aguilar-Díaz ◽  
José E. Vara-Pastrana ◽  
Diego Pescador-Pérez ◽  
...  
Keyword(s):  
Amino Acid ◽  
New Technologies ◽  
Bioinformatic Analysis ◽  
Amino Acid Sequences ◽  
Bioinformatics Analyses ◽  
Control And Prevention ◽  
Potential Vaccine ◽  
Bovine Anaplasmosis ◽  
First Time ◽  
New Strategies

Omics sciences and new technologies to sequence full genomes provide valuable data that are revealed only after detailed bioinformatic analysis is performed. In this work, we analyzed the genomes of seven Mexican Anaplasma marginale strains and the data from a transcriptome analysis of the tick Rhipicephalus microplus. The aim of this analysis was to identify protein sequences with predicted features to be used as potential targets to control the bacteria or tick-vector transmission. We chose three amino acid sequences different to all proteins previously reported in A. marginale that have been used as potential vaccine candidates, and also, we report, for the first time, the presence of a peroxinectin protein sequence in the transcriptome of R. microplus, a protein associated with the immune response of ticks. The bioinformatics analyses revealed the presence of B-cell epitopes in all the amino acid sequences chosen, which opens the way for their likely use as single or arranged peptides to develop new strategies for the control and prevention of bovine anaplasmosis transmitted by ticks.

scholarly journals Expression and characterisation of the ryegrass mottle virus non-structural proteins

2010 ◽  
Vol 64 (5-6) ◽  
pp. 215-222
Author(s):  
Ina Baļķe ◽  
Gunta Resēviča ◽  
Dace Skrastiņa ◽  
Andris Zeltiņš
Keyword(s):  
Amino Acid ◽  
Expression System ◽  
Protein Structures ◽  
Amino Acid Sequences ◽  
Host Cells ◽  
Structural Proteins ◽  
Mottle Virus ◽  
Expression Vectors ◽  
Structural Protein ◽  
E Coli

Expression and characterisation of the ryegrass mottle virus non-structural proteins The Ryegrass mottle virus (RGMoV) single-stranded RNA genome is organised into four open reading frames (ORF) which encode several proteins: ORF1 encodes protein P1, ORF2a contains the membrane-associated 3C-like serine protease, genome-linked protein VPg and a P16 protein gene. ORF2b encodes replicase RdRP and the only structural protein, coat protein, is synthesised from ORF3. To obtain the non-structural proteins in preparative quantities and to characterise them, the corresponding RGMoV gene cDNAs were cloned in pET- and pColdI-derived expression vectors and overexpressed in several E. coli host cells. For protease and RdRP, the best expression system containing pColdI vector and E. coli WK6 strain was determined. VPg and P16 proteins were obtained from the pET- or pACYC- vectors and E. coli BL21 (DE3) host cells and purified using Ni-Sepharose affinity chromatography. Attempts to crystallize VPg and P16 were unsuccessful, possibly due to non-structured amino acid sequences in both protein structures. Methods based on bioinformatic analysis indicated that the entire VPg domain and the C-terminal part of the P16 contain unstructured amino acid stretches, which possibly prevented the formation of crystals.

scholarly journals Structural and antigenic variance between novel influenza A/H1N1/2009 and influenza A/H1N1/2008 viruses

2009 ◽  
Vol 4 (01) ◽  
pp. 001-006 ◽  
Author(s):  
Shailendra K Saxena ◽  
Niraj Mishra ◽  
Rakhi Saxena ◽  
ML Arvinda Swamy ◽  
Pranshu Sahgal ◽  
...  
Keyword(s):  
Amino Acid ◽  
Influenza A ◽  
Vaccine Development ◽  
Amino Acid Sequences ◽  
Host Cells ◽  
Antigenic Analysis ◽  
Amino Acid Homology ◽  
Viral Attachment ◽  
Influenza A H1n1 ◽  
Significant Difference

Background: The emergence of influenza A/H1N1/2009 is alarming. The severity of previous epidemics suggests that the susceptibility of the human population to H1N1 is directly proportional to the degree of changes in hemagglutinin/HA and neuraminidase/NA; therefore, H1N1/2009 and H1N1/2008 were analyzed for their sequence as well as structural divergence. Methodology: The structural and sequence divergence of H1N1/2009 and H1N1/2008 strains were analyzed by aligning HA and NA amino acid sequences by using ClustalW and ESyPred3D software. To determine the variations in sites of viral attachment to host cells, a comparison between amino acid sequences of HA and NA glycosylation sites was performed with NetNGlyc software. The antigenic divergence was executed by CTL epitope prediction method.  Results: The amino acid homology levels of H1N1/2009 were 20.32% and 18.73% compared to H1N1/2008 for HA and NA genes, respectively.  In spite of the high variation in HA and NA amino acid composition, there was no significant difference in their structures. Antigenic analysis proposes that great antigenic differences exist between both the viral strains, but no addition of a new site of glycosylation was observed. Conclusions: To our knowledge, this is the first report suggesting that the circulating novel influenza virus A/H1N1/2009 attaches to the same glycosylation receptor sites as its predecessor influenza A/H1N1/2008 virus, but is antigenically different and may have the potential for initiating a significant pandemic. Our study may facilitate the development of better therapeutics and preventive strategies, as well as impart clues for novel H1N1 diagnostic and vaccine development.

scholarly journals Insights into the mysterious genetic variation profile oftprKinTreponema pallidumunder the development of natural human syphilis infection

2019 ◽  
Author(s):  
Dan Liu ◽  
Man-Li Tong ◽  
Yong Lin ◽  
Li-Li Liu ◽  
Li-Rong Lin ◽  
...  
Keyword(s):  
Amino Acid ◽  
Immune Evasion ◽  
High Frequency ◽  
Critical Role ◽  
Treponema Pallidum ◽  
Secondary Syphilis ◽  
Human Infection ◽  
Amino Acid Sequences ◽  
Potential Vaccine

AbstractAlthough the variations of thetprKgene inTreponema pallidumwere considered to play a critical role in the pathogenesis of syphilis, how actual variable characteristics oftprKin the course of natural human infection enabling the pathogen’s survive has thus far remained unclear. Here, we performed NGS to investigatetprKofT. pallidumdirectly from primary and secondary syphilis samples. Compared with diversity intprKof the strains from primary syphilis samples, there were more mixture variants found within seven V regions of thetprKgene among the strains from secondary syphilis samples, and the frequencies of predominant sequences within V regions oftprKwere generally decreased (less than 80%) with the proportion of minor variants in 10-60% increasing. Noteworthy, the variations within V regions oftprKalways obeyed a strict 3 bp changing pattern. AndtprKin the strains from the two-stage samples kept some stable amino acid sequences within V regions. Particularly, the amino acid sequences IASDGGAIKH and IASEDGSAGNLKH in V1 not only presented a high proportion of inter-population sharing, but also presented a relatively high frequency (above 80%) in the populations. Besides,tprKalways demonstrated remarkable variability in V6 at both the intra- and inter-strain levels regardless of the course. These findings unveiled that the different profile oftprK in T. pallidumdirectly from primary and secondary syphilis samples, indicating that throughout the development of syphilisT. pallidumconstantly varies its domaintprKgene to obtain the best adaptation to the host. While this changing was always subjected a strict gene conversion mechanism to keep an abnormal TprK. The highly stable peptides found in V1 would probably be promising potential vaccine components. And the highly heterogenetic regions (e.g. V6) could provide insight into the mysterious role oftprKin immune evasion.Author summaryAlthough the variations of thetprKgene inTreponema pallidumwere considered to play a critical role in the pathogenesis of syphilis, how actual variable characteristics oftprKin the course of natural human infection enabling the pathogen’s survive has thus far remained unclear. Here, we performed next-generation sequencing, a more sensitive and reliable approach, to investigatetprKofTreponema pallidumdirectly from primary and secondary syphilis patients, revealing that the profile oftprKinT. pallidumfrom the two-stage samples was different. Within the strains from secondary syphilis patients, more mixture variants within seven V regions oftprKwere found, the frequencies of their predominant sequences were generally decreased with the proportion of minor variants in 10-60% was increased. And the variations within V regions oftprKalways obeyed a strict 3 bp changing pattern. Noteworthy, the amino acid sequences IASDGGAIKH and IASEDGSAGNLKH in V1 presented a high proportion of inter-population sharing and presented a relatively high frequency in the populations. And V6 region always demonstrated remarkable variability at intra- and inter-patient levels regardless of the course. These findings provide insights into the mysterious role of TprK in immune evasion and for further exploring the potential vaccine components.

scholarly journals World-wide Sequence Variant and Non-synonymous Amino Acid Substitution Signature in SARS-COV-2 Structural Proteins

2020 ◽  
Author(s):  
Jayanta Das ◽  
Swarup Roy
Keyword(s):  
Amino Acid ◽  
Amino Acid Substitution ◽  
World Wide ◽  
Protein Structures ◽  
Biochemical Properties ◽  
Host Cells ◽  
Structural Proteins ◽  
Single Point Mutation ◽  
Country Specific ◽  
S Proteins

Like other viruses, SARS-COV-2 too mutating and thus creating divergent variants across the world. Protein sequence variation occurs due to non-synonymous single-nucleotide polymorphism (SNP) that alter the amino acid. Amino acid substitutions on homooligomer interfaces may change the structure of the protein and hence alter the regular or known functional activities of a viral protein. Studies reveal that even a single point mutation in virus protein can significantly change their biology, leads to peculiar pathogenic properties. Therefore, an in-depth investigation of the amino acid substitution in the genomic signature of a protein is highly essential for the rapidly evolving virus-like SARS-COV-2. Investigation of world-wide and country-specific substitution features may be crucial and highly essential to decipher pathogenicity. These might be also helpful to precise structure prediction and identification of possible therapeutic targets for effective drug design. We perform extensive analysis towards highlighting and characterizing the amino acid substitution signature occurs in the four structural proteins (Spike-S, Nucleocapsid-N, Membrane-M, Envelope-E) of SARS-COV-2. We use a total of 9587 viral sequences reported from 49 different countries across the globe. In this study, we try to study the amino acid substitution patterns and its impact on change in biochemical properties, thereby possible changes in protein structures. We perform the following analysis: a) isolating and grouping variants we considered, for different protein sequences; b) identifying amino acid substitution type that are frequently and rarely occurring and reporting their location within the sequence; c) change in chemical properties due to amino acid substitution; and f) highlight country-specific divergent variation and substitution signature. In terms of mutational changes, E and M proteins are relatively stable than N and S proteins. A significant quantity of variations is observed in spike (S) proteins. Our study further reveals an interesting fact that the substitution location is random in N protein, whereas the substitution sites in M protein is less varying and almost stable. Substitutions specific to active sub-domains in S and N proteins reveals that sub-domains like Heptapeptide Repeat (HR2), Fusion peptides (FP), and Transmembrane (TM), which are involved in cellular membrane fusion and entry of the virus into the host cells, are significantly mutated. Majority of the substitutions leads to change in biochemical properties (side chain and hydropathy) of amino acid. A good number of exclusive variants are found specific to a particular country. We strongly believe that the current findings will be helpful for protein structure analysis of viral structural proteins and antiviral drug discovery.

Assessment of cathepsin D and L-like proteinases of poultry red mite, Dermanyssus gallinae (De Geer), as potential vaccine antigens

Parasitology ◽  
2012 ◽  
Vol 139 (6) ◽  
pp. 755-765 ◽  
Author(s):  
KATHRYN BARTLEY ◽  
JOHN F. HUNTLEY ◽  
HARRY W. WRIGHT ◽  
MINTU NATH ◽  
ALASDAIR J. NISBET
Keyword(s):  
Amino Acid ◽  
Cathepsin D ◽  
Proportional Hazards ◽  
Proportional Hazards Model ◽  
Dermanyssus Gallinae ◽  
Poultry Red Mite ◽  
Acid Protein ◽  
Vaccine Antigens ◽  
Potential Vaccine ◽  
Amino Acid Protein

SUMMARYVaccination is a feasible strategy for controlling the haematophagous poultry red mite Dermanyssus gallinae. A cDNA library enriched for genes upregulated after feeding was created to identify potential vaccine antigens. From this library, a gene (Dg-CatD-1) encoding a 383 amino acid protein (Dg-CatD-1) with homology to cathepsin D lysosomal aspartyl proteinases was identified as a potential vaccine candidate. A second gene (Dg-CatL-1) encoding a 341 amino acid protein (Dg-CatL-1) with homology to cathepsin L cysteine proteinases was also selected for further study. IgY obtained from naturally infested hens failed to detect Dg-CatD-1 suggesting that it is a concealed antigen. Conversely, Dg-CatL-1 was detected by IgY derived from natural-infestation, indicating that infested hens are exposed to Dg-CatL-1. Mortality rates 120 h after mites had been fed anti-Dg-CatD-1 were significantly higher than those fed control IgY (PF<0·01). In a survival analysis, fitting a proportional hazards model to the time of death of mites, anti-Dg-CatD-1 and anti-Dg-CatL-1 IgY had 4·42 and 2·13 times higher risks of dying compared with controls (PF<0·05). Dg-CatD-1 and L-1 both have potential as vaccine antigens as part of a multi-component vaccine and have the potential to be improved as vaccine antigens using alternative expression systems.

scholarly journals Sequence Conservation and Antigenic Variation of the Structural Proteins of Equine Rhinitis A Virus

2001 ◽  
Vol 75 (21) ◽  
pp. 10550-10556 ◽  
Author(s):  
Annalisa Varrasso ◽  
Heidi E. Drummer ◽  
Jin-an Huang ◽  
Rachel A. Stevenson ◽  
Nino Ficorilli ◽  
...  
Keyword(s):  
Monoclonal Antibodies ◽  
Amino Acid ◽  
Antigenic Variation ◽  
Amino Acid Sequences ◽  
Sequence Conservation ◽  
Structural Proteins ◽  
Serum Neutralization ◽  
Prototype Virus

ABSTRACT The nucleotide and deduced amino acid sequences of the P1 region of the genomes of 10 independent equine rhinitis A virus (ERAV) isolates were determined and found to be very closely related. A panel of seven monoclonal antibodies to the prototype virus ERAV.393/76 that bound to nonneutralization epitopes conserved among all 10 isolates was raised. In serum neutralization assays, rabbit polyclonal sera and sera from naturally and experimentally infected horses reacted in a consistent and discriminating manner with the 10 isolates, which indicated the existence of variation in the neutralization epitopes of these viruses.

scholarly journals Identification of Adomavirus Virion Proteins

2018 ◽  
Author(s):  
Nicole L. Welch ◽  
Michael J. Tisza ◽  
Gabriel J. Starrett ◽  
Anna K. Belford ◽  
Diana V. Pastrana ◽  
...  
Keyword(s):  
Dna Helicase ◽  
Amino Acid Sequences ◽  
Host Cells ◽  
Structural Proteins ◽  
Replicase Gene ◽  
Virion Protein ◽  
Virus Family ◽  
Animal Virus ◽  
Tumor Viruses ◽  
Emerging Virus

AbstractAdenoviruses, papillomaviruses, and polyomaviruses are collectively known as small DNA tumor viruses. Although it has long been recognized that small DNA tumor virus oncoproteins and capsid proteins show a variety of structural and functional similarities, it is unclear whether these similarities reflect descent from a common ancestor, convergent evolution, horizontal gene transfer among virus lineages, or acquisition of genes from host cells. Here, we report the discovery of a dozen new members of an emerging virus family, the Adomaviridae, that unite a papillomavirus/polyomavirus-like replicase gene with an adenovirus-like virion maturational protease. Adomaviruses were initially discovered in a lethal disease outbreak among endangered Japanese eels. New adomavirus genomes were found in additional commercially important fish species, such as tilapia, as well as in reptiles. The search for adomavirus sequences also revealed an additional candidate virus family, which we refer to as xenomaviruses, in mollusk datasets. Analysis of native adomavirus virions and expression of recombinant proteins showed that the virion structural proteins of adomaviruses are homologous to those of both adenoviruses and another emerging animal virus family called adintoviruses. The results pave the way toward development of vaccines against adomaviruses and suggest a framework that ties small DNA tumor viruses into a shared evolutionary history.Author SummaryIn contrast to cellular organisms, viruses do not encode any universally conserved genes. Even within a given family of viruses, the amino acid sequences encoded by homologous genes can diverge to the point of unrecognizability. Although members of an emerging virus family, the Adomaviridae, encode replicative DNA helicase proteins that are recognizably similar to those of polyomaviruses and papillomaviruses, the functions of other adomavirus genes have been difficult to identify. Using a combination of laboratory and bioinformatic approaches, we identify the adomavirus virion structural proteins. The results link adomavirus virion protein operons to those of other midsize non-enveloped DNA viruses, including adenoviruses and adintoviruses.

scholarly journals Typing complex meningococcal vaccines to understand diversity and population structure of key vaccine antigens

2018 ◽  
Vol 3 ◽  
pp. 151 ◽  
Author(s):  
Charlene M. C. Rodrigues ◽  
Hannah Chan ◽  
Caroline Vipond ◽  
Keith Jolley ◽  
Odile B. Harrison ◽  
...  
Keyword(s):  
Capsular Polysaccharide ◽  
Vaccine Development ◽  
Membrane Vesicles ◽  
Shotgun Proteomics ◽  
Outer Membrane Vesicles ◽  
Amino Acid Sequences ◽  
Protein Antigens ◽  
Structured Population ◽  
Vaccine Antigens ◽  
Successful Approach

Background:Protein-conjugate capsular polysaccharide vaccines can potentially control invasive meningococcal disease (IMD) caused by five (A, C, W, X, Y) of the six IMD-associated serogroups.  Concerns raised by immunological similarity of the serogroup B capsule, to human neural cell carbohydrates, has meant that ‘serogroup B substitute’ vaccines target more variable subcapsular protein antigens.  A successful approach using outer membrane vesicles (OMVs) as major vaccine components had limited strain coverage. In 4CMenB (Bexsero®), recombinant proteins have been added to ameliorate this problem. Methods:Here, scalable, portable, genomic techniques were used to investigate the Bexsero®OMV protein diversity in meningococcal populations. Shotgun proteomics identified 461 proteins in the OMV, defining a complex proteome. Amino acid sequences for the 24 proteins most likely to be involved in cross-protective immune responses were catalogued within thePubMLST.org/neisseriadatabase using a novel OMV peptide Typing (OMVT) scheme.Results:Among these proteins there was variation in the extent of diversity and association with meningococcal lineages, identified as clonal complexes (ccs), ranging from the most conserved peptides (FbpA, NEISp0578, and putative periplasmic protein, NEISp1063) to the most diverse (TbpA, NEISp1690).  There were 1752 unique OMVTs identified amongst 2492/3506 isolates examined by whole-genome sequencing (WGS). These OMVTs were grouped into clusters (sharing ≥18 identical OMVT peptides), with 45.3% of isolates assigned to one of 27 OMVT clusters. OMVTs and OMVT clusters were strongly associated with cc, genogroup, and Bexsero®antigen variants, demonstrating that combinations of OMV proteins exist in discrete, non-overlapping combinations associated with genogroup and Bexsero®Antigen Sequence Type. This highly structured population of IMD-associated meningococci is consistent with strain structure models invoking host immune selection.Conclusions:The OMVT scheme facilitates region-specific WGS investigation of meningococcal diversity and is an open-access, portable tool with applications for vaccine development, especially in the choice of antigen combinations, assessment and implementation.

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