scholarly journals DNA Polymorphisms in the pepA and PPE18 Genes among Clinical Strains of Mycobacterium tuberculosis: Implications for Vaccine Efficacy

2007 ◽  
Vol 75 (12) ◽  
pp. 5798-5805 ◽  
Author(s):  
Andrea M. Hebert ◽  
Sarah Talarico ◽  
Dong Yang ◽  
Riza Durmaz ◽  
Carl F. Marrs ◽  
...  
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Amino Acid ◽  
Genomic Diversity ◽  
Dna Polymorphisms ◽  
Effective Vaccine ◽  
Nucleotide Polymorphisms ◽  
T Cell Epitopes ◽  
Phase I Clinical Trials ◽  
Clinical Strains ◽  
Different Strains

ABSTRACT Tuberculosis continues to be a leading cause of death worldwide. Development of an effective vaccine against Mycobacterium tuberculosis is necessary to reduce the global burden of this disease. Mtb72F, consisting of the protein products of the pepA and PPE18 genes, is the first subunit tuberculosis vaccine to undergo phase I clinical trials. To obtain insight into the ability of Mtb72F to induce an immune response capable of recognizing different strains of M. tuberculosis, we investigated the genomic diversity of the pepA and PPE18 genes among 225 clinical strains of M. tuberculosis from two different geographical locations, Arkansas and Turkey, representing a broad range of genotypes of M. tuberculosis. A combination of single nucleotide polymorphisms (SNPs) and insertion/deletions resulting in amino acid changes in the PPE18 protein occurred in 47 (20.9%) of the 225 study strains, whereas SNPs resulted in amino acid changes in the PepA protein in 14 (6.2%) of the 225 study strains. Of the 122 Arkansas study strains and the 103 Turkey study strains, 32 (26.2%) and 15 (14.6%), respectively, had at least one genetic change leading to an alteration of the amino acid sequence of the PPE18 protein, and many of the changes occurred in regions previously reported to be potential T-cell epitopes. Thus, immunity induced by Mtb72F may not recognize a proportion of M. tuberculosis clinical strains.

scholarly journals rpoB Mutations in Multidrug-Resistant Strains of Mycobacterium tuberculosis Isolated in Italy

1999 ◽  
Vol 37 (4) ◽  
pp. 1197-1199 ◽  
Author(s):  
G. Pozzi ◽  
M. Meloni ◽  
E. Iona ◽  
G. Orrù ◽  
O. F. Thoresen ◽  
...  
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Amino Acid ◽  
Amino Acid Change ◽  
Multidrug Resistant ◽  
Single Base Substitution ◽  
Base Substitution ◽  
Single Base ◽  
Clinical Strains ◽  
Resistant Strains ◽  
Rifampin Resistance

Mutations of rpoB associated with rifampin resistance were studied in 37 multidrug-resistant (MDR) clinical strains ofMycobacterium tuberculosis isolated in Italy. At least one mutated codon was found in each MDR strain. It was always a single-base substitution leading to an amino acid change. Nine differentrpoB alleles, three of which had not been reported before, were found. The relative frequencies of specific mutations in this sample were different from those previously reported from different geographical areas, since 22 strains (59.5%) carried the mutated codon TTG in position 531 (Ser→Leu) and 11 (29.7%) had GAC in position 526 (His→Asp).

scholarly journals Bioinformatics analysis of calcium-dependent protein kinase 4 (CDPK4) as Toxoplasma gondii vaccine target

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Masoud Foroutan ◽  
Ali Dalir Ghaffari ◽  
Shahrzad Soltani ◽  
Hamidreza Majidiani ◽  
Ali Taghipour ◽  
...  
Keyword(s):  
Amino Acid ◽  
Toxoplasma Gondii ◽  
Average Molecular Weight ◽  
Alpha Helix ◽  
Effective Vaccine ◽  
Amino Acid Residues ◽  
T Cell Epitopes ◽  
Calcium Dependent ◽  
Aliphatic Index ◽  
Dependent Protein

Abstract Objectives Toxoplasma gondii (T. gondii), an obligate intracellular apicomplexan parasite, could affect numerous warm-blooded animals, such as humans. Calcium-dependent protein kinases (CDPKs) are essential Ca2+ signaling mediators and participate in parasite host cell egress, outer membrane motility, invasion, and cell division. Results Several bioinformatics online servers were employed to analyze and predict the important properties of CDPK4 protein. The findings revealed that CDPK4 peptide has 1158 amino acid residues with average molecular weight (MW) of 126.331 KDa. The aliphatic index and GRAVY for this protein were estimated at 66.82 and – 0.650, respectively. The findings revealed that the CDPK4 protein comprised 30.14% and 34.97% alpha-helix, 59.84% and 53.54% random coils, and 10.02% and 11.49% extended strand with SOPMA and GOR4 tools, respectively. Ramachandran plot output showed 87.87%, 8.40%, and 3.73% of amino acid residues in the favored, allowed, and outlier regions, respectively. Also, several potential B and T-cell epitopes were predicted for CDPK4 protein through different bioinformatics tools. Also, antigenicity and allergenicity evaluation demonstrated that this protein has immunogenic and non-allergenic nature. This paper presents a basis for further studies, thereby provides a fundamental basis for the development of an effective vaccine against T. gondii infection.

scholarly journals Evidence for Recombination in Mycobacterium tuberculosis

2006 ◽  
Vol 188 (23) ◽  
pp. 8169-8177 ◽  
Author(s):  
Xiaoming Liu ◽  
Michaela M. Gutacker ◽  
James M. Musser ◽  
Yun-Xin Fu
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Hot Spot ◽  
Living Environment ◽  
Major Contributor ◽  
Nucleotide Polymorphisms ◽  
Clonal Structure ◽  
Single Nucleotide ◽  
Polymorphic Pattern ◽  
History Of ◽  
Different Strains

ABSTRACT Due to its mostly isolated living environment, Mycobacterium tuberculosis is generally believed to be highly clonal, and thus recombination between different strains must be rare and is not critical for the survival of the species. To investigate the roles recombination could have possibly played in the evolution of M. tuberculosis, an analysis was conducted on previously determined genotypes of 36 synonymous single nucleotide polymorphisms (SNPs) in 3,320 M. tuberculosis isolates. The results confirmed the predominant clonal structure of the M. tuberculosis population. However, recombination between different strains was also suggested. To further resolve the issue, 175 intergenic SNPs and 234 synonymous SNPs were genotyped in 37 selected representative strains. A clear mosaic polymorphic pattern ahead of the MT0105 locus encoding a PPE (Pro-Pro-Glu) protein was obtained, which is most likely a result of recombination hot spot. Given that PPE proteins are thought to be critical in host-pathogen interactions, we hypothesize that recombination has been influential in the history of M. tuberculosis and possibly a major contributor to the diversity observed ahead of the MT0105 locus.

scholarly journals A high-frequency single nucleotide polymorphism in the MtrB sensor kinase in clinical strains of Mycobacterium tuberculosis alters its biochemical and physiological properties

PLoS ONE ◽  
2021 ◽  
Vol 16 (9) ◽  
pp. e0256664
Author(s):  
Uchenna Watson Waturuocha ◽  
Athira P. J. ◽  
Krishna Kumar Singh ◽  
Vandana Malhotra ◽  
M. S. Krishna ◽  
...  
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Pathogenic Bacteria ◽  
Physiological Role ◽  
Dna Polymorphisms ◽  
Membrane Properties ◽  
Sensor Kinase ◽  
Bacterial Cell Division ◽  
Clinical Strains ◽  
The Impact

The DNA polymorphisms found in clinical strains of Mycobacterium tuberculosis drive altered physiology, virulence, and pathogenesis in them. Although the lineages of these clinical strains can be traced back to common ancestor/s, there exists a plethora of difference between them, compared to those that have evolved in the laboratory. We identify a mutation present in ~80% of clinical strains, which maps in the HATPase domain of the sensor kinase MtrB and alters kinase and phosphatase activities, and affects its physiological role. The changes conferred by the mutation were probed by in-vitro biochemical assays which revealed changes in signaling properties of the sensor kinase. These changes also affect bacterial cell division rates, size and membrane properties. The study highlights the impact of DNA polymorphisms on the pathophysiology of clinical strains and provides insights into underlying mechanisms that drive signal transduction in pathogenic bacteria.

scholarly journals Computational Mapping of Cytotoxic T Lymphocyte epitopes of Mycobacterium Tuberculosis and their Potential Role in Vaccine Design

2021 ◽  
Author(s):  
Esakkimuthu Thangamariappan ◽  
Manikandan Mohan ◽  
Krishnan Sundar
Keyword(s):  
Mycobacterium Tuberculosis ◽  
T Lymphocyte ◽  
Potential Role ◽  
Cytotoxic T Lymphocyte ◽  
Class I ◽  
Effective Vaccine ◽  
T Cell Epitopes ◽  
Multiple Allele ◽  
Ctl Epitopes ◽  
Cell Mediated Immune Response

Objective: Tuberculosis (TB) caused by Mycobacterium tuberculosis (M. tb) is one of the deadliest diseases causing millions of deaths worldwide. Bacillus Calmette-Guérin (BCG) is the only vaccine that has been used in many countries where TB is prevalent. Despite vaccination, this disease prevails in many of the developing countries, necessitating the development of an effective vaccine against TB. Since M. tb acts as an intracellular pathogen, cell-mediated immune response plays an important role in disease control. Therefore, screening of CD8+ T cell epitopes of M. tb antigens could aid in the development of an effective vaccine against TB. In the current study, a reverse vaccinology approach was utilized to predict and map cytotoxic T lymphocyte (CTL) epitopes in the virulent proteins that are also essential for M. tb. Materials and Methods: Database of Essential Genes and Virulence Factor Database were used for identifying the virulent proteins of M. tb and their antigenicity was assessed using VaxiJen server. Various immunoinformatics tools were used to predict MHC class I binding, MHC processing, immunogenicity, toxicity and allergenicity. Results: Twelve M. tb antigens were selected for the prediction analyses using various tools. The results indicated the presence of 20 novel CTL epitopes predicted against human HLA-A alleles. This study has also screened for multiple allele binding epitopes that could be used as a vaccine component. Conclusion: This study has yielded a few hitherto unreported CTL epitopes binding to class I HLA-A alleles. Further experimental validation is necessary for confirming their potential as vaccine candidates.

scholarly journals Negligible Genetic Diversity of Mycobacterium tuberculosis Host Immune System Protein Targets: Evidence of Limited Selective Pressure

Genetics ◽  
2000 ◽  
Vol 155 (1) ◽  
pp. 7-16 ◽  
Author(s):  
James M Musser ◽  
Amol Amin ◽  
Srinivas Ramaswamy
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Immune System ◽  
Amino Acid ◽  
Genomic Diversity ◽  
Host Immune System ◽  
Protein Targets ◽  
Amino Acid Sequence Variation ◽  
Medical Microbiology ◽  
Antigenic Proteins ◽  
Amino Acid Diversity

Abstract A common theme in medical microbiology is that the amount of amino acid sequence variation in proteins that are targets of the host immune system greatly exceeds that found in metabolic enzymes or other housekeeping proteins. Twenty-four Mycobacterium tuberculosis genes coding for targets of the host immune system were sequenced in 16 strains representing the breadth of genomic diversity in the species. Of the 24 genes, 19 were invariant and only six polymorphic nucleotide sites were identified in the 5 genes that did have variation. The results document the highly unusual circumstance that prominent M. tuberculosis antigenic proteins have negligible structural variation worldwide. The data are best explained by a combination of three factors: (i) evolutionarily recent global dissemination in humans, (ii) lengthy intracellular quiescence, and (iii) active replication in relatively few fully immunocompetent hosts. The very low level of amino acid diversity in antigenic proteins may be cause for optimism in the difficult fight to control global tuberculosis.

scholarly journals Characterization of T-cell immunogenicity of two PE/PPE proteins of Mycobacterium tuberculosis

2008 ◽  
Vol 57 (9) ◽  
pp. 1079-1086 ◽  
Author(s):  
M. G. Chaitra ◽  
M. S. Shaila ◽  
R. Nayak
Keyword(s):  
Mycobacterium Tuberculosis ◽  
T Cell ◽  
Antigenic Variation ◽  
T Cell Response ◽  
Interleukin 4 ◽  
Specific Response ◽  
T Cell Epitopes ◽  
High Affinity ◽  
High Gamma ◽  
Different Strains

The PE and PPE proteins of Mycobacterium tuberculosis form a source of antigenic variation among different strains of this bacterium. Two of the PE_PGRS protein-encoding genes, rv3812 and rv3018c, are expressed in pathogenic mycobacteria and are implicated, respectively, in the persistence of the organism in macrophages and in virulence. Peptides derived from these proteins have been predicted to bind major histocompatibility complex (MHC) class I with high affinity on the basis of immunoinformatics analysis, suggesting a possible role for these proteins in antimycobacterial immunity. In the present work, using DNA constructs containing the rv3812 and rv3018c genes of M. tuberculosis, the immunogenicity of these proteins was demonstrated in BALB/c mice. Immunization with either DNA construct induced a significant number of CD8+-type T cells and a strong Th1-type response, with high gamma interferon (IFN-γ) and low interleukin-4 responses. Three nonameric peptides of Rv3812 and two of Rv3018c elicited a strong T-cell response in an MHC-restricted manner. An epitope-specific response was demonstrated by the lysis of peptide-pulsed antigen-presenting cells, release of perforin and IFN-γ production. Experimentally, these peptides bound with high affinity to MHC H-2Kd and showed low dissociation rates of peptide–MHC complexes. This study suggests that the identified T-cell epitopes may contribute to immunity against tuberculosis if included in a vaccine.

scholarly journals Distribution and Identification of Mycobacterium tuberculosis Lineage in Kashgar Prefecture

2021 ◽  
Author(s):  
Ai-Min Xu ◽  
Chuan-Jiang He ◽  
Xiang Chen ◽  
Li Li ◽  
AniKiz Abuduaini ◽  
...  
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Phylogenetic Tree ◽  
Geographical Location ◽  
Principal Component ◽  
Nucleotide Polymorphisms ◽  
Clinical Strains ◽  
Lineage 2 ◽  
Composition Structure ◽  
And Control ◽  
Kashgar Prefecture

Abstract Objectives In order to understand the composition of Mycobacterium tuberculosis(M.tb) lineage and find specific tags to distinguish lineage of the M.tb in Kashgar prefecture, so as to provide a basis for the prevention of tuberculosis in this area. Methods Whole genome sequencing (WGS) of M.tb clinical strains (161 cases) was conducted. The phylogenetic tree was constructed by Maximum Likelihood (ML) on the basis of single nucleotide polymorphisms (SNPs) and verified via principal component analysis (PCA). The composition structure of M.tb in different regions was analyzed by combining geographic information. Results The M.tb clinical strains were composed of lineage 2 (73/161, 45.34%), lineage 3 (52/161, 32.30%) and lineage 4 (36/161, 22.36%) in Kashgar prefecture. And the 3 lineages were subdivided into 11 sublineages, among which lineage 2 includes lineage 2.2.2/Asia Ancestral 1(9/73, 12.33%),lineage 2.2.1-Asia Ancestral 2(9/73, 12.33%)༌lineage 2.2.1-Asia Ancestral 3(18/73, 24.66%) and lineage 2.2.1-Modern Beijing(39/73, 53.42%).Lineage 3 includes lineage 3.2(14/52, 26.92%)and lineage 3.3(38/52, 73.08%)༌lineage 4 includes lineage 4.1(3/36, 8.33%)༌lineage 4.2(2/36, 5.66%)༌lineage 4.4.2(1/36, 2.78%)༌lineage 4.5(28/36, 77.78%) and lineage 4.8(2/36, 5.66%)༌all of which were consistent with the PCA results. Among the identified 21438 SNPs ,there are 136 markers proposed to discriminate known circulating strains. Reconstruction of a phylogenetic tree using the 136 SNPs for all 161 samples resulted in a tree with the same number of delineated clades. Based on geographical location analysis, the composition of Lineage 2 in Kashgar prefecture (45.34%) is lower than other regions level in China(54.35%-90.27%), and the composition of Lineage 3 (32.30%)is much higher than other regions level in China (0.92%-2.01%), but it is lower than the bordering Pakistan (70.40%). Conclusion In summary, M.tb clinical strains from Kashgar prefecture were identifed 3 lineages and 11 sublineages, with 136 Branch-Specific SNP. Kashgar borders countries with a high incidence of tuberculosis such as Pakistan and India, resulting in a large difference between the M.tb lineage and sublineage distribution in this region and other provinces in China. This research provides a theoretical basis for the prevention and control of tuberculosis in Xinjiang.

scholarly journals Peptide Microarray-Based Identification of Mycobacterium tuberculosis Epitope Binding to HLA-DRB1*0101, DRB1*1501, and DRB1*0401

2009 ◽  
Vol 17 (1) ◽  
pp. 168-175 ◽  
Author(s):  
Simani Gaseitsiwe ◽  
Davide Valentini ◽  
Shahnaz Mahdavifar ◽  
Marie Reilly ◽  
Anneka Ehrnst ◽  
...  
Keyword(s):  
Mycobacterium Tuberculosis ◽  
T Cell ◽  
Mhc Class Ii ◽  
Class Ii ◽  
T Cell Response ◽  
Effective Vaccine ◽  
T Cell Epitopes ◽  
Peptide Microarray ◽  
Active Pulmonary Tuberculosis ◽  
Clinical Phase

ABSTRACT A more effective vaccine against Mycobacterium tuberculosis is needed, and a number of M. tuberculosis vaccine candidates are currently in preclinical or clinical phase I and II studies. One of the strategies to select M. tuberculosis (protein) targets to elicit a CD8+ or CD4+ T-cell response is to gauge the binding of candidate peptides to major histocompatibility complex (MHC) class I or class II molecules, a prerequisite for successful peptide presentation and to expand antigen-specific T cells. We scanned 61 proteins from the M. tuberculosis proteome for potential MHC class II-presented epitopes that could serve as targets for CD4+ T-cell responses. We constructed a peptide microarray consisting of 7,466 unique peptides derived from 61 M. tuberculosis proteins. The peptides were 15-mers overlapping by 12 amino acids. Soluble recombinant DRB1*0101 (DR1), DRB1*1501 (DR2), and DRB1*0401 (DR4) monomers were used to gauge binding to individual peptide species. Out of 7,466 peptides, 1,282, 674, and 1,854 peptides formed stable complexes with HLA-DR1, -DR2, and -DR4, respectively. Five hundred forty-four peptides bound to all three MHC class II molecules, 609 bound to only two, and 756 bound to only a single MHC class II molecule. This allowed us to rank M. tuberculosis proteins by epitope density. M. tuberculosis proteins contained “hot spots,” i.e., regions with enriched MHC class II binding epitopes. Two hundred twenty-two peptides that formed MHC class II-peptide complexes had previously been described as exclusively recognized by IgG in sera from patients with active pulmonary tuberculosis, but not in sera from healthy individuals, suggesting that these peptides serve as B-cell and CD4+ T-cell epitopes. This work helps to identify not only M. tuberculosis peptides with immunogenic potential, but also the most immunogenic proteins. This information is useful for vaccine design and the development of future tools to explore immune responses to M. tuberculosis.

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