Mycobacterial species as case-study of comparative genome analysis

Each alignment was visually inspected to detect short misalignments or poorly aligned regions. Conclusion Mycobacteria include important pathogenic species for human and animals and the Mycobacterium tuberculosis complex is the most cause of death of the humankind.

The distance between two strains is the sum of the branch lengths between them. Identification of NTM homologs of immunogenic proteins warrants further investigation of their ability to cause cross-reactive immune responses with MTBC antigens.

Interestingly, the rpoBsequence of one strain Kan among the 32 clinical isolates ofM.

Mycobacterial species as case-study of comparative genome analysis

Moreover, according to the recent archeological studies carried out on the Siberian skeletal remains from the iron age and based on the single-nucleotide polymorphic loci PCR and the analysis of the regions of difference RDs of the MTBC, Taylor et al. In this present study, we aim to highlight a comparative genome, proteome and phylogeny analysis between twenty-one mycobacterial Tuberculosis and non tuberculosis strains using a set of computational and bioinformatics tools Pan and Core genome plotting, BLAST matrix and phylogeny analysis.

The members of the complex Mycobacterium tuberculosis are the most virulent microorganisms that have killed human and other mammals since millennia.

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The analyses included the first and second codon positions usually associated with nonsynonymous substitutions and the third codon positions usually resulting in synonymous substitutions due to codon wobbling.

We took a compiled list of virulence genes from Forrellad et al. Defining these protein coding genes which are essential for the bacterial growth and its survival is believed to be important in identifying both key biological processes and potential targets for rational drug development [ 7 ].

As it has been shown in Table 315 proteins from the proposed target lists interact with human. Viewing the BLAST matrix a high similarity was found among the species of the complex Mycobacterium tuberculosis and less conservation is found with other slow growing pathogenic mycobacteria.

Pasteur P2, with some of the free living Mycobacterial genomes M. Shortest path length distribution. This analysis gives accurate genomic information in respect of the genetic differences between these species, which are useful for better understanding of their evolution, pathogenesis mechanism, basis for virulence, and consequently to deal with the scientific priorities of better drugs, vaccines, and diagnostics tools for Mycobacterial diseases 6, 9.

The shortest path length distribution between pairwise protein interactions has been shown in Figure 2. We have adopted a stringent measure of listing out only those enzymes which have no similarity or negligible similarity above the -value threshold of 0.

Mycobacterium fortuitum and to a lesser extent M. The amplified region bp; from R to H using the codon numbering system for Escherichia coli lies within the C2 region, one of four conserved domains C1 to C4. Amino acid sequences of reference strains. These two species were previously identified and characterized as novel NTM Gcebe et al.

The purified protein derivatives from M. TubercuList and TB database TBDB [ 2324 ] and with the huge amount of mycobacterial sequences, there is a crucial need for the visualization, simplification and comparative genomics of their data for better understanding their evolutionary events and consequently, the conception of their environmental niches, mechanisms of adaptation into human and animal being, pathogencity, virulence determinants that paved the way for appropriate conditions of survival within their hosts and the development of new tools of diagnosis and drug targets for better controlling those threatening diseases [ 25 ].

Sorted lists of proteins proposed as potential drug targets which have solved structure. These genes are those which are indispensable for the survival and growth of the pathogen. To calculate the numbers of synonymous dS and nonsynonymous dN nucleotide substitutions per site in five M.

The pe35 and ppe68 genes were found to occur next to each other in the genomes of the four newly sequenced NTM. Nucleotide sequence accession numbers.

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Therefore use of these antigens in BTB diagnosis may be hampered by the exposure of humans and animals to pathogenic NTM leading to false positive BTB immunological test results. In recent times, many mycobacterial virulence genes that are essential for the virulence of Mycobacterium tuberculosis complex MTBC species have been reported by a number of studies.

Nucleotide sequence variations of rpoB among the clinical isolates were observed. The positions of the immunogenic proteins of interest in the reference genomes are also highlighted.

The liquid cultures were screened for contaminants before PPDs were prepared by spread plating each culture on two nutrient agar plates.

Also, the genomes of two M. The comparative genome analysis could provide a new insight for better controlling and preventing these diseases.Comparative sequence analysis of rpoB DNAs provided the basis for species differentiation within the genusMycobacterium.

Slowly and rapidly growing groups of mycobacteria were clearly separated, and each mycobacterial species was differentiated as a distinct entity in the phylogenetic tree.

Mar 27,  · Identification of Mycobacterial Species by Comparative Sequence Analysis of the RNA Polymerase Gene (rpoB) The rpoB gene has been studied to help the identification of certain mycobacterium species, which in some cases can cause serious infections.

Comparative Genomics and Proteomic Analysis of Four Non-tuberculous Mycobacterium Species and Mycobacterium tuberculosis Complex: Occurrence of Shared Immunogenic Proteins. Comparative genomic studies of rapidly growing mycobacteria (RGM).

Mycobacteria have been reported to cause a wide range of human diseases. We present the first whole-genome study of a Non-Tuberculous Mycobacterium, Mycobacterium sp. UM_CSW (referred to hereafter as UM_CSW), isolated from a patient diagnosed with bronchiectasis.

Our data suggest that this clinical isolate is likely a novel mycobacterial species, supported by clear evidence from molecular. Potential drug targets of Mycobacterium tuberculosis H37Rv were identified through systematically integrated comparative genome and network centrality analysis.

The comparative analysis of the complete genome of Mycobacterium tuberculosis H37Rv against Database of Essential Genes (DEG) yields a list of proteins which are essential for the growth and survival of the pathogen.

Jan 03,  · To improve our understanding of the genetic landscape and diversity of M. avium and its role in disease, we performed a comparative genome analysis of 79 M. avium strains. Our analysis demonstrated that MAH is an open pan-genome species.

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Mycobacterial species as case-study of comparative genome analysis
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