Mycobacterial species as case-study of comparative genome analysis

The existence of false positives and false negatives is widely anticipated in the networks of these types which are being constructed by using the currently available methods [ 13 ]. Peptide identifications were accepted if they could be established at greater than 9.

Immunogenic proteins of interest are highlighted in red also see Table 1. The unannotated genes in NTM encode for hypothetical proteins. 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.

The number of contigs, the length of the largest contig as well as the N50 the length for which the set of contigs of that length or longer contains at least half the assembly bases and L50 the number of contigs of that length for each assembly is presented.

The rpoBgene sequences determined for the mycobacterial reference strains and other microorganisms have been deposited in GenBank accession no. Received Mar 15; Accepted Aug 2. The GenBank accession number for the nucleotide sequence of the full-length rpoB gene of M. As the degree distribution of the resulting network has also been shown in Figure 3it exhibits scale-free property like many biological networks in which the degree distribution of proteins approximates a power lawwith the degree exponent.

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

Phylogeny analysis based on both protein conservation, as well as rRNA clearly resolve known relationships between slow growing mycobacteria. This tree was constructed by the neighbor-joining method. In this database, a combined score has been assigned for each protein-protein linkage based on the evidence from various sources.

Table 1 summarizes a number of characteristics for each of the analyzed genome, such as size, number of predicted genes, rRNA operons, tRNA genes and GC content. The reason for the presence of only few overlaps could be due to the fact that the host-pathogen interaction dataset is not comprehensive or the host interacting proteins are not necessarily essential to the pathogen and nonhomologous with human.

Different aspects indicated in this diagram are identification of essential genes, comparative analysis, construction of protein-protein interaction network, and network centrality analysis and validation. Thus, from this small world property of the network, we can understand that the network is efficient in the communication of biological information.

The Venn diagram Figure 6 shows the overlaps among these lists of drug targets and the proposed potential target list. For the substitution values, M. Taken together, the results described above indicate that M. Network Centrality Analysis Comparative genome analysis was helpful in filtering out nonhomologous and essential proteins of Mycobacterium tuberculosis H37Rv.

Nucleotide sequence accession numbers. The distribution indicated that most of the candidate drug targets are involved in cell wall and cell processes, followed by a significant proportion of proteins in intermediary metabolism and respiration, conserved hypothetical, and those belong to information pathway.

All tested species showed good separation. Since it was previously shown by hybridization experiments that ESX-5 might be absent in Mycobacterium nonchromogenicum we verified the presence of esxN ortholog situated in ESX-5 locus in M. A phylogenetic tree of the mycobacteria was constructed by using the MEGA program To gauge the similarity of the NTM genomes to those of M.

Sorted lists of proteins proposed as potential drug targets which have solved structure. However, the sequence variation justified assigning a new species for the new organism instead of classifying it as a variant of M. The one strain that showed a low level of similarity to theM.

Interestingly, the rpoBsequence of one strain Kan among the 32 clinical isolates ofM. Leprosy, one of the oldest human diseases, remains a significant public health problem in many developing countries 8. The dS and dN values were also much higher than those for other closest pairs of mycobacteria.

BLAST matrix, Comparative genome analysis, Evolution, Mycobacterium tuberculosis, Pan- core genome, Phylogeny Background The genus Mycobacterium comprises more than species, among them the most contagious and infectious bacteria [ 1 ]. Mascot was set up to search the Mycobacterium database derived from UniProtKB, entries assuming the digestion enzyme trypsin.

Shortest path length distribution. Amino acid and nucleotide sequences from M.

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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. By referring to the phylogenetic tree and by using reference strains, we applied this procedure to the clinical isolates and thus could identify various mycobacterial species, which had been confirmed in the conventional way.

Table 1 Characteristics of 21 mycobacterial genomes Genome.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.

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 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. 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.

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avium strains. Our analysis demonstrated that MAH is an open pan-genome species. 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.

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).

Mycobacterial species as case-study of comparative genome analysis
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