Transcriptional regulation of topology modulators and transcription regulators of Mycobacterium tuberculosis

Ghosh, Soumitra; Padmanabhan, Bhavna; Godbole, Adwait Anand; Tare, Priyanka; Ahmed, Wareed; Vasu, K.I.; China, Arnab; Kumar, Rupesh; Mitra, Anirban P.; Nagaraja, Valakunja

doi:10.1016/j.bbrc.2016.05.078

Cited by 2 publications

(2 citation statements)

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“…SIFT revealed that most of these mutations were with a high probability of affecting protein function. Genes under positive selection enriched for transcriptional function have been reported ( Liu et al, 2022 ), and the responses of Mtb at the level of transcription and translational regulation will adapt themselves to the external and host environmental conditions ( Ghosh et al, 2016 ). Functional enrichment analysis indicated that positively selected genes are highly enriched for transcriptional regulators, especially resR ( Liu et al, 2022 ).…”

Section: Discussionmentioning

confidence: 99%

Identification of positively selected genes in Mycobacterium tuberculosis from southern Xinjiang Uygur autonomous region of China

Deng,

Wang,

Liu

et al. 2024

Front. Microbiol.

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BackgroundTuberculosis (TB), mainly caused by Mycobacterium tuberculosis (Mtb), remains a serious public health problem. Increasing evidence supports that selective evolution is an important force affecting genomic determinants of Mtb phenotypes. It is necessary to further understand the Mtb selective evolution and identify the positively selected genes that probably drive the phenotype of Mtb.MethodsThis study mainly focused on the positive selection of 807 Mtb strains from Southern Xinjiang of China using whole genome sequencing (WGS). PAML software was used for identifying the genes and sites under positive selection in 807 Mtb strains.ResultsLineage 2 (62.70%) strains were the dominant strains in this area, followed by lineage 3 (19.45%) and lineage 4 (17.84%) strains. There were 239 codons in 47 genes under positive selection, and the genes were majorly associated with the functions of transcription, defense mechanisms, and cell wall/membrane/envelope biogenesis. There were 28 codons (43 mutations) in eight genes (gyrA, rpoB, rpoC, katG, pncA, embB, gid, and cut1) under positive selection in multi-drug resistance (MDR) strains but not in drug-susceptible (DS) strains, in which 27 mutations were drug-resistant loci, 9 mutations were non-drug-resistant loci but were in drug-resistant genes, 2 mutations were compensatory mutations, and 5 mutations were in unknown drug-resistant gene of cut1. There was a codon in Rv0336 under positive selection in L3 strains but not in L2 and L4 strains. The epitopes of T and B cells were both hyper-conserved, particularly in the T-cell epitopes.ConclusionThis study revealed the ongoing selective evolution of Mtb. We found some special genes and sites under positive selection which may contribute to the advantage of MDR and L3 strains. It is necessary to further study these mutations to understand their impact on phenotypes for providing more useful information to develop new TB interventions.

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Section: Discussionmentioning

confidence: 99%

Identification of positively selected genes in Mycobacterium tuberculosis from southern Xinjiang Uygur autonomous region of China

Deng,

Wang,

Liu

et al. 2024

Front. Microbiol.

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“…79 M. tuberculosis transcriptomics is currently an active field of study, but the techniques have not yet been applied to historical or ancient human remains. 80,81 This is clearly an area where important insights should be obtained, provided suitable wellpreserved specimens containing sufficient M. tuberculosis aDNA are available for analysis, such as historical remains from the permafrost or possibly the 18 th century Hungarian Vá c mummies. The combination of epigenetics, proteomics, and transcriptomics should throw light on the differences in gene expression and virulence between M. tuberculosis strains and lineages.…”

Section: Recent Findings From Epigenetics and Transcriptomicsmentioning

confidence: 99%

Insights gained from ancient biomolecules into past and present tuberculosis—a personal perspective

Donoghue

2017

International Journal of Infectious Diseases

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Ancient and historical tuberculosis (TB) can be recognized by its typical paleopathology in human remains. Using paleomicrobiology, it is possible to detect many more individuals infected with TB but with no visible lesions. Due to advances in molecular analysis over the past two decades, it is clear that TB was widespread in humans from the Neolithic period and has remained so until the present day. Past human populations were associated with different lineages of the Mycobacterium tuberculosis complex, thereby elucidating early human migrations. Using paleomicrobiology, it is possible to detect individuals infected with TB who are also co-infected with other bacteria or parasites. TB is also found in hosts with co-morbidities such as neoplasms, or metabolic disorders such as rickets and scurvy. In well-preserved human skeletal or mummified tissue, whole genome sequencing has detected individuals with multiple infections of different M. tuberculosis strains. Such studies put modern findings into context and emphasize the importance of human population density in such circumstances.

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Transcriptional regulation of topology modulators and transcription regulators of Mycobacterium tuberculosis

Cited by 2 publications

References 38 publications

Identification of positively selected genes in Mycobacterium tuberculosis from southern Xinjiang Uygur autonomous region of China

Identification of positively selected genes in Mycobacterium tuberculosis from southern Xinjiang Uygur autonomous region of China

Insights gained from ancient biomolecules into past and present tuberculosis—a personal perspective

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