Omics analysis of Mycobacterium tuberculosis isolates uncovers Rv3094c, an ethionamide metabolism-associated gene

[1]  Nisheeth Agarwal,et al.  Proteomic Landscape of a Drug-Tolerant Persister Subpopulation of Mycobacterium tuberculosis. , 2021, Journal of proteome research.

[2]  R. Kulkarni,et al.  “Omics” and “epi-omics” underlying the β-cell adaptation to insulin resistance , 2019, Molecular metabolism.

[3]  S. Fortune,et al.  Bacterial Genome-Wide Association Identifies Novel Factors That Contribute to Ethionamide and Prothionamide Susceptibility in Mycobacterium tuberculosis , 2019, mBio.

[4]  T. Clark,et al.  Genome-wide analysis of Mycobacterium tuberculosis polymorphisms reveals lineage-specific associations with drug resistance , 2019, BMC genomics.

[5]  B. Gicquel,et al.  Genome-Wide Transcriptional Responses of Mycobacterium to Antibiotics , 2019, Front. Microbiol..

[6]  Lianhua Qin,et al.  A deletion in the RD105 region confers resistance to multiple drugs in Mycobacterium tuberculosis , 2019, BMC Biology.

[7]  Ying Zhou,et al.  Multi-omics comparisons of p-aminosalicylic acid (PAS) resistance in folC mutated and un-mutated Mycobacterium tuberculosis strains , 2019, Emerging microbes & infections.

[8]  R. Hasan,et al.  Efflux pump as alternate mechanism for drug resistance in Mycobacterium tuberculosis. , 2019, The Indian journal of tuberculosis.

[9]  W. Degrave,et al.  Integrated analysis of ethionamide resistance loci in Mycobacterium tuberculosis clinical isolates. , 2018, Tuberculosis.

[10]  Enrique Merino,et al.  Operon-mapper: a web server for precise operon identification in bacterial and archaeal genomes , 2018, Bioinform..

[11]  S. Gagneux Ecology and evolution of Mycobacterium tuberculosis , 2018, Nature Reviews Microbiology.

[12]  Ruth McNerney,et al.  A standardised method for interpreting the association between mutations and phenotypic drug resistance in Mycobacterium tuberculosis , 2017, European Respiratory Journal.

[13]  A. Earl,et al.  Whole-Transcriptome and -Genome Analysis of Extensively Drug-Resistant Mycobacterium tuberculosis Clinical Isolates Identifies Downregulation of ethA as a Mechanism of Ethionamide Resistance , 2017, Antimicrobial Agents and Chemotherapy.

[14]  Xin Ma,et al.  Identification of Missing Proteins in the Phosphoproteome of Kidney Cancer. , 2017, Journal of proteome research.

[15]  L. Bi,et al.  Quantitative proteomic analysis of host responses triggered by Mycobacterium tuberculosis infection in human macrophage cells , 2017, Acta biochimica et biophysica Sinica.

[16]  L. Bi,et al.  Structural analysis of the regulatory mechanism of MarR protein Rv2887 in M. tuberculosis , 2017, Scientific Reports.

[17]  L. Bi,et al.  Cyclic di-GMP regulates Mycobacterium tuberculosis resistance to ethionamide , 2017, Scientific Reports.

[18]  C. Locht,et al.  Reversion of antibiotic resistance in Mycobacterium tuberculosis by spiroisoxazoline SMARt-420 , 2017, Science.

[19]  K. Tan,et al.  Analysis of Reproducibility of Proteome Coverage and Quantitation Using Isobaric Mass Tags (iTRAQ and TMT). , 2017, Journal of proteome research.

[20]  G. Lamichhane,et al.  Drug resistance mechanisms and novel drug targets for tuberculosis therapy. , 2017, Journal of genetics and genomics = Yi chuan xue bao.

[21]  Liliana K. Rutaihwa,et al.  Mycobacterium tuberculosis Lineage 4 comprises globally distributed and geographically restricted sublineages , 2016, Nature Genetics.

[22]  P. Xu,et al.  Recombinant expression, refolding, purification and characterization of Pseudomonas aeruginosa protease IV in Escherichia coli. , 2016, Protein expression and purification.

[23]  Christian Stolte,et al.  Genetic Determinants of Drug Resistance in Mycobacterium tuberculosis and Their Diagnostic Value. , 2016, American journal of respiratory and critical care medicine.

[24]  A. Earl,et al.  Baeyer-Villiger Monooxygenases EthA and MymA Are Required for Activation of Replicating and Non-replicating Mycobacterium tuberculosis Inhibitors. , 2016, Cell chemical biology.

[25]  L. Bi,et al.  An automated approach for global identification of sRNA-encoding regions in RNA-Seq data from Mycobacterium tuberculosis. , 2016, Acta biochimica et biophysica Sinica.

[26]  Tao Zhang,et al.  Quantitative Proteomics Reveals Membrane Protein-Mediated Hypersaline Sensitivity and Adaptation in Halophilic Nocardiopsis xinjiangensis. , 2016, Journal of proteome research.

[27]  Xing-wang Li,et al.  MicroRNA signatures from multidrug-resistant Mycobacterium tuberculosis , 2015, Molecular medicine reports.

[28]  J. Bader,et al.  Deficiency of the Novel Exopolyphosphatase Rv1026/PPX2 Leads to Metabolic Downshift and Altered Cell Wall Permeability in Mycobacterium tuberculosis , 2015, mBio.

[29]  R. Pathak,et al.  Differential expression of efflux pump genes of Mycobacterium tuberculosis in response to varied subinhibitory concentrations of antituberculosis agents. , 2015, Tuberculosis.

[30]  S. Gagneux,et al.  Consequences of genomic diversity in Mycobacterium tuberculosis. , 2014, Seminars in immunology.

[31]  Jun-mei Lu,et al.  Mutations in the embC-embA Intergenic Region Contribute to Mycobacterium tuberculosis Resistance to Ethambutol , 2014, Antimicrobial Agents and Chemotherapy.

[32]  R. Brosch,et al.  Evolutionary history of tuberculosis shaped by conserved mutations in the PhoPR virulence regulator , 2014, Proceedings of the National Academy of Sciences.

[33]  K. Wan,et al.  Prevalence and Molecular Characteristics of Drug-Resistant Mycobacterium tuberculosis in Hunan, China , 2014, Antimicrobial Agents and Chemotherapy.

[34]  Björn Usadel,et al.  Trimmomatic: a flexible trimmer for Illumina sequence data , 2014, Bioinform..

[35]  A. Darby,et al.  Integrated transcriptomic and proteomic analysis of the global response of Wolbachia to doxycycline-induced stress , 2013, The ISME Journal.

[36]  Wei Shi,et al.  featureCounts: an efficient general purpose program for assigning sequence reads to genomic features , 2013, Bioinform..

[37]  Dongfang Li,et al.  Genome sequencing of 161 Mycobacterium tuberculosis isolates from China identifies genes and intergenic regions associated with drug resistance , 2013, Nature Genetics.

[38]  S. Niemann,et al.  Clade-Specific Virulence Patterns of Mycobacterium tuberculosis Complex Strains in Human Primary Macrophages and Aerogenically Infected Mice , 2013, mBio.

[39]  Thomas R. Gingeras,et al.  STAR: ultrafast universal RNA-seq aligner , 2013, Bioinform..

[40]  Randy J. Read,et al.  Overview of the CCP4 suite and current developments , 2011, Acta crystallographica. Section D, Biological crystallography.

[41]  Anuj Gupta,et al.  jefA (Rv2459), a drug efflux gene in Mycobacterium tuberculosis confers resistance to isoniazid & ethambutol. , 2010, The Indian journal of medical research.

[42]  Stefan Niemann,et al.  Functional Genetic Diversity among Mycobacterium tuberculosis Complex Clinical Isolates: Delineation of Conserved Core and Lineage-Specific Transcriptomes during Intracellular Survival , 2010, PLoS pathogens.

[43]  Randy J. Read,et al.  Acta Crystallographica Section D Biological , 2003 .

[44]  Mark D. Robinson,et al.  edgeR: a Bioconductor package for differential expression analysis of digital gene expression data , 2009, Bioinform..

[45]  Steven J. M. Jones,et al.  Circos: an information aesthetic for comparative genomics. , 2009, Genome research.

[46]  George M Church,et al.  Tuberculosis Drug Resistance Mutation Database , 2009, PLoS medicine.

[47]  T. Parish,et al.  Electroporation of mycobacteria. , 2009, Methods in molecular biology.

[48]  M. Mann,et al.  MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification , 2008, Nature Biotechnology.

[49]  James C. Sacchettini,et al.  Mechanism of thioamide drug action against tuberculosis and leprosy , 2007, The Journal of experimental medicine.

[50]  Feng Wang,et al.  Crystal structure and activity studies of the Mycobacterium tuberculosis beta-lactamase reveal its critical role in resistance to beta-lactam antibiotics. , 2006, Antimicrobial agents and chemotherapy.

[51]  M. Hazbón,et al.  The Mycobacterium tuberculosis iniA gene is essential for activity of an efflux pump that confers drug tolerance to both isoniazid and ethambutol , 2005, Molecular microbiology.

[52]  Fei Long,et al.  REFMAC5 dictionary: organization of prior chemical knowledge and guidelines for its use. , 2004, Acta crystallographica. Section D, Biological crystallography.

[53]  Kevin Cowtan,et al.  research papers Acta Crystallographica Section D Biological , 2005 .

[54]  D. van Soolingen,et al.  Mutations in Putative Mutator Genes of Mycobacterium tuberculosis Strains of the W-Beijing Family , 2003, Emerging infectious diseases.

[55]  G. Besra,et al.  Overexpression of inhA, but not kasA, confers resistance to isoniazid and ethionamide in Mycobacterium smegmatis, M. bovis BCG and M. tuberculosis , 2002, Molecular microbiology.

[56]  F. Portaels,et al.  Resazurin Microtiter Assay Plate: Simple and Inexpensive Method for Detection of Drug Resistance in Mycobacterium tuberculosis , 2002, Antimicrobial Agents and Chemotherapy.

[57]  P. Ortiz de Montellano,et al.  The Antituberculosis Drug Ethionamide Is Activated by a Flavoprotein Monooxygenase* , 2002, The Journal of Biological Chemistry.

[58]  C. Locht,et al.  Activation of the pro-drug ethionamide is regulated in mycobacteria. , 2000, The Journal of biological chemistry.

[59]  Z. Otwinowski,et al.  Processing of X-ray diffraction data collected in oscillation mode. , 1997, Methods in enzymology.

[60]  D. Ballou,et al.  Reactions of the 4a-hydroperoxide of liver microsomal flavin-containing monooxygenase with nucleophilic and electrophilic substrates. , 1986, The Journal of biological chemistry.