Structural Implications of Mutations Conferring Rifampin Resistance in Mycobacterium leprae

• Published in: Scientific reports 2018-03, Vol.8 (1), p.5016-12, Article 5016
• Main Authors: Vedithi, Sundeep Chaitanya, Malhotra, Sony, Das, Madhusmita, Daniel, Sheela, Kishore, Nanda, George, Anuja, Arumugam, Shantha, Rajan, Lakshmi, Ebenezer, Mannam, Ascher, David B., Arnold, Eddy, Blundell, Tom L.
• Format: Article
• Language: English
• Subjects: 45/22; 45/23; 45/29; 45/77; 631/114/2411; 631/326/22/1434; 631/326/325/1506; 631/535/1267; Adolescent; Adult; Bacterial Proteins - genetics; Binding sites; DNA, Bacterial - genetics; DNA-directed RNA polymerase; DNA-Directed RNA Polymerases - genetics; Drug Resistance, Bacterial - genetics; Female; Humanities and Social Sciences; Humans; Hydrophobicity; India; Leprostatic Agents - pharmacology; Leprostatic Agents - therapeutic use; Leprosy; Leprosy - drug therapy; Leprosy - microbiology; Male; Microbial Sensitivity Tests; Middle Aged; Missense mutation; multidisciplinary; Mutation; Mycobacterium leprae; Mycobacterium leprae - drug effects; Mycobacterium leprae - genetics; Mycobacterium leprae - isolation & purification; Nucleic acids; Polymerase chain reaction; Protein Binding - genetics; Protein Stability - drug effects; Recurrence; Rifampin; Rifampin - pharmacology; Rifampin - therapeutic use; RNA polymerase; RpoB protein; Science; Science (multidisciplinary); Sequence Analysis, DNA; Skin; Structure-Activity Relationship; Structure-function relationships; Transcription; Treatment Outcome; Tuberculosis; Young Adult
• ISSN: 2045-2322; 2045-2322
• DOI: 10.1038/s41598-018-23423-1

The rpoB gene encodes the β subunit of RNA polymerase holoenzyme in Mycobacterium leprae (M . leprae) . Missense mutations in the rpoB gene were identified as etiological factors for rifampin resistance in leprosy. In the present study, we identified mutations corresponding to rifampin resistance in relapsed leprosy cases from three hospitals in southern India which treat leprosy patients. DNA was extracted from skin biopsies of 35 relapse/multidrug therapy non-respondent leprosy cases, and PCR was performed to amplify the 276 bp rifampin resistance-determining region of the rpoB gene. PCR products were sequenced, and mutations were identified in four out of the 35 cases at codon positions D441Y, D441V, S437L and H476R. The structural and functional effects of these mutations were assessed in the context of three-dimensional comparative models of wild-type and mutant M . leprae RNA polymerase holoenzyme (RNAP), based on the recently solved crystal structures of RNAP of Mycobacterium tuberculosis, containing a synthetic nucleic acid scaffold and rifampin. The resistance mutations were observed to alter the hydrogen-bonding and hydrophobic interactions of rifampin and the 5′ ribonucleotide of the growing RNA transcript. This study demonstrates that rifampin-resistant strains of M . leprae among leprosy patients in southern India are likely to arise from mutations that affect the drug-binding site and stability of RNAP.