title: Phylogenetic and Structural Significance of Dihydrofolate Synthase (folC) Mutations in Drug-Resistant Mycobacterium tuberculosis.
abstract: The aim of this study is to investigate the mutation pattern of the folC gene in drug-resistant Mycobacterium tuberculosis (MTB) clinical isolates of global and Hong Kong cohorts. The public sequence read archives of 1,124 MTB genomes from three independent studies were retrieved and folC mutations existing solely in drug-resistant MTB strains were identified. A phylogenetic tree was constructed to analyze the segregation of mutation-related amino acid residues in the FolC structure. These mutation sites were further supported by direct Sanger sequencing of the folC gene among 254 clinical MTB isolates in a Hong Kong cohort. Homology modeling of wild-type and mutated FolC was performed, and the predicted structures were docked with hydroxydihydropteroate, the metabolic derivative of para-aminosalicylic acid (PAS), to evaluate the resultant binding affinity changes. Combining the results of three previous cohorts and our cohort, E40, I43, S150, and E153 are the most frequently affected amino acid residues in resistant isolates. Based on the distribution of mutations in the genome-based phylogenetic tree, lineage-specific mutation patterns were observed. Regarding the segregation of affected amino acid residues, the four most frequently affected residues are all in close proximity of the binding pocket for the PAS derivative. Molecular modeling results showed that mutations at E40, I43, and S150 can alter the structure of FolC putative binding pocket, causing the PAS derivative to bind outside of the now deformed pocket. This might ablate the interaction between the protein and the PAS derivative. To conclude, this study is the first comprehensive mutation pattern and bioinformatics analysis of the folC gene in MTB drug-resistant isolates. The distribution of mutations in phylogenetic lineages and protein structure is reported, analyzed, and discussed.
authors.affiliation: 1 School of Biomedical Sciences, The Chinese University of Hong Kong , Shatin, NT, Hong Kong .
authors.forename: Vincent Wing-Sang
authors.initials: VW
authors.lastname: Cheng
authors.affiliation: 1 School of Biomedical Sciences, The Chinese University of Hong Kong , Shatin, NT, Hong Kong .
authors.forename: Kenneth Siu-Sing
authors.initials: KS
authors.lastname: Leung
authors.affiliation: 1 School of Biomedical Sciences, The Chinese University of Hong Kong , Shatin, NT, Hong Kong .
authors.forename: Jamie Sui-Lam
authors.initials: JS
authors.lastname: Kwok
authors.affiliation: 1 School of Biomedical Sciences, The Chinese University of Hong Kong , Shatin, NT, Hong Kong .|2 Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong , Shatin, NT, Hong Kong .
authors.forename: Ross Ka-Kit
authors.initials: RK
authors.lastname: Leung
authors.affiliation: 1 School of Biomedical Sciences, The Chinese University of Hong Kong , Shatin, NT, Hong Kong .|2 Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong , Shatin, NT, Hong Kong .
authors.forename: Kevin Yi
authors.initials: KY
authors.lastname: Yang
authors.affiliation: 3 Department of Microbiology, The Chinese University of Hong Kong , Shatin, NT, Hong Kong .
authors.forename: Raphael Chiu-Yeung
authors.initials: RC
authors.lastname: Chan
authors.affiliation: 3 Department of Microbiology, The Chinese University of Hong Kong , Shatin, NT, Hong Kong .|4 Tuberculosis Reference Laboratory, Department of Health, Public Health Laboratory Centre , Shatin, NT, Hong Kong .
authors.forename: Kai-Man
authors.initials: KM
authors.lastname: Kam
authors.affiliation: 1 School of Biomedical Sciences, The Chinese University of Hong Kong , Shatin, NT, Hong Kong .|2 Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong , Shatin, NT, Hong Kong .|5 Centre for Microbial Genomics and Proteomics, The Chinese University of Hong Kong , Shatin, NT, Hong Kong .
authors.forename: Stephen Kwok-Wing
authors.initials: SK
authors.lastname: Tsui
mesh_terms: D000995:Antitubercular Agents / Q000737:chemistry* / Q000494:pharmacology; D001426:Bacterial Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D001665:Binding Sites; D019295:Computational Biology; D024881:Drug Resistance, Bacterial / Q000235:genetics; D015870:Gene Expression; D005838:Genotype; D006723:Hong Kong; D006801:Humans; D008826:Microbial Sensitivity Tests; D062105:Molecular Docking Simulation; D009154:Mutation; D009169:Mycobacterium tuberculosis / Q000145:classification / Q000187:drug effects / Q000201:enzymology / Q000235:genetics*; D010453:Peptide Synthases / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D010802:Phylogeny; D011485:Protein Binding; D011622:Pterins / Q000737:chemistry* / Q000494:pharmacology; D018088:Tuberculosis, Multidrug-Resistant / Q000188:drug therapy / Q000382:microbiology; D014397:Tuberculosis, Pulmonary / Q000188:drug therapy / Q000382:microbiology
chemical_list: D000995:Antitubercular Agents; D001426:Bacterial Proteins; D011622:Pterins; D010453:Peptide Synthases; C020041:dihydrofolate synthetase
keywords: Mycobacterium tuberculosis; dihydrofolate synthase; drug resistance; mutation