A role for 16S rRNA dimethyltransferase (ksgA) in intrinsic clarithromycin resistance in Mycobacterium tuberculosis

Phunpruch, Saranya; Warit, Saradee; Suksamran, Rungaroon; Billamas, Pamaree; Jaitrong, Sarinya; Palittapongarnpim, Prasit; Prammananan, Therdsak

doi:10.1016/j.ijantimicag.2013.02.011

Cited by 16 publications

(11 citation statements)

References 25 publications

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“…In humans, genetic defects resulting in imperfect ribosome biogenesis are the cause of various ribosomopathies (4)(5)(6)(7). Thus, a better understanding of ribosome biogenesis is a fundamental requirement to develop antimicrobials and various therapies (8)(9)(10)(11)(12).…”

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confidence: 99%

An evolutionarily conserved element in initiator tRNAs prompts ultimate steps in ribosome maturation

Shetty

Varshney

2016

Proc. Natl. Acad. Sci. U.S.A.

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Ribosome biogenesis, a complex multistep process, results in correct folding of rRNAs, incorporation of >50 ribosomal proteins, and their maturation. Deficiencies in ribosome biogenesis may result in varied faults in translation of mRNAs causing cellular toxicities and ribosomopathies in higher organisms. How cells ensure quality control in ribosome biogenesis for the fidelity of its complex function remains unclear. Using Escherichia coli, we show that initiator tRNA (i-tRNA), specifically the evolutionarily conserved three consecutive GC base pairs in its anticodon stem, play a crucial role in ribosome maturation. Deficiencies in cellular contents of i-tRNA confer cold sensitivity and result in accumulation of ribosomes with immature 3′ and 5′ ends of the 16S rRNA. Overexpression of i-tRNA in various strains rescues biogenesis defects. Participation of i-tRNA in the first round of initiation complex formation licenses the final steps of ribosome maturation by signaling RNases to trim the terminal extensions of immature 16S rRNA.cold sensitivity | ribosome biogenesis | 3GC base pairs | RNase PH/RNAse R | 16S rRNA maturation R ibosomes are large and the most complex of the molecular machines in cells, using up to 40% of the cellular energy for their biogenesis (1). Ribosome biogenesis is a multistep process involving a coordinated network of RNA-RNA, RNA-protein, and protein-protein interactions. The process begins with the transcription of rRNA, its processing, nucleoside modifications, structural rearrangements, synthesis, and interaction of ribosomal proteins (r-proteins) (2). In cells, RNA processing enzymes, modification systems, and chaperone-like factors facilitate ribosome biogenesis. Any deficiencies in this process may produce ribosomes that fail to maintain the fidelity of protein synthesis and cause cellular toxicity/ death (3). Deficiencies in biogenesis factors impart cold sensitivity to Escherichia coli and affect bacterial drug resistance and virulence. In humans, genetic defects resulting in imperfect ribosome biogenesis are the cause of various ribosomopathies (4-7). Thus, a better understanding of ribosome biogenesis is a fundamental requirement to develop antimicrobials and various therapies (8-12).Of the two ribosomal subunits in E. coli, the small subunit contains a 1,542 nucleotide long rRNA (16S rRNA) along with 21 r-proteins, whereas the large subunit contains two rRNAs of 2,904 (23S rRNA) and 120 (5S rRNA) nucleotide lengths along with 33 r-proteins. The three rRNAs are synthesized as parts of a single transcript and the assembly of r-proteins begins cotranscriptionally. As the assembly advances, the precursor rRNA is cleaved by RNase III into immature units of 16S rRNA (as 17S), 23S rRNA (as 25S), and 5S rRNA (as 9S) rRNAs. The 17S rRNA retains unprocessed extensions of 110 and 33 nucleotides on the 5′ and 3′ ends, respectively. Trimming of the extensions by RNase G and other RNases matures 16S rRNA. Incorporation of r-proteins occurs in three stages. The primary r-proteins interact di...

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confidence: 99%

An evolutionarily conserved element in initiator tRNAs prompts ultimate steps in ribosome maturation

Shetty

Varshney

2016

Proc. Natl. Acad. Sci. U.S.A.

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“…In addition, researchers have focused on the relationship between drug resistance and the M. tuberculosis complex (MTC) (Madsen et al 2005;Phunpruch et al 2013). For example, Phunpruch et al suggested that the methylation pattern in Mycobacterium smegmatis (M. smegmatis) could be used to understand the resistance toward lincosamides and erythromycin (Phunpruch et al 2013). Therefore, we speculate that DNA methylation may be closely related to LOF resistance in the M. tuberculosis H37Rv strain.…”

Section: Introductionmentioning

confidence: 86%

“…Moreover, previous studies have highlighted occurrence of DNA methylation remodeling in dendritic cells upon infection with M. tuberculosis (Pacis et al 2019(Pacis et al , 2015. In addition, researchers have focused on the relationship between drug resistance and the M. tuberculosis complex (MTC) (Madsen et al 2005;Phunpruch et al 2013). For example, Phunpruch et al suggested that the methylation pattern in Mycobacterium smegmatis (M. smegmatis) could be used to understand the resistance toward lincosamides and erythromycin (Phunpruch et al 2013).…”

Section: Introductionmentioning

confidence: 99%

Potential Genes Related to Levofloxacin Resistance in Mycobacterium tuberculosis Based on Transcriptome and Methylome Overlap Analysis

Guo

Chen

et al. 2020

J Mol Evol

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Drug-resistant Mycobacterium tuberculosis (M. tuberculosis) has become an increasingly serious public health problem and has complicated tuberculosis (TB) treatment. Levofloxacin (LOF) is an ideal anti-tuberculosis drug in clinical applications. However, the detailed molecular mechanisms of LOF-resistant M. tuberculosis in TB treatment have not been revealed. Our study performed transcriptome and methylome sequencing to investigate the potential biological characteristics of LOF resistance in M. tuberculosis H37Rv. In the transcriptome analysis, 953 differentially expressed genes (DEGs) were identified; 514 and 439 DEGs were significantly downregulated and upregulated in the LOF-resistant group and control group, respectively. The KEGG pathway analysis revealed that 97 pathways were enriched in this study. In the methylome analysis, 239 differentially methylated genes (DMGs) were identified; 150 and 89 DMGs were hypomethylated and hypermethylated in the LOF-resistant group and control group, respectively. The KEGG pathway analysis revealed that 74 pathways were enriched in this study. The overlap study suggested that 25 genes were obtained. It was notable that nine genes expressed downregulated mRNA and upregulated methylated levels, including pgi, fadE4, php, cyp132, pckA, rpmB1, pfkB, acg, and ctpF, especially cyp132, pckA, and pfkB, which were vital in LOF-resistant M. tuberculosis H37Rv. The overlapping genes between transcriptome and methylome could be essential for studying the molecular mechanisms of LOF-resistant M. tuberculosis H37Rv. These results may provide informative evidence for TB treatment with LOF.

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“…Resistance is caused indirectly because of unstable interactions between helix 45 (where A1519 and A1518 are located) and helix 44 (primary binding site of kasugamycin) (8). Recent data suggest a new role for KsgA in resistance of M. tuberculosis to the macrolide clarithromycin (11). While the molecular basis of ksgA-mediated macrolide resistance is unknown, macrolides bind to the 50S subunit, causing premature detachment of incomplete polypeptide chains, resulting in impaired protein synthesis (41).…”

Section: Fig 1 Ksga Deficiency Decreases the Ability Of S Enteritidimentioning

confidence: 99%

“…In contrast, a ksgA mutant of Staphylococcus aureus was more sensitive to kanamycin and paromomycin, probably due to the conformational changes distal to the aminoglycoside binding site in the SSU, which are further propagated from the KsgA methylation site (10). Recently, disruption of ksgA in a clarithromycin-resistant Mycobacterium tuberculosis strain resulted in abolishment of resistance (11), suggesting that KsgAmediated drug resistance is likely to be strain and species dependent.…”

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confidence: 99%

Dimethyl Adenosine Transferase (KsgA) Deficiency in Salmonella enterica Serovar Enteritidis Confers Susceptibility to High Osmolarity and Virulence Attenuation in Chickens

Chiok

Addwebi

Guard

et al. 2013

Appl Environ Microbiol

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bDimethyl adenosine transferase (KsgA) performs diverse roles in bacteria, including ribosomal maturation and DNA mismatch repair, and synthesis of KsgA is responsive to antibiotics and cold temperature. We previously showed that a ksgA mutation in Salmonella enterica serovar Enteritidis results in impaired invasiveness in human and avian epithelial cells. In this study, we tested the virulence of a ksgA mutant (the ksgA::Tn5 mutant) of S. Enteritidis in orally challenged 1-day-old chickens. The ksgA:: Tn5 mutant showed significantly reduced intestinal colonization and organ invasiveness in chickens compared to those of the wild-type (WT) parent. Phenotype microarray (PM) was employed to compare the ksgA::Tn5 mutant and its isogenic wild-type strain for 920 phenotypes at 28°C, 37°C, and 42°C. At chicken body temperature (42°C), the ksgA::Tn5 mutant showed significantly reduced respiratory activity with respect to a number of carbon, nitrogen, phosphate, sulfur, and peptide nitrogen nutrients. The greatest differences were observed in the osmolyte panel at concentrations of >6% NaCl at 37°C and 42°C. In contrast, no major differences were observed at 28°C. In independent growth assays, the ksgA::Tn5 mutant displayed a severe growth defect in high-osmolarity (6.5% NaCl) conditions in nutrient-rich (LB) and nutrient-limiting (M9 minimum salts) media at 42°C. Moreover, the ksgA::Tn5 mutant showed significantly reduced tolerance to oxidative stress, but its survival within macrophages was not impaired. Unlike Escherichia coli, the ksgA::Tn5 mutant did not display a cold-sensitivity phenotype; however, it showed resistance to kasugamycin and increased susceptibility to chloramphenicol. To the best of our knowledge, this is the first report showing the role of ksgA in S. Enteritidis virulence in chickens, tolerance to high osmolarity, and altered susceptibility to kasugamycin and chloramphenicol.

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A role for 16S rRNA dimethyltransferase (ksgA) in intrinsic clarithromycin resistance in Mycobacterium tuberculosis

Cited by 16 publications

References 25 publications

An evolutionarily conserved element in initiator tRNAs prompts ultimate steps in ribosome maturation

An evolutionarily conserved element in initiator tRNAs prompts ultimate steps in ribosome maturation

Potential Genes Related to Levofloxacin Resistance in Mycobacterium tuberculosis Based on Transcriptome and Methylome Overlap Analysis

Dimethyl Adenosine Transferase (KsgA) Deficiency in Salmonella enterica Serovar Enteritidis Confers Susceptibility to High Osmolarity and Virulence Attenuation in Chickens

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