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Identification of novel mutations in LprG (rv1411c), rv0521, rv3630, rv0010c, ppsC, cyp128 associated with pyrazinoic acid/pyrazinamide resistance in Mycobacterium tuberculosis

By Wanliang Shi, Jiazhen Chen, Shuo Zhang, Wenhong Zhang, Ying Zhang

Posted 17 Jan 2018
bioRxiv DOI: 10.1101/249201 (published DOI: 10.1128/aac.00430-18)

There is currently considerable interest in understanding the mechanisms of action of pyrazinamide (PZA), a critical frontline tuberculosis (TB) drug that plays a unique role in shortening TB therapy due to its unique activity against Mycobacterium tuberculosis persisters. PZA is a prodrug that is converted to its active form pyrazoic acid (POA) by PncA enzyme. However, the mechanisms of action and resistance of PZA are complex and are not well understood. So far, pncA, rpsA, panD, and clpC1 are known to be involved in PZA resistance, however, we still find some PZA/POA-resistant strains still do not have any mutations in the above known genes involved in PZA resistance, indicating that new mechanisms of PZA/POA resistance must exist. Here, to identify possible new mechanisms of PZA resistance, we characterized 109 POA-resistant mutants and found that most (101/109=93%) of POA-resistant mutants had panD mutations. Among the 8 POA-resistant mutants that did not have panD mutations, 4 had the same clpC1 mutation (S91G), while the remaining 4 did not have any mutations in the known PZA resistance genes. Whole genome sequencing of the 4 POA-resistant mutants revealed that they all had the same two mutations rv1411c (Lipoprotein LprG C672T change leading to W224STOP) and rv0521 (Methyltransferase, C295T causing amino acid substitution R99W). However, one strain (3G1) had only the two identical mutations in LprG (rv1411c) and rv0521 while the remaining 3 mutants had additional low percentage of heterogeneous mutations in rv3630 (hypothetical protein), rv0010c (hypothetical protein), ppsC (phenolpthiocerol synthesis type-I polyketide synthase C) and cyp128 (cytochrome P450 128). LprG-Rv1410 participates in triacylglyceride (TAG) transport in M. tuberculosis and loss of its function leads to intracellular TAG accumulation, and is critical for regulating bacterial growth and metabolism during carbon starvation and infection. The finding that all 4 POA-resistant mutants have the same W224Stop mutation in LprG suggests that the non-functional LprG may lead to higher TAG accumulation and thus causing higher metabolism, which is known to antagonize PZA/POA activity. This provides a plausible explanation for loss of function mutation in LprG being a likely cause for PZA/POA resistance. Our findings shed new light on the mechanisms of action and resistance of PZA/POA. Future studies are needed to address the role of the identified mutations in PZA resistance and how they might be involved in the action of PZA in M. tuberculosis.

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