Thanks Federico

You can look at this:

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Nat Genet. 2013 Oct;45(10):1190-7. doi: 10.1038/ng.2743. Epub 2013 Sep 1.

Evolution of high-level ethambutol-resistant tuberculosis through interacting mutations in decaprenylphosphoryl-β-D-arabinose biosynthetic and utilization pathway genes.

Safi H1, Lingaraju S, Amin A, Kim S, Jones M, Holmes M, McNeil M, Peterson SN, Chatterjee D, Fleischmann R, Alland D.

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Abstract

To study the evolution of drug resistance, we genetically and biochemically characterized Mycobacterium tuberculosis strains selected in vitro for ethambutol resistance. Mutations in decaprenylphosphoryl-β-D-arabinose (DPA) biosynthetic and utilization pathway genes Rv3806c, Rv3792, embB and embC accumulated to produce a wide range of ethambutol minimal inhibitory concentrations (MICs) that depended on mutation type and number. Rv3806c mutations increased DPA synthesis, causing MICs to double from 2 to 4 μg/ml in a wild-type background and to increase from 16 to 32 μg/ml in an embB codon 306 mutant background. Synonymous mutations in Rv3792 increased the expression of downstream embC, an ethambutol target, resulting in MICs of 8 μg/ml. Multistep selection was required for high-level resistance. Mutations in embC or very high embC expression were observed at the highest resistance level. In clinical isolates, Rv3806c mutations were associated with high-level resistance and had multiplicative effects with embB mutations on MICs. Ethambutol resistance is acquired through the acquisition of mutations that interact in complex ways to produce a range of MICs, from those falling below breakpoint values to ones representing high-level resistance.

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Complex genetics of drug resistance in Mycobacterium tuberculosis. [Nat Genet. 2013]

It is of course possible by SNPs in promotor regions those affecting bindings sites, small RNAs etc

Dear Emma,

We have identified a silent mutation A46A in pncA gene in one PZA-resistant isolate of our collection. This SNP is reported to serve as a marker of M. canettii, a variant of M. tuberculosis, which is naturally resistant to PZA (efflux pumps), but not as a result of pncA mutations.

When looking to the morphology, these colonies were smooth that is characteristic of M. canettii.

In inh-resistant isolate, we have identified another silent mutation in inhA gene ( GGA/GGC -> G3G) that was in combination with the well known mutation -15 C/T in the inhA promoter region.

Interestingly one susceptible isolate that was left in MGIT tube + INH for more than 21 days (induction of resistance), have shown this silent mutation G3G. Further analysis are required to look if this SNP is a precursor for other mutation associated with resistance. I don't think that this SNP is responsible for resistance when enzymatic activity (KatG, inhA, embB, pncA) or conformationnal change (rpoB) are involved, ruther than a precursor for other mutations.

Many thanks for all your answers, 

Emma.

Synonymous mutation can be related to misfolding and dysfunction of the protein.

I recently proposed that translational rate is modulated by pairs of consecutive codons or bicodons [1]. By a statistical analysis of coding sequences, we compute a rate translational measure of all bicodons. We found that bicodons associated with sequences encoding low abundant proteins are involved in translational rate attenuation. Furthermore, we observe that the misfolding in many protein, such MDR1 gene [2], is better explained by a big change in the translational rate due to the synonymous bicodon variant, rather than by a relatively small change in the codon usage.

1.- Coding translational rates: the hidden genetic code

http://biorxiv.org/content/early/2016/07/08/062935

2.- Kimchi-Sarfaty, et al. A silent polymorphism in the MDR1 gene changes substrate specificity.

Science 315, 525–528 (2007).