Frameshift mutations in the mmpR5 gene can have a bedaquiline-susceptible phenotype by retaining a protein structure and function similar to wild-type Mycobacterium tuberculosis.

Abstract

Bedaquiline (BDQ) is crucial for the treatment of rifampicin-resistant tuberculosis, yet resistance threatens its effectiveness, mainly linked to mutations in the mmpR5 (Rv0678) gene. While frameshift mutations are thought to produce non-functional proteins, we hypothesize that they can result in conserved proteins through late-stop codons or alternative reading frames and remain BDQ susceptible. We extracted 512 isolates harboring frameshift mutations in mmpR5 from the World Health Organization (WHO) catalog and 68 isolates with minimum inhibitory concentration (MIC) in mycobacterial growth indicator tube (MGIT) through a literature review. Using BioPython and AlphaFold2 we computed open (ORF) and alternative reading frames (ARFs) sequences and protein structures and assessed similarity to the wild type using an alignment and template modeling (TM)-score. Among the WHO 512 isolates, 24.8% were BDQ-sensitive. Out of 184 unique frameshift mutations with available nucleotide information, a late-stop codon in the ORF occurred for 32% of the mutations. Also, 40.7% resulted in a conserved sequence, through the ORF or one of the forward ARFs. In 68 isolates with available MGIT MIC data, the presence of late-stop codons in the ORF (OR 4.71, 95% CI 1.36-19.3) or a conserved reading frame (OR 10.4, 95% CI 2.07-102.9) were associated with BDQ sensitivity. Protein structures from the conserved sequences showed high similarity (TM > 0.8). We show that frameshift mutations may retain BDQ susceptibility through late-stop codons in the ORF or conserved ARFs. These findings could improve the prediction of the BDQ phenotype from genomic data and have important implications for treatment decisions. Research Foundation-Flanders, Academy of Medical Sciences, the Wellcome Trust, the Government Department of Business, Energy and Industrial Strategy, the British Heart Foundation and Diabetes UK, and the Global Challenges Research Fund.IMPORTANCETuberculosis (TB), caused by Mycobacterium tuberculosis, remains the deadliest infectious disease and is particularly challenging to treat when it becomes drug-resistant. Bedaquiline (BDQ) is a recently recommended core drug for treating drug-resistant TB. However, resistance to bedaquiline is already emerging, primarily due to mutations in the mmpR5 gene. Identifying which mutations cause resistance and which do not is a critical knowledge gap. In particular, little is known about the effect of frameshift mutations, typically thought to make TB bacteria resistant to bedaquiline by producing non-functional proteins. Yet, one-quarter of isolates with a frameshift mutation are still susceptible to bedaquiline. How the bacteria produce a functional protein despite the frameshift mutation is unknown. We analyzed over 500 frameshift mutations using computational methods to model their effects on protein structure and bedaquiline resistance. Our findings revealed that some frameshift mutations can still produce functional proteins, allowing bacteria to remain sensitive to bedaquiline. Specifically, bacteria can produce a functional protein despite frameshift mutations if the mutation occurs near the end of the protein or if an alternative reading frame is available. These insights improve our ability to interpret mutations associated with bedaquiline, the most important drug for drug-resistant TB, allowing more accurate and effective treatment decisions.