A novel mutation alters the stability of PapA2 resulting in the complete abrogation of sulfolipids in clinical mycobacterial strains

Abstract

The analysis of whole genomes has revealed specific geographical distribution of Mycobacterium tuberculosis (Mtb) strains across the globe suggestive of unique niche dependent adaptive mechanisms. We provide an important correlation of a genome‐based mutation to a molecular phenotype across two predominant clinical Mtb lineages of the Indian subcontinent. We have identified a distinct lineage specific mutation‐G247C, translating into an alanine‐proline conversion in the papA2 gene of Indo‐oceanic lineage 1 (L1) Mtb strains, and restoration of cell wall sulfolipids by simple genetic complementation of papA2 from lineage 3 (L3) or from H37Rv (lineage 4‐L4) attributed the loss of this glycolipid to this specific mutation in Indo‐Oceanic L1 Mtb. The investigation of structure of Mtb PapA2 revealed a distinct nonribosomal peptide synthetase (NRPS) C domain conformation with an unconventional presence of a zinc binding motif. Surprisingly, the A83P mutation did not map to either the catalytic center in the N‐terminal subdomain or any of the substrate‐binding region of the protein. On the contrary, the inherent ability of mutant PapA2 to form insoluble aggregates and molecular simulations with the wild‐type/mutant (Wt/mut) PapA2 purports an important role for the surface associated 83rd residue in protein conformation. This study demonstrates the importance of a critical structural residue in the papA2 protein of Mtb and helps establish a link between observed genomic alteration and its molecular consequence in the successful human pathogen Mtb. Significance We demonstrate the effect of a unique SNP in PapA2 gene of Indo‐oceanic Mycobacterium tuberculosis (Mtb) strains leading to the loss of sulfolipid from these strains. By X‐ray crystallographic analysis and molecular dynamics (MD) simulations, we show the importance of this residue in the global PapA2 structure. The presence of a Zn atom has not been reported before for this class of proteins. Here, we provide an important link between genomic alteration and its molecular consequence in Mtb highlighting one of the many adaptive mechanisms that have contributed to its success as a human pathogen. A high degree of identity with PapA1, 3, or 4 would help in interpreting the structure of these PapA proteins and other acyl transferases of other biological systems.

SLeuthing Tuberculous Cough

“…This idea would certainly be consistent with its evolutionary history. It would also fit with a recent paper showing that a clade of M. tuberculosis prevalent in South India does not produce SL-1 owing to a mutation in a metabolic pathway enzyme (Panchal et al, 2019).…”

Mycobacterium tuberculosis (Mtb) lipid mediated lysosomal rewiring in infected macrophages modulates intracellular Mtb trafficking and survival

“…Similarly, it will be interesting to extend these studies to clinical isolates of Mtb, which differ in SL-1 gene expression and lipid levels (82)(83)(84). Some strains of the "ancestral" Clade 2 show reduced expression of genes in the SL-1 biosynthetic pathway (85), whereas a recent report shows an Mtb strain belonging to the ancestral lineage with a point mutation in the papA2 gene, which confers it a loss of SL-1 phenotype (86). The contribution of the lysosomal alterations and their differential subcellular localization to the distinct inflammatory responses elicited by these phylogenetically distant strains will be interesting to explore.…”

Acyltransferase families that act on thioesters: Sequences, structures, and mechanisms

“…The only structure available to date in family AT10 (6AEF), a PKS associate enzyme from M. tuberculosis , shows an unconventional presence of a zinc finger motif in the N‐terminal region, but still presents a classical CoA‐dependent acyltransferase fold with a large β sheet flanked by α‐helices. The N‐terminal subdomain also shows seven mixed‐type beta strands, parallel and antiparallel, whereas the C‐terminal subdomain contains six mixed beta strands 86 …”

“…The N-terminal subdomain also shows seven mixed-type beta strands, parallel and antiparallel, whereas the C-terminal subdomain contains six mixed beta strands. 86 AT11 has a single crystallized structure (3K2I) from Homo sapiens;…”