Toxin-mediated tRNATrp depletion drives Trp-codon-dependent reprogramming in Mycobacterium tuberculosis while selectively enriching the PDIM biosynthetic machinery

Abstract

Mycobacterium tuberculosis (Mtb) must adapt to host-imposed stresses that limit its growth and ability to establish an infection. One important immune-regulated host defense mechanism involves competition between host and pathogen for tryptophan (Trp). Although Mtb is a Trp prototroph capable of synthesizing its own Trp, it normally acquires this amino acid from host macrophages because of the high energetic cost of its synthesis. However, interferon-γ-activated macrophages attempt to restrict Mtb growth by inducing indoleamine 2,3-dioxygenase 1 (IDO1) that degrades Trp. In response, Mtb senses and adapts to limitation of this essential amino acid by inducing its own Trp biosynthetic pathway, although the mechanisms coupling Trp limitation and compensatory Trp biosynthesis remain unknown. Here, we studied the Mtb VapC37 toxin and demonstrate that it arrests growth and is a highly selective tRNase that exclusively depletes tRNA Trp . Consequently, VapC37 triggers a state of perceived Trp starvation to upregulate production of Trp biosynthetic enzymes. Therefore, this toxin appears to link intracellular Trp availability—a well-established regulator of Mtb growth—to a codon-dependent adaptive response to increase the Trp concentration. VapC37 also broadly reprograms the Mtb transcriptome and translatome toward synthesis of mRNAs and proteins with low or no Trp codons. However, there is one striking exception: key enzymes in the phthiocerol dimycocerosate (PDIM) biosynthetic pathway were robustly synthesized despite being large and Trp-numerous, resulting in a > 2-fold increase in PDIM lipid production upon VapC37 expression. Thus, Mtb selectively preserves PDIM production under conditions of tRNA Trp limitation. Finally, VapBC37 and PDIM transcripts are upregulated in Mtb cells subjected to nitrosative stress and upon Mtb infection of THP-1 macrophage-like cells. This might implicate early macrophage-associated stresses as activators of VapC37, possibly enabling this toxin to reallocate metabolic priorities toward Trp biosynthesis while selectively preserving PDIM production critical for Mtb early immune escape and virulence.