Toxin-mediated tRNATrp depletion drives Trp-codon-dependent reprogramming in Mycobacterium tuberculosis while selectively enriching the PDIM biosynthetic machinery
- 1Department of Biochemistry and Molecular Biology, Rutgers Health, Robert Wood Johnson Medical School, Piscataway, New Jersey, United States of America
- 2Division of Infecti ous Diseases, Department of Pediatrics, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
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 tRNATrp. 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 tRNATrp 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. Author summary: Tryptophan (Trp), the least abundant amino acid in Escherichia coli, is likely also limiting in Mycobacterium tuberculosis (Mtb) since intracellular Trp concentration acts as a growth regulating switch. Although Mtb is a prototroph capable of synthesizing its own Trp, this pathway is energetically costly. Macrophage-residing Mtb cells are therefore thought to exploit the host environment as an exogenous source of Trp. In response, the host innate immune system restricts bacterial growth through interferon-γ-induced degradation of Trp. Although Trp availability is essential to establish an infection in mice, it is unclear how Mtb senses and adapts to host-imposed Trp limitation. Here we report that the VapC37 toxin might help Mtb adapt to the Trp-restricted environment encountered during macrophage infection. VapC37-mediated tRNATrp inactivation mimics Trp starvation and triggers the Trp biosynthetic pathway that may counter host-imposed Trp stress while simultaneously remodeling Mtb physiology and upregulating the phthiocerol dimycocerosate (PDIM) lipid biosynthetic pathway essential for Mtb virulence. VapC37 and PDIM biosynthetic transcripts are upregulated during infection of THP-1 macrophage-like cells, and VapC37 transcripts are also induced by nitrosative stress. Together, these findings implicate VapC37 as a possible mediator that links growth arrest, Trp biosynthesis, metabolic adaptation, and preservation of virulence during infection.
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BibTeX
@article{sain2026toxinmediated,
title = {{Toxin-mediated tRNATrp depletion drives Trp-codon-dependent reprogramming in Mycobacterium tuberculosis while selectively enriching the PDIM biosynthetic machinery}},
author = {Safreen Sain and Unnati Chauhan and Valdir C. Barth Jr and Eduardo A. Troian and Bruno L. Abbadi and Basanti Malakar and Robert N. Husson and Nancy A. Woychik},
journal = {PLOS Pathogens},
year = {2026},
month = oct,
doi = {10.1371/journal.ppat.1014679},
url = {https://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1014679},
note = {CC BY},
}
RIS
TY - JOUR
TI - Toxin-mediated tRNATrp depletion drives Trp-codon-dependent reprogramming in Mycobacterium tuberculosis while selectively enriching the PDIM biosynthetic machinery
AU - Safreen Sain
AU - Unnati Chauhan
AU - Valdir C. Barth Jr
AU - Eduardo A. Troian
AU - Bruno L. Abbadi
AU - Basanti Malakar
AU - Robert N. Husson
AU - Nancy A. Woychik
PY - 2026
DA - 2026/10/01
JO - PLOS Pathogens
DO - 10.1371/journal.ppat.1014679
UR - https://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1014679
AB - 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 tRNATrp. 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 tRNATrp 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. Author summary: Tryptophan (Trp), the least abundant amino acid in Escherichia coli, is likely also limiting in Mycobacterium tuberculosis (Mtb) since intracellular Trp concentration acts as a growth regulating switch. Although Mtb is a prototroph capable of synthesizing its own Trp, this pathway is energetically costly. Macrophage-residing Mtb cells are therefore thought to exploit the host environment as an exogenous source of Trp. In response, the host innate immune system restricts bacterial growth through interferon-γ-induced degradation of Trp. Although Trp availability is essential to establish an infection in mice, it is unclear how Mtb senses and adapts to host-imposed Trp limitation. Here we report that the VapC37 toxin might help Mtb adapt to the Trp-restricted environment encountered during macrophage infection. VapC37-mediated tRNATrp inactivation mimics Trp starvation and triggers the Trp biosynthetic pathway that may counter host-imposed Trp stress while simultaneously remodeling Mtb physiology and upregulating the phthiocerol dimycocerosate (PDIM) lipid biosynthetic pathway essential for Mtb virulence. VapC37 and PDIM biosynthetic transcripts are upregulated during infection of THP-1 macrophage-like cells, and VapC37 transcripts are also induced by nitrosative stress. Together, these findings implicate VapC37 as a possible mediator that links growth arrest, Trp biosynthesis, metabolic adaptation, and preservation of virulence during infection.
SN - 1553-7374
SN - 1553-7366
ER -