A bacterial enzyme that marks mRNA for destruction in tuberculosis

Bacteria survive stress by changing which genes they make and how quickly they destroy the messages called mRNAs. In Escherichia coli, a known enzyme called RppH triggers mRNA destruction by cutting a chemical group from the front end of mRNA molecules. Researchers led by corresponding author Scarlet S. Shell set out to find the equivalent enzyme in Mycobacterium tuberculosis (Mtb), the bacterium that causes tuberculosis. To do this, they focused on the family of Nudix hydrolase genes, which includes enzymes with similar chemical activities. The team deleted each non-essential Nudix gene from Mtb one at a time and looked for changes in mRNA phosphorylation states — that is, whether mRNA 5’-ends carried three phosphate groups (5’-triphosphates) or had been converted to a single phosphate (5’-monophosphates). This systematic genetic approach allowed the researchers to test which gene changes altered the balance of phosphorylated mRNA across the whole transcriptome, and to identify candidates that behave like the RppH enzyme known from E. coli.

The experiments showed that deleting mutT4 (Rv3908) caused an increased relative abundance of 5’-triphosphates on many mRNAs across the transcriptome, pointing to a role in converting triphosphates to monophosphates. The team purified the MutT4 protein and demonstrated that it converted mRNA 5’-triphosphates into monophosphates in vitro, and that this conversion stimulated degradation by RNase E and RNase J. Sequence features of MutT4 include intrinsically disordered regions (IDRs), which are protein segments known to promote biomolecular condensate formation. Using microscopy, the researchers observed that MutT4 forms condensates inside cells; these condensates dissociated when rifampicin was added. They also found that the N-terminal IDR of MutT4 is sufficient to drive condensate formation and that these MutT4 condensates localize with RNase E and RNase J. Deleting mutT4 in Mtb altered cell properties, producing higher outer membrane permeability and increased resistance to oxidative stress. From these results, the authors conclude that MutT4 acts as the RppH homolog in Mtb and assembles in condensates that could serve as degradation hubs.

These findings reshape how we think about mRNA control in Mycobacterium tuberculosis. By identifying MutT4 as the RppH-like enzyme, the work links a specific protein to the first chemical step that makes many mRNAs vulnerable to rapid breakdown. The observation that MutT4 forms biomolecular condensates together with RNase E and RNase J suggests cells may concentrate the machinery for mRNA decay into localized hubs, which could allow rapid, coordinated changes in gene expression during stress. The fact that removing mutT4 changes outer membrane permeability and makes cells more resistant to oxidative stress hints that altering mRNA decay has broader effects on cell physiology and stress responses. The authors also note that MutT4 is unlikely to be primarily involved in DNA repair or in cleansing the nucleotide pool, functions sometimes ascribed to related proteins, and therefore suggest the name RppH more accurately reflects its role. Altogether, the study adds a new piece to the picture of how tuberculosis bacteria regulate their messages and respond to antibiotics or immune pressures, by showing a molecular link between a specific enzyme, condensate behavior, and mRNA stability.