Biology subjects

Goormaghtigh, F.

Publications and source records attributed to Goormaghtigh, F..

3 recordsLinked to original sources

bioRxiv2026

Codon usage determines tRNA-modification requirements for bacterial virulence

Bacterial virulence genes exhibit distinctive codon usage that may impose tRNA-modification requirements for efficient translation, but a comprehensive understanding is lacking. Here, a curated codon-tRNA modification map for Salmonella predicted six modifications that could preferentially support virulence gene translation. Mutant phenotypes in infected mice confirmed requirements for iA37 and C5 modification of U34, whereas essential k2C34 could not be tested. Q34, Cm32/Um32, and Cm34 had limited impact consistent with weak decoding effects in other systems. Non-predicted tRNA modifications were not required. Synonymous reporter variants, proteomics, and targeted recoding demonstrated that virulence-associated codons directly conferred modification dependence. Additionally, four Leu-TTA codons in ssrB, the master regulator of Salmonella pathogenicity island 2 (SPI-2), contributed to MiaA-dependent SPI-2 gene expression. Extending our analysis to other pathogens predicted shared and divergent virulence dependencies consistent with published mutant phenotypes. Thus, codon usage explains tRNA-modification requirements for bacterial virulence.

microbiology↗

bioRxiv2026

Repurposing a chromosome segregation ParB-CTPase fold into an ATPase toxin for contact-dependent growth inhibition in plant and animal pathogens

Bacterial competition drives the evolution of antibacterial mechanisms, yet how new activities arise remains poorly understood. A major route to innovation is the reuse of pre-existing genetic systems, whereby conserved protein modules are repurposed in new biological contexts to generate new capabilities. Here, we show that the ParB-CTPase fold, a conserved nucleotide-binding module best known for its role in chromosome segregation, can be functionally repurposed as an antibacterial toxin. We identify ToxB, a ParB-like domain embedded within the polymorphic toxin region of contact-dependent inhibition systems and show that it functions as a potent antibacterial effector. Structural and biochemical analyses reveal that ToxB retains the core architecture of the ParB-CTPase fold but lacks DNA-binding capability and preferentially binds ATP. This shift in nucleotide specificity underpins a distinct mode of action, in which ATP binding and hydrolysis trigger rapid nucleoid compaction, chromosome segregation defects, oxidative stress, cell chaining, and ultimately cell lysis. ToxB also exhibits toxic activity in plant cells, suggesting that it targets conserved cellular processes. Together, these findings provide direct experimental evidence that the ParB-NTPase fold is biologically versatile and can be repurposed for biological roles fundamentally distinct from its ancestral function in DNA segregation.

microbiology↗

bioRxiv2026

tRNA modifications enable codon usage signatures to coordinate bacterial virulence in Salmonella

Virulence genes in bacterial pathogens are often A/T-rich and horizontally acquired, yet they must be translated efficiently under stress and nutrient limitation encountered during infection. Here we show that synonymous codon usage contributes directly to this problem. Using CodonPipe, a genome-scale framework for synonymous codon-usage analysis, we find that bacterial genomes contain functionally organized codon-usage landscapes that extend well beyond previous knowledge. In Salmonella enterica, virulence genes form a codon signature that is distinct from ribosomal genes and other mobile elements. This signature favors wobble decoding, increased use of rare tRNA isoacceptors, and enrichment of codons previously shown to better preserve translation during amino-acid limitation. Using codon-recoded fluorescent reporters, we show that virulence codon usage outperforms ribosomal codon usage selectively during nutrient starvation and, more strongly, in host-mimicking conditions. In mouse infections, overexpression of virulence-recoded reporters imposes a strong selective cost. Comparative analyses further indicate that related decoding signatures are conserved across diverse Enterobacteriaceae pathogens. These findings support stress-adapted codon usage as a mechanism that promotes virulence-gene expression during infection. More broadly, our work contributes to explain the long-observed A/T-rich codon bias of virulence genes and identifies tRNA charging and modifications as promising broad anti-virulence targets.

microbiology↗