Biology subjects

Cabales, A.

Publications and source records attributed to Cabales, A..

3 recordsLinked to original sources

bioRxiv2026

Genetic code expansion enables plant-directed control of bacterial activity

Programmable control of microbial gene expression by plant hosts could enable a new generation of precision agricultural biotechnology. Here, using O-methyl-L-tyrosine (OMY) as a model compound, we establish non-canonical amino acids (ncAAs) as a tool for plant-based control of associated microbial activity. We use genetic code expansion to engineer OMY-dependent control of protein synthesis in the soil bacterium Bacillus subtilis. Then, we engineer agronomically diverse plants, including Arabidopsis, tomato and poplar, to biosynthesize OMY. We show that plant-derived OMY can stimulate gene expression in both model and wild soil bacteria while also demonstrating that inducible and tissue-specific expression of a single biosynthetic enzyme by the plant enables on-demand control over microbial activity. This work establishes ncAAs as a tool for programming plant-microbe partnerships.

synthetic biology↗

bioRxiv2026

A nitrogen assimilation bottleneck can limit Bacillus subtilis growth in plant culture media

Microbial engineering offers potential for improving the sustainability of agriculture by providing greater control of desired microbial functions. However, successful control of engineered functions requires greater understanding of their robustness under diverse conditions including those used for plant hydroponics. Here, we studied biomass accumulation and surfactin biosynthesis by an engineered derivative of Bacillus subtilis PY79 in common plant culture media as a model system for interrogating metabolic robustness. We report the observation that PY79 and all other B. subtilis strains that we tested, including natural isolates, exhibited difficulty growing under shaking incubation in defined media where the only nitrogen sources were inorganic. In contrast, assimilation of inorganic nitrogen sources functioned relatively robustly under static incubation in these same media. Our findings may offer some guidance for use of B. subtilis in controlled environment agriculture and could aid future efforts to identify the molecular basis for the agitation-dependent effect on nitrogen assimilation.

microbiology↗

bioRxiv2025

The influence of surfactin and glutamate on tomato root association by plant growth promoting rhizobacteria Bacillus subtilis

The influence of microbially and plant synthesized compounds on attachment of plant growth promoting rhizobacteria (PGPR) to various regions of the plant root are underexplored. Here, we examine the influence of surfactin and glutamate on the level and specificity of attachment of Bacillus subtilis along different regions of tomato root using chemical and genetic perturbations. First, we modify Bacillus subtilis PY79 to express a full-length phosphopantetheinyl transferase (sfp) native to other B. subtilis strains, and we observe surfactin biosynthesis under static incubation at 25{degrees}C in plant culturing media. We then perform microscopy using the wild-type PY79 strain, the sfp+ strain, and the wild isolate B. subtilis UD1022 to map the attachment of each strain along the entire root of young tomato plants incubated at 25{degrees}C, including when exogenously supplementing surfactin or glutamate. Through root mapping, we show that these strains prefer to attach near the mature region (MR) of the root and that colonization patterns vary based on exogenous metabolite concentration. Inclusion of glutamate in the media or through transient priming of the plant prior to bacterial inoculation strongly promoted root colonization by B. subtilis strains (both surfactin null and producers). In addition, the data shows that the domesticated strains were less efficient in binding compared to the wild B. subtilis strain. Interestingly, in the presence of glutamate, microbes lost their preference for association at the mature region, instead colonizing along the entire root. Overall, our work reveals a preference for association of these B. subtilis strains to the mature region of tomato in the absence of glutamate supplementation, confirms a strong influence of glutamate on root association, and demonstrates a smaller than anticipated role of biosynthesized or supplemented surfactin on root association, at least in a hydroponic culturing format.

plant biology↗