Biology subjects

Cai, Y.-M.

Publications and source records attributed to Cai, Y.-M..

4 recordsLinked to original sources

bioRxiv2026

Evolutionary Rewiring of Root Cell-Type Nitrogen Responses

Nitrate induces widespread transcriptional reprogramming in plants, but how transcription factors coordinate these responses across cell types and evolve across species with divergent root patterning remains unclear. Using single-cell transcriptomics in Arabidopsis thaliana and Solanum lycopersicum (tomato) under varying nitrate conditions, we demonstrate that many transcriptional responses are cell type and developmental stage-specific. Arabidopsis NIN-LIKE PROTEIN 7 (NLP7) directly modulates both broadly expressed and cell-type-specific targets, but is not required to establish the cell type specific nature of these patterns. Comparative analysis reveals evolutionary shifts; key nitrogen programs are localized to different cell types in tomato, with the exodermis as a major regulatory hub. Identification of tomato NLP7a and NLP7b direct targets at cellular resolution supports their role in direct modulation of cell type N-transcriptional programs. This is evidenced by NLP7-controlled exodermal cell wall remodeling in low nitrate, highlighting functional conservation despite divergent cellular topographies.

plant biology↗

bioRxiv2024

Identification of echinacoside as a tobramycin potentiator against Pseudomonas aeruginosa aggregates

Cyclic diguanylate (c-di-GMP) is a central biofilm regulator, where increased intracellular levels promote biofilm formation and antibiotic tolerance. Targeting the c-di-GMP network is a promising anti-biofilm approach. Most agents reported previously decreased c-di-GMP to eliminate surface-attached biofilms, which did not recapitulate in vivo biofilms well and may thus impede their clinical impact. Here, the expression profile of genes encoding proteins associated with c-di-GMP metabolism was analysed among 32 Pseudomonas aeruginosa strains grown as suspended aggregates in synthetic sputum or planktonic cells. A diguanylate cyclase, SiaD, proved essential for auto-aggregation under in vivo-like conditions. Virtual screening against SiaD identified echinacoside as an inhibitor, which reduced intracellular c-di-GMP levels and aggregate sizes and potentiated the efficacy of tobramycin against aggregates established by >80% of tested strains. This synergistic effect was also observed for in vivo-like 3-D alveolar cells infected by cytotoxic P. aeruginosa, demonstrating its high potential as an adjunctive therapy for recalcitrant P. aeruginosa infections.

microbiology↗

bioRxiv2023

Tuning plant promoters using a simple split luciferase method for quantifying transcription factor binding affinity

Sequence features, including the binding affinity of binding motifs for their cognate transcription factors, are important contributors to promoter behavior. The ability to predictably recode affinity enables the development of synthetic promoters with varying levels of response to known cellular signals. Here we describe a luminescence-based microplate assay for comparing the interactions of transcription factors with short DNA probes. We then demonstrate how this data can be used to design synthetic plant promoters of varying strengths that respond to the same transcription.

synthetic biology↗

bioRxiv2019

Differential impact on motility and biofilm dispersal of closely related phosphodiesterases in Pseudomonas aeruginosa

Bacteria typically occur either as free-swimming planktonic cells or within a sessile, biofilm mode of growth. In Pseudomonas aeruginosa, the transition between these lifestyles is known to be modulated by the intracellular secondary messenger cyclic dimeric-GMP (c-di-GMP). We are interested in the control of distinct biofilm-relevant phenotypes in P. aeruginosa through the modulation of intracellular c-di-GMP. Here, we characterise motility and associated biofilm formation and dispersal in two pairs of related multi-domain proteins with putative c-di-GMP turnover domains, selected to contain additional PAS (Per-Arnt-Sim) homology domains known for their ability to process environmental stimuli. The enzymes PA0861 (RbdA) and PA2072 have distinct functions despite their similar domain structures. The {Delta}rbdA deletion mutant showed significantly increased biofilm formation while biofilm formation was impaired in {Delta}PA2072. Using a GFP transcriptional reporter fused to the cyclic di-GMP-responsive cdrA promoter, we show correlation between biofilm phenotype and c-di-GMP levels. Both proteins are shown to play a role in nitric oxide (NO) induced biofilm dispersal. We further studied pseudo-enzymes of similar architecture. PA5017 (DipA) is an inactive cyclase, and PA4959 (FimX) is described here as an inactive cyclase/phosphodiesterase. Loss of swimming and twitching motilities, respectively, is observed in deletion variants, which correlated with NO-induced biofilm dispersal phenotypes, as {Delta}dipA dispersed less well while {Delta}fimX dispersed better than wild type. The study highlights how Pseudomonas differentiates c-di-GMP output - in this case motility - using structurally very similar proteins and underlines a significant role for pseudo-enzymes in motility regulation and associated biofilm dispersal.\n\nImportanceBacterial biofilms exert pervasive economic and societal impact across a range of environmental, engineered and clinical contexts. The secondary messenger cyclic guanosine di-phosphate, c-di-GMP, is known to control the ability of many bacteria to form biofilms. The opportunistic human pathogen Pseudomonas aeruginosa PAO1 has 38 putative enzymes that can regulate c-di-GMP turnover, and these proteins modulate various cellular functions and influence bacterial lifestyle. The specific protein sensory domains and mechanisms of motility that lead to biofilm dispersal remain to be fully understood. Here we studied multi-domain proteins with the PAS (Per-Arnt-Sim) homology domains, these being classic sensors to environmental stimuli. Our study demonstrates the significant roles for the pseudo-enzymes PA4959 (FimX) and PA5017 (DipA) in regulation of biofilm phenotype and motility. Further, enzymes with highly homologous structures, such as PA0861 (RbdA) and PA2072, have almost orthogonal function in biofilm and motility control.

microbiology↗