Biology subjects

Rillema, R.

Publications and source records attributed to Rillema, R..

3 recordsLinked to original sources

bioRxiv2026

Identifying Novel Targets of the Stringent Response in Plants and Cyanobacteria using chemoproteomics

Survival in dynamic environments requires photosynthetic organisms to rapidly sense and respond to stress. The stringent response, mediated by the signaling molecule guanosine-3,5-bisdiphosphate (ppGpp), is crucial for acclimation to environmental changes such as darkness and nitrogen limitation. While it has been extensively characterized in heterotrophic bacteria such as Escherichia coli, the molecular mechanisms and regulatory targets of ppGpp in photosynthetic organisms remain less understood. Here, we report large-scale chemoproteomic identification of ppGpp-binding proteins across plant chloroplasts and cyanobacteria, revealing both conserved and novel targets compared to E. coli. In plants, we found that ppGpp regulates pyrimidine metabolism by inhibiting the chloroplastic enzyme aspartate transcarbamoylase (PyrB). In cyanobacteria, we found that ppGpp activates glucose-1-phosphate adenylyltransferase (GlgC) involved in glycogen synthesis, activates citrate synthase (GltA), and induces carboxysome aggregation. These findings expand the known ppGpp regulatory network in photosynthetic organisms and provide a foundation for understanding how ppGpp coordinates adaptation to nutrient and environmental stresses.

systems biology↗

bioRxiv2022

Developing cyanobacterial quorum sensing toolkits: towards interspecies coordination in mixed autotroph/heterotroph communities

1.There has been substantial recent interest in the promise of sustainable, light-driven bioproduction using cyanobacteria, including developing efforts for microbial bioproduction using mixed autotroph/heterotroph communities, which could provide useful properties, such as division of metabolic labor. However, building stable mixed-species communities of sufficient productivity remains a challenge, partly due to the lack of strategies for synchronizing and coordinating biological activities across different species. To address this obstacle, we developed an inter-species communication system using quorum sensing (QS) modules derived from well-studied pathways in heterotrophic microbes. In the model cyanobacterium, Synechococcus elongatus PCC 7942 (S. elongatus), we designed, integrated, and characterized genetic circuits that detect acyl-homoserine lactones (AHLs), diffusible signals utilized in many QS pathways. We showed that these receiver modules sense exogenously supplied AHL molecules and activate gene expression in a dose-dependent manner. We characterized these AHL receiver circuits in parallel in Escherichia coli W (E. coli W) to dissect species-specific properties, finding broad agreement, albeit with increased basal expression in S. elongatus. Our engineered "sender" E. coli strains accumulated biologically synthesized AHLs within the supernatant and activated receiver strains similarly to exogenous AHL activation. Our results will bolster the design of sophisticated genetic circuits in cyanobacterial/heterotroph consortia and the engineering of QS-like behaviors across cyanobacterial populations. HighlightsO_LIDesigned, built, and tested an inter-species quorum sensing-based communication system. C_LIO_LIThese genetic circuits can sense and respond to exogenous and secreted signals. C_LIO_LICircuit function in S. elongatus was comparable to E. coli, albeit with increased basal expression and lower induction ratios C_LIO_LIDemonstrated inter-species communication in direct co-cultivation C_LIO_LIFirst demonstration of inducible promoters and cross-species gene regulation in S. elongatus based on quorum sensing C_LI

synthetic biology↗

bioRxiv2020

Cyanobacterial growth and morphology are influenced by carboxysome positioning and temperature

Cyanobacteria are the prokaryotic group of phytoplankton responsible for a significant fraction of global CO2 fixation. Like plants, cyanobacteria use the enzyme Ribulose 1,5-bisphosphate Carboxylase/Oxidase (RuBisCO) to fix CO2 into organic carbon molecules via the Calvin-Benson-Bassham cycle. Unlike plants, cyanobacteria evolved a carbon concentrating organelle called the carboxysome - a proteinaceous compartment that encapsulates and concentrates RuBisCO along with its CO2 substrate. In the rod-shaped cyanobacterium Synechococcus elongatus PCC7942, we recently identified the McdAB system responsible for uniformly distributing carboxysomes along the cell length. It remains unknown what role carboxysome positioning plays with respect to cellular physiology. Here, we show for the first time that a failure to distribute carboxysomes leads to a temperature-dependent decrease in cell growth rate, cell division arrest, cell elongation, asymmetric cell division, and a significant reduction in cellular levels of RuBisCO. Unexpectedly, we also report that even wild-type S. elongatus undergoes filamentous growth at the cool, but environmentally-relevant, growth temperature of 20{degrees}C. The findings suggest that carboxysome positioning by the McdAB system functions to maintain the carbon-fixation efficiency of RuBisCO by preventing carboxysome aggregation, which is particularly important at temperatures where rod-shaped cyanobacteria adopt a filamentous morphology. IMPORTANCEPhotosynthetic cyanobacteria are responsible for almost half of global CO2 fixation. Due to eutrophication, rising temperatures, and increasing atmospheric CO2 concentrations, cyanobacteria have recently gained notoriety for their ability to form massive blooms in both freshwater and marine ecosystems across the globe. Like plants, cyanobacteria use the most abundant enzyme on Earth, RuBisCO, to provide the sole source of organic carbon required for its photosynthetic growth. Unlike plants, cyanobacteria have evolved a carbon-concentrating organelle called the carboxysome that encapsulates and concentrates RuBisCO with its CO2 substrate to significantly increase carbon-fixation efficiency and cell growth. We recently identified the positioning system that distributes carboxysomes in cyanobacteria. However, the physiological consequence of carboxysome mispositioning in the absence of this distribution system remains unknown. Here we find that carboxysome mispositioning triggers temperature-dependent changes in cell growth and morphology as well as a significant reduction in cellular levels of RuBisCO.

cell biology↗