Analysis of Bacterial Ribonucleoprotein Bodies

Our experts have a keen interest in the study of liquid-liquid and liquid-solid phase transitions in bacterial cells. We have cutting-edge super-resolution imaging or infinite diffraction microscopy apparently combined with single molecule trafficking methods, and computer analysis platforms to analyze key microbial biomolecular condensates undergoing LLPS, as well as the formation and organization of biomolecular condensates within the intracellular space. Here, CD BioSciences is committed to analyzing intrinsically disordered bacterial ribonucleoprotein bodies (BR-bodies).

BR-Bodies as Bacterial Biomolecular Condensates

Bacterial ribonucleoprotein bodies (BR-bodies) consist of C. crescentus ribonuclease E (Ccr-RNase E), RNA degradation components, and RNA. BR-bodies are biomolecular condensates in bacteria that have been shown to be directly assembled by liquid-liquid phase separation (LLPS), primarily through intrinsically disordered regions (IDRs) of RNase E scaffold proteins and RNA degradant client proteins phase-separated from RNA. BR-bodies serve as sites for sequestration, storage and regulation of intracellular RNA molecules in bacteria and are involved in a variety of cellular processes, including stress response, adaptation to changing environments and regulation of gene expression.

Fig. 1. Phase-separated BR-bodies organize mRNA decay. (Muthunayake NS, et al., 2020)

Customized Services

Like eukaryotic P-bodies and stress granules, BR-bodies provide a broadly conserved transbacterial gene regulatory mechanism that organizes the mRNA decay/processing machinery. CD BioSciences offers specialized services to analyze the structural dynamics and biochemical function in tissue mRNA decay of intrinsically disordered BR-bodies. Our services include:

• Characterization of RNase E LLPS of BR-Bodies
  RNase E has an intrinsically disordered C-terminal structural domain (CTD) that contains multiple RNA binding sites and protein partner interaction motifs. Our laboratory has the latest super-resolution microscopy and single-molecule trafficking methods to detect RNase E LLPS in vitro and in vivo.
• Identification of Bacteria with the Ability to Assemble BR-Bodies
  The phylogenetic range of BR-bodies in bacteria has not been fully determined. We provide bioinformatic sequence analysis of bacterial mRNA decay nucleases to predict the possibility of BR-bodies formation in bacteria, including analysis of bacterial mRNA decay nucleases such as RNase E, RNase Y, RNase J, and RNase G.
  We can detect the potential of BR-bodies in the following bacteria by genetic tools, including E. coli, C. crescentus, Rhizobium chinensis, Agrobacterium rhizogenes, Cyanobacteria, Bacillus subtilis, and H. pylori, etc. Our technical team will select representatives of each major bacterial evolutionary branch and plant chloroplast, and will provide disorder content and propensity scores based on pi stacking of phase separation.
• Determine the Functional Role of Different RNA Degradosomal Proteins on mRNA Decay
  RNA degradosomes have evolved to form a diverse set of proteins that are associated with major scaffolding nucleases. We have successfully analyzed the effect of the biochemical activities of major canonical RNase E partners on BR-bodies in the model Gram-negative bacterium Escherichia coli, such as the dead box decapping enzyme RhlB, the phosphoribonucleic acid exonuclease polynucleotide phosphorylase (PNPase) and the glycolytic enzyme enolase.

CD BioSciences offers a simple modular biomolecular platform to characterize the LLPS of intrinsically disordered BR-bodies. We aim to help our clients understand and manipulate the underlying organizing principles of BR-bodies condensates, ultimately allowing disease modeling and developing new therapeutic approaches. If you have any special requirements for our services, please feel free to contact us.