ABSTRACT
Biomolecular condensates play a key role in organizing RNAs and proteins into membraneless organelles. Bacterial RNP-bodies (BR-bodies) are a biomolecular condensate containing the RNA degradosome mRNA decay machinery, but the biochemical function of such organization remains poorly defined. Here, we define the RNA substrates of BR-bodies through enrichment of the bodies followed by RNA sequencing (RNA-seq). We find that long, poorly translated mRNAs, small RNAs, and antisense RNAs are the main substrates, while rRNA, tRNA, and other conserved non-coding RNAs (ncRNAs) are excluded from these bodies. BR-bodies stimulate the mRNA decay rate of enriched mRNAs, helping to reshape the cellular mRNA pool. We also observe that BR-body formation promotes complete mRNA decay, avoiding the buildup of toxic endo-cleaved mRNA decay intermediates. The combined selective permeability of BR-bodies for both enzymes and substrates together with the stimulation of the sub-steps of mRNA decay provide an effective organization strategy for bacterial mRNA decay.
Subject(s)
Caulobacter crescentus/metabolism , Endoribonucleases/metabolism , Escherichia coli/metabolism , Multienzyme Complexes/metabolism , Organelles/metabolism , Polyribonucleotide Nucleotidyltransferase/metabolism , RNA Helicases/metabolism , RNA Stability , RNA, Messenger/metabolism , Caulobacter crescentus/genetics , Caulobacter crescentus/growth & development , Endoribonucleases/genetics , Escherichia coli/genetics , Escherichia coli/growth & development , Humans , Multienzyme Complexes/genetics , Organelles/genetics , Polyribonucleotide Nucleotidyltransferase/genetics , RNA Helicases/genetics , RNA, Antisense/genetics , RNA, Antisense/metabolism , RNA, Messenger/genetics , RNA, Ribosomal/genetics , RNA, Ribosomal/metabolism , RNA, Small Untranslated/genetics , RNA, Small Untranslated/metabolism , RNA, Transfer/genetics , RNA, Transfer/metabolism , RNA, Untranslated/genetics , RNA, Untranslated/metabolismABSTRACT
Ribonucleoprotein (RNP) granules play an important role in organizing eukaryotic mRNA metabolism via liquid-liquid phase separation (LLPS) of mRNA decay factors into membrane-less organelles in the cytoplasm. Here we show that the bacterium Caulobacter crescentus Ribonuclease (RNase) E assembles RNP LLPS condensates that we term bacterial RNP-bodies (BR-bodies), similar to eukaryotic P-bodies and stress granules. RNase E requires RNA to assemble a BR-body, and disassembly requires RNA cleavage, suggesting BR-bodies provide localized sites of RNA degradation. The unstructured C-terminal domain of RNase E is both necessary and sufficient to assemble the core of the BR-body, is functionally conserved in related α-proteobacteria, and influences mRNA degradation. BR-bodies are rapidly induced under cellular stresses and provide enhanced cell growth under stress. To our knowledge, Caulobacter RNase E is the first bacterial protein identified that forms LLPS condensates, providing an effective strategy for subcellular organization in cells lacking membrane-bound compartments.
Subject(s)
Caulobacter crescentus/metabolism , Cytoplasmic Granules/physiology , Ribonucleoproteins/metabolism , Alphaproteobacteria/metabolism , Caulobacter crescentus/genetics , Cytoplasmic Granules/metabolism , Endoribonucleases/metabolism , Liquid-Liquid Extraction , Multienzyme Complexes/metabolism , Polyribonucleotide Nucleotidyltransferase/metabolism , RNA Helicases/metabolism , RNA StabilityABSTRACT
Objective: To determine if dermoscopy, a technique widely utilized in dermatology for improved diagnosis of skin lesions, can be used comfortably for evaluating periorbital, eyelid, and conjunctival lesions. Design: Proof-of-concept study in which a technique for performing dermoscopy near the eye was developed, related educational material was prepared, and a protocol for dermoscopic image capture was created. Methods: Technicians used the developed materials to learn to take high-quality pictures with a 10x dermoscope attached to a standard cell phone camera. The images were assessed for diagnostic utility by an oculoplastic surgeon and two dermatologists. Participants: 115 patients recruited from ophthalmology clinics from July 2021 to April 2023 were photographed, yielding 129 lesions with high-quality dermoscopic images as assessed by an oculoplastic surgeon and two dermatologists. Results: Technicians reported a significant increase in confidence (measured on a 1-10 scale) with dermoscopy after training (pre-instruction mean = 1.72, median = 1, mode = 1, IQR = 1.25 vs mean = 7.69, median = 7.75, mode = 7 and 8, IQR = 1.5 post-instruction. Wilcoxon rank sum test with continuity correction, W = 0, p < 0.001, paired t = 13.95, p < 0.0001). Incorporating a contact plate with a 4 × 4mm reticule on the dermoscope aided in photographing ocular and periocular lesions. Conclusion: Medical support staff in eye-care offices can be taught to use dermoscopes to capture high-quality images of periorbital, eyelid, and conjunctival lesions. Dermoscopy illuminates diagnostic features of lesions and thus offers a new avenue to improve decision-making in ophthalmology. Dermoscopy can be incorporated into telemedicine evaluations by ophthalmologists, oculoplastic surgeons, or affiliated dermatologists for triage of or rendering advice to patients and for planning of surgery if needed.