Spatial organization and dynamics of RNase E and ribosomes in Caulobacter crescentus

• Published in: Proceedings of the National Academy of Sciences - PNAS 2018-04, Vol.115 (16), p.E3712-E3721
• Main Authors: Bayas, Camille A., Wang, Jiarui, Lee, Marissa K., Schrader, Jared M., Shapiro, Lucy, Moerner, W. E.
• Format: Article
• Language: English
• Subjects: Bacterial Proteins - analysis; Bacterial Proteins - metabolism; Biological Sciences; Biosynthesis; Caulobacter crescentus; Caulobacter crescentus - enzymology; Caulobacter crescentus - metabolism; Caulobacter crescentus - ultrastructure; Cell Cycle; Cell Polarity; Chromosomes, Bacterial - genetics; Chromosomes, Bacterial - ultrastructure; Clustering; Confinement; Cytoplasm; Degradation; E coli; Endoribonucleases - analysis; Endoribonucleases - metabolism; Gene expression; Gene Expression Regulation, Bacterial; Luminescent Proteins - analysis; Membranes; MicroRNAs; Microscopy; Microscopy, Fluorescence - methods; Multienzyme Complexes - metabolism; Particle tracking; PNAS Plus; Polyribonucleotide Nucleotidyltransferase - metabolism; Position (location); Protein synthesis; Proteins; Ribonuclease E; Ribonucleic acid; Ribosomal protein L1; Ribosomes; Ribosomes - metabolism; RNA; RNA Helicases - metabolism; RNA processing; RNA, Bacterial - biosynthesis; RNA, Bacterial - genetics; RNA, Ribosomal - biosynthesis; RNA, Ribosomal - genetics; rRNA; Single Molecule Imaging - methods; Subcellular Fractions - enzymology; Substrates; Templates, Genetic; Transcription; Transcription, Genetic
• ISSN: 0027-8424; 1091-6490
• DOI: 10.1073/pnas.1721648115

We report the dynamic spatial organization of Caulobacter crescentus RNase E (RNA degradosome) and ribosomal protein L1 (ribosome) using 3D single-particle tracking and superresolution microscopy. RNase E formed clusters along the central axis of the cell, while weak clusters of ribosomal protein L1 were deployed throughout the cytoplasm. These results contrast with RNase E and ribosome distribution in Escherichia coli, where RNase E colocalizes with the cytoplasmic membrane and ribosomes accumulate in polar nucleoid-free zones. For both RNase E and ribosomes in Caulobacter, we observed a decrease in confinement and clustering upon transcription inhibition and subsequent depletion of nascent RNA, suggesting that RNA substrate availability for processing, degradation, and translation facilitates confinement and clustering. Importantly, RNase E cluster positions correlated with the subcellular location of chromosomal loci of two highly transcribed rRNA genes, suggesting that RNase E’s function in rRNA processing occurs at the site of rRNA synthesis. Thus, components of the RNA degradosome and ribosome assembly are spatiotemporally organized in Caulobacter, with chromosomal readout serving as the template for this organization.