Polyribosomes of Escherichia coli. II. Experiments to determine the in vivo distribution of polysomes, ribosomes and ribosomal subunits

Glycogen phase separation drives macromolecular rearrangement and asymmetric division in E. coli

Bacteria often experience nutrient limitation in nature and the laboratory. While exponential and stationary growth phases are well characterized in the model bacterium Escherichia coli, little is known about what transpires inside individual cells during the transition between these two phases. Through quantitative cell imaging, we found that the position of nucleoids and cell division sites becomes increasingly asymmetric during transition phase. These asymmetries were coupled with spatial reorganization of proteins, ribosomes, and RNAs to nucleoid-centric localizations. Results from live-cell imaging experiments, complemented with genetic and 13C whole-cell nuclear magnetic resonance spectroscopy studies, show that preferential accumulation of the storage polymer glycogen at the old cell pole leads to the observed rearrangements and asymmetric divisions. In vitro experiments suggest that these phenotypes are likely due to the propensity of glycogen to phase separate in crowded environments, as glycogen condensates exclude fluorescent proteins under physiological crowding conditions. Glycogen-associated differences in cell sizes between strains and future daughter cells suggest that glycogen phase separation allows cells to store large glucose reserves without counting them as cytoplasmic space.

Interconnecting solvent quality, transcription, and chromosome folding in Escherichia coli

All cells fold their genomes, including bacterial cells, where the chromosome is compacted into a domain-organized meshwork called the nucleoid. How compaction and domain organization arise is not fully understood. Here, we describe a method to estimate the average mesh size of the nucleoid in Escherichia coli. Using nucleoid mesh size and DNA concentration estimates, we find that the cytoplasm behaves as a poor solvent for the chromosome when the cell is considered as a simple semidilute polymer solution. Monte Carlo simulations suggest that a poor solvent leads to chromosome compaction and DNA density heterogeneity (i.e., domain formation) at physiological DNA concentration. Fluorescence microscopy reveals that the heterogeneous DNA density negatively correlates with ribosome density within the nucleoid, consistent with cryoelectron tomography data. Drug experiments, together with past observations, suggest the hypothesis that RNAs contribute to the poor solvent effects, connecting chromosome compaction and domain formation to transcription and intracellular organization.

Nucleoid Size Scaling and Intracellular Organization of Translation across Bacteria

The scaling of organelles with cell size is thought to be exclusive to eukaryotes. Here, we demonstrate that similar scaling relationships hold for the bacterial nucleoid. Despite the absence of a nuclear membrane, nucleoid size strongly correlates with cell size, independent of changes in DNA amount and across various nutrient conditions. This correlation is observed in diverse bacteria, revealing a near-constant ratio between nucleoid and cell size for a given species. As in eukaryotes, the nucleocytoplasmic ratio in bacteria varies greatly among species. This spectrum of nucleocytoplasmic ratios is independent of genome size, and instead it appears linked to the average population cell size. Bacteria with different nucleocytoplasmic ratios have a cytoplasm with different biophysical properties, impacting ribosome mobility and localization. Together, our findings identify new organizational principles and biophysical features of bacterial cells, implicating the nucleocytoplasmic ratio and cell size as determinants of the intracellular organization of translation.

In vivo biochemistry in bacterial cells using FRAP: insight into the translation cycle

In vivo measurements of the mobility and binding kinetics of cellular components are essential to fully understand the biochemical processes occurring inside cells. Here, we describe a fluorescence recovery after photobleaching-based method that can be easily implemented to the study of reaction-diffusion processes in live bacteria despite their small size. We apply this method to provide new, to our knowledge, quantitative insight into multiple aspects of the bacterial translation cycle by measuring the binding kinetics and the micrometer-scale diffusive properties of the 50S ribosomal subunit in live Caulobacter cells. From our measurements, we infer that 70% of 50S subunits are engaged in translation and display, on average, limited motion on the micrometer scale, consistent with little mixing of transcripts undergoing translation. We also extract the average rate constants for the binding of 50S subunits to 30S initiation complexes during initiation and for their release from mRNAs when translation is completed. From this, we estimate the average time of protein synthesis and the average search time of 50S subunits before they engage in the next initiation event. Additionally, our experiments suggest that so-called free 50S subunits do not diffuse freely; instead their mobility is significantly slowed down, possibly through transient associations with mRNA.

Cellular organization of the transfer of genetic information

Each step involved in the transfer of genetic information is spatially regulated in eukaryotic cells, as transcription, translation and mRNA degradation mostly occur in distinct functional compartments (e.g., nucleus, cytoplasm and P-bodies). At first glance in bacteria, these processes seem to take place in the same compartment - the cytoplasm - because of the conspicuous absence of membrane-enclosed organelles. However, it is becoming increasingly evident that mRNA-related processes are also spatially organized inside bacterial cells, and that this organization affects cellular function. The aims of this review are to summarize the current knowledge about this organization and to consider the mechanisms and forces shaping the cell interior. The field stands at an exciting point where new technologies are making long-standing questions amenable to experimentation.

Evidence for synthesis of alkaline phosphatase on membrane-bound polysomes in Escherichia coli

Polysomes containing nascent chains of alkaline phosphatase have been isolated from a membrane-bound polysome preparation. Indirect immunoprecipitation using conformation-specific antibodies has been employed. This technique provides a good enrichment of these polyribosomes since routinely no more than than 10--15% of non-specific immunoprecipitation was observed. The yield of the procedure is generally 40% but can be increased if higher non-specific immunoprecipitation is tolerated. Antibodies, previously described, directed against uncoiled or folded monomers of alkaline phosphatase can be used as primary antibody to recognize the nascent chains contained in membrane-bound polysomes which suggests that these chains are partially folded.

Ribosome run through of the termination codon in the absence of the ribosome releasing factor

The ribosome releasing factor (RR factor) which releases ribosomes from mRNA at the termination codon has been examined for its effects on the amino acid incorporation programmed by wild type R17 Phage RNA and amB2 R17 RNA. When RR factor was added at the beginning of the incorporation, there was no effect on the initial rate of incorporation but it reduced the final level of incorporation. The reduction of the final level of incorporation was more pronounced for histidine incorporation than for valine incorporation suggesting that the translation of the RNA polymerase cistron was more influenced by RR factor. These experiments were carried out under conditions where no reinitiation of protein synthesis occurred. In the presence of RR factor, suppressor tRNA functioned better for the incorporation of amino acids into proteins with amB2 R17 RNA than did wild type tRNA. No such differential effect of suppressor tRNA was observed in the absence of RR factor. This suggests that the ribosome has to be released from mRNA by RR factor in order for the amber mutation to be effective.

Characterization of RNA from noninfectious virions produced by sarcoma positive-leukemia negative transformed 3T3 cells

RNA from noninfectious virions produced by two established clonal lines of sarcoma positive-leukemia negative (S+L-)-transformed 3T3 cells has been characterized. RNA from virions or nucleoids of S+L--(C243) cells consisted of three to four sizes: +/-44 S (6%), 28 S (17%), 18 S (38%), and <18 S (39%). 28S virion RNA contained some virus-specific information demonstrable by RNA.DNA hybridization with a DNA probe derived from the RNA-directed DNA polymerase product of murine sarcoma-leukemia virus, while parallel studies indicated that 28S ribosomal RNA from ribosomal subunits of transformed and nontransformed 3T3 cells did not contain virus-specific information. In contrast to the S+L-(C243) virions, RNA from virions or nucleoids of S+L-(D56) cells consisted of five sizes: 80 S (6%), 68 S (8%), 56 S (5%), 28 S (28%), and <28 S (53%). Thermal dissociation studies suggested that this S+L- genome is comprised of 28S RNA subunits. From these studies we postulate that the 28S viral RNA is most probably the monomeric genome of S+L- virions.

Ribosome crystallization in chicken embryos. II. Conditions for the formation of ribosome tetramers in vitro

Slow cooling of fertilized chicken eggs permits the elongation and termination of nascen(t) polypeptides in the polysomes but prevents the initiation of new protein chains. This leads to polysome disaggregation during the first 30 min of cooling, and to the formation, of a pool of inactive ribosomes prone to crystallization. After 2 hr these ribosomes began to form tetramers, which do not contain any labeled proteins synthesized during cooling. If protein synthesis is inhibited by cycloheximide, added to eggs before cooling, tetramer formation in the embryos is prevented. Puromycin, on the other hand, leads to polysome disassembly and does not prevent tetramer formation. Rapid cooling of explanted embryos after short incubation at 37 degrees C, with or without cycloheximide, largely prevents polysome disaggregation and the formation of tetramers. On the other hand, the addition of puromycin to explanted embryos promotes tetramer formation after rapid cooling. When cooled eggs are rewarmed, tetramers are disassembled into monomers, even if protein synthesis is inhibited. When those embryos were rapidly recooled tetramers reformed spontaneously from tetramer-derived monomers, even in the presence of cycloheximide. We conclude that the formation of tetramers at low temperature is an inherent property of the normal ribosomes.