Cleavage by ribonuclease III of the complex of 30 S pre-ribosomal RNA and ribosomal proteins of Escherichia coli

Uncovering a delicate balance between endonuclease RNase III and ribosomal protein S15 in E. coli ribosome assembly

The bacterial ribosomal protein S15 is located in the platform, a functional region of the 30S ribosomal subunit. While S15 is critical for in vitro formation of E. coli small subunits (SSUs), it is dispensable for in vivo biogenesis and growth. In this work, a novel synergistic interaction between rpsO, the gene that encodes S15, and rnc (the gene that encodes RNase III), was uncovered in E. coli. RNase III catalyzes processing of precursor ribosomal RNA (rRNA) transcripts and thus is involved in functional ribosome subunit maturation. Strains lacking S15 (ΔrpsO), RNase III (Δrnc) or both genes were examined to understand the relationship between these two factors and the impact of this double deletion on rRNA processing and SSU maturation. The double deletion of rpsO and rnc partially alleviates the observed cold sensitivity of ΔrpsO alone. A novel 16S rRNA precursor (17S∗ rRNA) that is detected in free 30S subunits of Δrnc is incorporated in 70S-like ribosomes in the double deletion. The stable accumulation of 17S∗ rRNA suggests that timing of processing events is closely coupled with SSU formation events in vivo. The double deletion has a suppressive effect on the cell elongation phenotype of ΔrpsO. The alteration of the phenotypes associated with S15 loss, due to the absence of RNase III, indicates that pre-rRNA processing and improvement of growth, relative to that observed for ΔrpsO, are connected. The characterization of the functional link between the two factors illustrates that there are redundancies and compensatory pathways for SSU maturation.

Differential decay of a polycistronic Escherichia coli transcript is initiated by RNaseE-dependent endonucleolytic processing

Differential expression of the genes expressing Pap pili in Escherichia coli was suggested to involve mRNAs with different stabilities. As the result of a post-transcriptional processing event, a papA gene-specific mRNA product (mRNA-A) accumulates in large excess relative to the primary mRNA-BA transcript. Our results show that the processed product, mRNA-A, is a translationally active molecule and that it is generated from the mRNA-BA precursor by an RNaseE-dependent mechanism. The processing did not occur under non-permissive conditions in an E. coli rne mutant strain with a temperature-sensitive RNaseE. The endonuclease RNaseE was previously described as being chiefly involved in the processing of the 9S precursor of 5S rRNA. A comparison of nucleotide sequences of mRNA-BA and three other RNAs processed by RNAseE revealed a conserved motif around the cleavage sites. Mutations abolishing the activity of either of two other endoribonucleases, RNaseIII and RNaseP, did not affect the pap mRNA processing event. However, a conditional mutation in the ams locus, causing altered stability of bulk mRNA in E. coli, led to reduced pap mRNA processing in a manner similar to the effect caused by RNaseE deficiency. Our findings are consistent with the idea that ams is related/allelic to rne. Absence of the processing event in the RNaseE mutant (rne-3071) strain led to a four-fold stabilization of the mRNA-BA primary transcript. We conclude that the RNaseE-dependent processing event is the rate-limiting step in the decay of the papB-coding part of the primary transcript and in the production of the stable mRNA-A product.(ABSTRACT TRUNCATED AT 250 WORDS)

Transcription of Escherichia coli ribosomal DNA in Proteus mirabilis

Transcription of Escherichia coli ribosomal DNA introduced into Proteus mirabilis on F14 is described. We have developed an assay for E. coli coded ribosomal RNA involving fingerprinting of ribonuclease T1 digests of RNA isolated from ribosomal subunits. Sequence differences in the ribosomal RNA of the two species have allowed us to detect E. coli coded 16S, 23S, and 5S ribosomal RNA in ribosomal subunits of the E. coli-P. mirabilis hybrid. The proportion of E. coli coded rRNA in the hybrid is found at a level which is compatible with the number of E. coli (and P. mirabilis) ribosomal DNA sequences. The resulting ribosomal RNA appears in ribosomes in a form which indicates extensive compatibility of E. coli coded ribosomal RNA with P. mirabilis ribosomal proteins and maturational factors.

Stability of "spacer" sequences of pre-ribosomal RNA in Escherichia coli

"SPACER" SEQUENCES OF AN RRNA gene transcript were detected with high efficiency by hybridization with DNA of the specilized transducing phase phi80rrn. Hybridization-competition studies revealed that 20 to 23% of the 30S precursor rRNA, obtained from E. coli mutant strain AB301/105, consist of "spacer" sequences. The "spacer" sequences formed hybrids with E. coli DNA, but not with Vibrio DNA. Experiments with RNA labeling in the presence of rifampicin showed that more than 80% of the spacer sequences arrive in full-length 30S pre rRNA chains before any cleavage of the RNA occurs. The hybridization assays also permitted the detection of "spacer" sequences in pulse-labeled rRNA of wild-type cells, in which the 30S pre-rRNA is already cleaved during its synthesis. Many of these "spacer" sequences degraded to alcohol-soluble materials with a half-life time of 1.2 min. The half-life was not lengthened by the treatment of cells with chloramphenicol, which stabilizes bulk mRNA. However, unstable "spacer" sequences transcribed in cells deficient in RNase III exhibited slower degradation, with a half-life time of about 9 min, whereas the cleavage of 30S pre-rRNA to smaller RNA species occurred with a half-life of about 3 min. These results are consistent with the notion that a rate-limiting action of RNase III in the initial attack leads to degradation of "spacer" sequences in rRNA gene transcript; and that degradation is not at all connected with ribosome translocation.