In vivo incorporation of the intrinsic photolabel 4-thiouridine into Escherichia coli RNAs.

The in vivo incorporation of the photoactivable uridine analogue 4-thiouridine into the RNAs of an Escherichia coli K12 pyrD strain has been optimised. s4Urd uptake in RNAs appears to be strikingly dependent upon the age of the preculture, i.e. the number of generations the cells have undergone immediately before dilution in the thiolation medium. Conditions have been set up where efficient RNA thiolation occurs in cells growing exponentially at 50 to 70% the rate of the control. The substitution level s4U/U is maximal after growth for 9 to 10 generations in the thiolation medium and reaches 17 +/- 3% in tRNA and bulk RNA. Most of ribosomal derived ribonucleoproteins, 65 +/- 5%, sediment as 70S ribosomes (s4U/U = 7 +/- 2%) on a high Mg2+ sucrose gradient. The thiolated RNAs were characterized by their migration on a thiol-specific affinity electrophoretic gel.     

Photochemistry of 4-thiouridine in Escherichia coli transfer RNA1Val

Irradiation of pure transfer RNA₁^Val with monochromatic light (334 nm) produces characteristic changes in the spectral properties of 4-thiouridine, the only base which strongly absorbs light at this wavelength. Variations in absorption and fluorescence of 4-thiouridine during irradiation are interpreted in terms of a specific, quantitative photoreaction which proceeds with a yield of about 5 × 10⁻³E/mole. The photoreaction occurs under conditions where tRNA₁^Val is biologically active but not under conditions that destroy the tertiary structure of the 4-thiouridine region.     

Oxidation of 4-thiouridine in intact Escherichia coli tRNAs.

Treatment of intact tRNAs from Escherichia coli B with mild oxidizing agents, such as KI-I₂, appears to quantitatively oxidize the 4-thiouridine present in these molecules to the disulfide form as judged by the loss of absorbance near 330 nm. Chromatography of these oxidized tRNAs on Sephadex G-75 did not reveal tRNA dimers or larger aggregates, suggesting intra- rather than intermolecular disulfide-bond formation. Enzymatic hydrolyses of both unlabeled and ³⁵S-labeled oxidized tRNAs followed by chromatography on columns of Sephadex G-25 indicated that 4-thiouridine did form covalent linkages with some component(s) in the tRNA that were reversible upon reduction. It was not clear whether 4-thiouridine formed disulfides only with itself, other sulfurcontaining nucleosides, or some non-sulfur-containing component. Data presented suggest that an earlier report on the isolation of 4-thiouridylate disulfide from oxidized tRNAs of E. coli was an artifact, resulting from oxidation of the thionucleotide during chromatography on Bio-Gel.     

Topography of the E site on the Escherichia coli ribosome.

Three photoreactive tRNA probes have been utilized in order to identify ribosomal components that are in contact with the aminoacyl acceptor end and the anticodon loop of tRNA bound to the E site of Escherichia coli ribosomes. Two of the probes were derivatives of E. coli tRNA(Phe) in which adenosines at positions 73 and 76 were replaced by 2-azidoadenosine. The third probe was derived from yeast tRNA(Phe) by substituting wyosine at position 37 with 2-azidoadenosine. Despite the modifications, all of the photoreactive tRNA species were able to bind to the E site of E. coli ribosomes programmed with poly(A) and, upon irradiation, formed covalent adducts with the ribosomal subunits. The tRNA(Phe) probes modified at or near the 3' terminus exclusively labeled protein L33 in the 50S subunit. The tRNA(Phe) derivative containing 2-azidoadenosine within the anticodon loop became cross-linked to protein S11 as well as to a segment of the 16S rRNA encompassing the 3'-terminal 30 nucleotides. We have located the two extremities of the E site-bound tRNA on the ribosomal subunits according to the positions of L33, S11 and the 3' end of 16S rRNA defined by immune electron microscopy. Our results demonstrate conclusively that the E site is topographically distinct from either the P site or the A site, and that it is located alongside the P site as expected for the tRNA exit site.     

Escherichia coli mutant lacking 4-thiouridine in its transfer ribonucleic acid.

A mutant of Escherichia coli has been isolated that lacks 4-thiouridine, a rare base in transfer ribonucleic acid. The mutant grows at the same rate as wild-type cells. It shows little near-ultraviolet-induced growth delay, thus supporting earlier hypotheses that 4-thiouridine in transfer ribonucleic acid is the chromophore for this growth delay.     

Quantitative analysis of ribosome binding sites in E.coli.

185 clones with randomized ribosome binding sites, from position -11 to 0 preceding the coding region of beta-galactosidase, were selected and sequenced. The translational yield of each clone was determined; they varied by more than 3000-fold. Multiple linear regression analysis was used to determine the contribution to translation initiation activity of each base at each position. Features known to be important for translation initiation, such as the initiation codon, the Shine/Dalgarno sequence, the identity of the base at position -3 and the occurrence of alternative ATGs, are all found to be important quantitatively for activity. No other features are found to be of general significance, although the effects of secondary structure can be seen as outliers. A comparison to a large number of natural E.coli translation initiation sites shows the information profile to be qualitatively similar although differing quantitatively. This is probably due to the selection for good translation initiation sites in the natural set compared to the low average activity of the randomized set.     

RNA-protein interactions in the Escherichia coli ribosome.

Over the last two decades essentially three different approaches have been used to study the topography of RNA-protein interactions in the ribosome. These are: (a) the analysis of binding sites for individual ribosomal proteins or groups of proteins on the RNA; (b) the determination of protein footprint sites on the RNA by the application of higher order structure analytical techniques; and (c) the localisation of RNA-protein cross-link sites on the RNA. This article compares and contrasts the types of data that the three different approaches provide, and gives a brief and highly simplified summary of the results that have been obtained for both the 16S and 23S ribosomal RNA from E coli.     

Promoter-like mutants with increased expression of the Escherichia coli uridine phosphorylase structural gene.

From an Escherichia coli K-12 strain lacking adenylate cyclase (cya) and cyclic AMP receptor protein (crp), two mutants were isolated that synthesize uridine phosphorylase constitutively. The mutations differ from one another and also from a wild type in the maximum rate of uridine phosphorylase synthesis. They have constitutive expression of the uridine phosphorylase gene (udp) in the presence of repressor protein coded by the cytR regulatory gene and decrease the sensitivity of the udp gene simultaneously with catabolite repression. Both mutations cause a high level of udp expression whether they are in a cya crp or in a cya+ crp+ background. Another mutation (udpP1) isolated previously alters the response of udp gene to the ctyR repressor and produces a higher constitutive level of uridine phosphorylase in a cytR+ than in a cytR background when bacteria are grown in glucose. The synthesis of uridine phosphorylase in this mutant is dependent on an intact cyclic AMP-cyclic AMP receptor protein complex. All mutations studied are cis-acting and extremely closely linked to the udp structural gene, and appear to affect the uridine phosphorylase promoter-operator region. The data obtained are in accordance with a suggestion that the cytR repressor protein normally asserts its function by preventing the positive action of cyclic AMP-cyclic AMP receptor protein complex.     

Recognition of the 70S ribosome and polysome by the RNA degradosome in Escherichia coli

The RNA degradosome is a multi-enzyme assembly that contributes to key processes of RNA metabolism, and it engages numerous partners in serving its varied functional roles. Small domains within the assembly recognize collectively a diverse range of macromolecules, including the core protein components, the cytoplasmic lipid membrane, mRNAs, non-coding regulatory RNAs and precursors of structured RNAs. We present evidence that the degradosome can form a stable complex with the 70S ribosome and polysomes, and we demonstrate the proximity in vivo of ribosomal proteins and the scaffold of the degradosome, RNase E. The principal interactions are mapped to two, independent, RNA-binding domains from RNase E. RhlB, the RNA helicase component of the degradosome, also contributes to ribosome binding, and this is favoured through an activating interaction with RNase E. The catalytic activity of RNase E for processing 9S RNA (the ribosomal 5S RNA precursor) is repressed in the presence of the ribosome, whereas there is little affect on the cleavage of single-stranded substrates mediated by non-coding RNA, suggestings that the enzyme retains capacity to cleave unstructured substrates when associated with the ribosome. We propose that polysomes may act as antennae that enhance the rates of capture of the limited number of degradosomes, so that they become recruited to sites of active translation to act on mRNAs as they become exposed or tagged for degradation.