Obed W. Odom

Relaxation time, interthiol distance, and mechanism of action of ribosomal protein S1

The two sulfhydryl groups of ribosomal protein S1 from Escherichia coli have been labeled with fluorescent maleimides and the distance between them has been determined by nonradiative energy transfer. This distance was found to be approximately 27 A for both free S1 and S1 bound to 30 S subunits. This value probably represents an upper limit. The position of the fluorescence emission maximum indicates that both sulfhydryl groups are in a relatively hydrophobic environment. When poly(U) is added to labeled S1, either free or in 30 S subunits, the emission maximum shifts to the red by about 3 nm but without a detectable change in the interthiol distance. S1 labeled at one or both of its sulfhydryl groups retains most of its ability to enhance poly(U)-directed polyphenylalanine synthesis. About the same concentration of poly(U) is required to give the maximum shift in fluorescence as is required to give maximum polyphenylalanine synthesis, indicating that S1 binds poly(U) during translation. The peptide initiation inhibitor aurintricarboxylic acid almost completely quenches the fluorescence from either labeled sulfhydryl groups in S1 bound to ribosomes or free in solution. This quenching probably is due to energy transfer from the labeled sulfhydryls to bound aurintricarboxylic acid. Fluorescence anisotropy measurements indicated that the C-terminal domain of S1 is relatively rigid, but retains some independent movement when attached to ribosomes. The overall data are consistent with a model in which a region near the two sulfhydryl groups in the elongated C-terminal domain functions to sequester and bind mRNA to the ribosome during peptide synthesis.

Interaction of rabbit reticulocyte elongation factor 1 with guanosine-triphosphate and aminoacyl-transfer ribonucleic acid

Abstract Elongation Factor 1 (EF-1) from rabbit reticulocytes interacts with GTP to form a complex that is retained on a nitrocellulose filter. EF-1 also interacts with GDP; however, the concentration of GDP required for maximal complex formation is higher than the concentration of GTP required and the extent of binding is lower. Interaction of EF-1 with GTP in the presence of various aminoacyl-tRNAs from rabbit liver or E. coli results in a 50–75% decrease in the amount of GTP complex retained on a filter. No reduction in the amount of GTP complex retained is observed with deacylated tRNA or with N -acetylphenylalanyl-tRNA. EF-1 is inactivated by heating at 37 °C in the presence of GTP. Aminoacyl-tRNA protects EF-1 from the inactivation observed in the presence of GTP. These data indicate that an interaction of reticulocyte EF-1 with GTP and aminoacyl-tRNA occurs; however, attempts to demonstrate the formation of a stable ternary complex by chromatography on Sephadex G-150 were unsuccessful. Also, no difference is observed between the rate of binding of aminoacyl-tRNA to reticulocyte ribosomes obtained with EF-1 and the rate obtained with EF-1 that had been incubated previously with GTP and aminoacyltRNA.

Mobile Self-Splicing Group I Introns from the psbA Gene of Chlamydomonas reinhardtii: Highly Efficient Homing of an Exogenous Intron Containing Its Own Promoter

ABSTRACT Introns 2 and 4 of the psbA gene of Chlamydomonas reinhardtii chloroplasts (Cr.psbA2 andCr.psbA4, respectively) contain large free-standing open reading frames (ORFs). We used transformation of an intronless-psbA strain (IL) to test whether these introns undergo homing. Each intron, plus short exon sequences, was cloned into a chloroplast expression vector in both orientations and then cotransformed into IL along with a spectinomycin resistance marker (16Srrn). For Cr.psbA2, the sense construct gave nearly 100% cointegration of the intron whereas the antisense construct gave 0%, consistent with homing. For Cr.psbA4, however, both orientations produced highly efficient cointegration of the intron. Efficient cointegration of Cr.psbA4 also occurred when the intron was introduced as a restriction fragment lacking any known promoter. Deletion of most of the ORF, however, abolished cointegration of the intron, consistent with homing. TheCr.psbA4 constructs also contained a 3-(3,4-dichlorophenyl)-1,1-dimethylurea resistance marker in exon 5, which was always present when the intron integrated, thus demonstrating exon coconversion. Remarkably, primary selection for this marker gave >100-fold more transformants (>10,000/μg of DNA) than did the spectinomycin resistance marker. A trans homing assay was developed for Cr.psbA4; the ORF-minus intron integrated when the ORF was cotransformed on a separate plasmid. This assay was used to identify an intronic region between bp −88 and −194 (relative to the ORF) that stimulated homing and contained a possible bacterial (−10, −35)-type promoter. Primer extension analysis detected a transcript that could originate from this promoter. Thus, this mobile, self-splicing intron also contains its own promoter for ORF expression. The implications of these results for horizontal intron transfer and organelle transformation are discussed.

BINDING OF AN N-TERMINAL RHODANESE PEPTIDE TO DNAJ AND TO RIBOSOMES

A peptide corresponding to the N-terminal 17 amino acids of bovine rhodanese was fluorescently labeled with a coumarin derivative at its primary amino group(s) and then purified by high performance liquid chromatography. This peptide interacted with the molecular chaperone DnaJ in the absence of other chaperones and ATP. In the presence of ATP, the molecular chaperone DnaK bound to the DnaJ-peptide complex, but not to the peptide alone. The chaperone GrpE appeared to cause the release of the peptide bound to the ternary complex in the presence of ATP but not in the presence of ADP. This nucleotide apparently stabilized the complex. The peptide also bound to salt-washed Escherichia coli 70 S ribosomes, specifically to 50 S ribosomal subunits, not to 30 S subunits. DnaJ plus DnaK interacted with the peptide on the ribosome. GrpE caused dissociation of the peptide from the ribosome; ATP was required for this reaction. It was inhibited by ADP. A comparable series of chaperone-mediated reactions is assumed to occur with the N-terminal segment of the nascent polypeptide to facilitate its folding on ribosomes.

Ribosome function determined by fluorescence

Five different fluorescence phenomena are considered in relation to their use to study the structure and function of ribosomes. These are: quantum yield or emission intensity; emission wavelength maximum; fluorescence anisotropy; collisional quenching; and nonradiative energy transfer. Results from a number of studies in which these techniques were used are described and summarized in relation to the movement and conformation of tRNA, the nascent peptide, and mRNA in a ribosome during the reaction steps of peptide elongation.

An apparent conformational change in tRNAPhe that is associated with the peptidyl transferase reaction

Fluorescence techniques were used to detect changes in the conformation of tRNA(Phe) that may occur during the peptidyl transferase reaction in which the tRNA appears to move between binding sites on ribosomes. Such a conformational change may be a fundamental part of the translocation mechanism by which tRNA and mRNA are moved through ribosomes. E. coli tRNA(Phe) was specifically labeled on acp3U47 and s4U8 or at the D positions 16 and 20. The labeled tRNAs were bound to ribosomes as deacylated tRNA(Phe) or AcPhe-tRNA. Changes in fluorescence quantum yield and anisotropy were measured upon binding to the ribosomes and during the peptidyl transferase reaction. In one set of experiments non-radiative energy transfer was measured between a coumarin probe at position 16 or 20 and a fluorescein attached to acp3U47 on the same tRNA(Phe) molecule. The results indicate that the apparent distance between the probes increases during deacylation of AcPhe-tRNA as a result of peptide bond formation. All of the results are consistent with but in themselves do not conclusively establish that tRNA undergoes a conformational change as well as movement during the peptidyl transferase reaction.

[11] Fluorescence labeling and isolation of labeled RNA and ribosomal proteins

Publisher Summary The development of highly sensitive fluorometers to measure steady state intensity and lifetime of fluorescence coupled with computerized data analysis has vastly enhanced the utility of fluorescence techniques for investigation of systems of biological origin. Estimation of the distance between an energy donor fluorophore and an acceptor by non radiative energy transfer has proven to be particularly useful. Precautions must be taken throughout the labeling and isolation procedure to use reagents, solvents, and glassware that are as free as possible of contaminating fluorescent material and degradative enzymes. In this laboratory, distilled water is passed through a deionizing column and then a column of activated charcoal before it is redistilled in glass. High-performance liquid chromatography (HPLC) was carried out with a Beckman system which included a 421 controller unit for generating elution gradients and a 165 variable wavelength detector with which absorption was monitored at two wavelengths simultaneously.

The extension of polyphenylalanine and polylysine peptides on Escherichia coli ribosomes

Fluorescence techniques were used to examine aminoacyl-tRNA binding to Escherichia coli ribosomes and the subsequent extension of polyphenylalanine and polylysine nascent peptides. The results demonstrate that deacylated tRNA, an analogue of peptidyl-tRNA and puromycin (an analogue of aminoacyl-tRNA) can be bound simultaneously to the same ribosome. Moreover, the fluorescence properties of nascent polyphenylalanine and polylysine peptides with a fluorophore attached to their amino termini were determined and found to be quite different. This difference is reflected in the effects that erythromycin has in each case.

Efficient polyphenylalanine synthesis with proflavine and ethidium labeled tRNAPhe from yeast in the reticulocyte ribosomal system

Abstract Yeast tRNAPhe containing fluorescent dyes in place of the Y base is bound to the acceptor site of reticulocyte ribosomes and participates efficiently in polyphenylalanine synthesis. Apparently the particular chemical characteristics of the Y base are not required for the recognition process but the proper conformation of the anticodon loop has to be maintained.

Reverse Transcription of Spliced psbA mRNA in Chlamydomonas spp. and Its Possible Role in Evolutionary Intron Loss

Reverse transcription of mRNA is thought to be an important first step in a model that explains certain evolutionary changes within genes, such as the loss of introns or RNA editing sites. In this model, reverse transcription of mRNA produces cDNA molecules that replace part of the parental gene by homologous recombination. In vivo evidence of reverse transcription of physiologically relevant mRNAs is generally lacking, however, except in genetically engineered cells. Here, we provide in vivo evidence for reverse transcription of the chloroplast psbA mRNA in two naturally occurring species of Chlamydomonas (raudensis and subcaudata) that is based on the presence of spliced cDNAs in both organisms. The psbA cDNAs, which lack the group II intron of the genomic gene, are nearly full length, and the majority of them--though not all--are in the form of RNA-cDNA hybrids. Moreover, the presence in these species of psbA cDNAs is correlated with the loss of an early group I intron from the same psbA gene. The group II intron that interrupts psbA in C. raudensis and C. subcaudata potentially encodes a protein with a reverse transcriptase domain, and the C. raudensis protein was shown to have reverse transcriptase activity in vitro. These results provide strong evidence for reverse transcription of a physiologically important mRNA (psbA) in two species of Chlamydomonas that have also lost an intron from the same gene, possibly through recombination with the cDNA.