In vitro synthesis of the first dipeptide of the beta subunit of Escherichia coli RNA polymerase

Mapping of sequences required for the translation of the beta subunit of Escherichia coli RNA polymerase

Previous experiments using expression plasmids which overproduce the beta and beta' subunits of Escherichia coli RNA polymerase suggested that regions considerably upstream of the start of the rpoB gene, which encodes the beta subunit, are required for its efficient synthesis. To further delineate the required regions, a collection of genetic constructs that contained varying amounts of the region either upstream or downstream of the translational start of rpoB was assembled. Measurements of beta and beta' synthesis and rpoB mRNA production from a series of rpoBC expression plasmids indicated that sequences extending more than 43 bp but less than 79 bp upstream of rpoB are required for the efficient translation of rpoB mRNA. This result was confirmed by beta-galactosidase measurements from a series of rpoB-lacZ fusions that have the same set of end points upstream of rpoB as the expression plasmids. A second set of gene fusions containing differing amounts of the sequence distal to the start of rpoB fused in frame to lacZ revealed that more than 29 bp but less than 70 bp of rpoB was required for efficient translation.

Post-transcriptional regulation of RNA polymerase II levels in Caenorhabditis elegans

To investigate the regulation of RNA polymerase II levels in Caenorhabditis elegans, we have constructed nematode strains having one, two, or three copies of ama-1, the gene for the largest subunit of RNA polymerase II. Steady-state levels of RNA polymerase II polypeptides and solubilized enzyme activity are invariant with gene dosage, indicating regulatory compensation. However, steady-state levels of ama-1 mRNA are directly proportional to gene dosage. These results imply that RNA polymerase II levels in C. elegans are regulated post-transcriptionally.

Alterations in the hydrophilic segment of the maltose-binding protein (MBP) signal peptide that affect either export or translation of MBP

Mutations that reduce the net positive charge within the hydrophilic segments of the signal peptides of several prokaryotic exported proteins can result in a reduction in the rate of protein export, as well as a reduction in protein synthesis (M. N. Hall, J. Gabay, and M. Shwartz, EMBO J. 2:15-19, 1983; S. Inouye, X. Soberon, T. Franceschini, K. Nakamura, K. Itakura, and M. Inouye, Proc. Natl. Acad. Sci. USA 79:3438-3441, 1982; J. W. Puziss, J. D. Fikes, and P. J. Bassford, Jr., J. Bacteriol. 171:2302-2311, 1989). This result has been interpreted as evidence that the hydrophilic segment is part of a mechanism that obligatorily couples translation to protein export. We have investigated the role of the hydrophilic segment of the Escherichia coli maltose-binding protein (MBP) signal peptide in the export and synthesis of MBP. Deletion of the entire hydrophilic segment from the MBP signal peptide resulted in a defect in MBP export, as well as a dramatic reduction in total MBP synthesis. Suppressor mutations that lie upstream of the malE coding region were isolated. These mutations do not affect MBP export but instead were shown to partially restore MBP synthesis by increasing the efficiency of MBP translational initiation. In addition, analysis of a series of substitution mutations in the second codon of certain malE alleles demonstrated that MBP export and synthesis can be independently affected by mutations in the hydrophilic segment. Finally, analysis of alterations in the hydrophilic segment of the ribose-binding protein signal peptide fused to the mature moiety of the MBP has revealed that the role of the hydrophilic segment in the export process can be functionally separated from any role in translation. Taken together, these results strongly suggest that the hydrophilic segment of the MBP signal peptide is not involved in a mechanism that couples MBP translation to export and argue against the presence of a mechanism that obligatorily couples translation to protein export in Escherichia coli.

Transcription frequency modulates the efficiency of an attenuator preceding the rpoBC RNA polymerase genes of Escherichia coli: possible autogenous control

Expression of the rpoBC genes encoding the beta and beta' RNA polymerase subunits of Escherichia coli is autogenously regulated. Although previous studies have demonstrated a post-transcriptional feedback mechanism, complex transcriptional controls of rpoBC expression may also contribute. We show that an attenuator (rpoBa) separating the ribosomal protein (rpl) genes from the rpoBC genes in the rplKAJLrpoBC gene cluster is modulated in its efficiency in response to changes in the frequency of transcription initiated by promoters located upstream. A series of rplJLrpoBalacZ transcriptional fusions was constructed on lambda vectors in which transcription into the rpoBa attenuator was varied by using a variety of promoters with different strengths. beta-galactosidase assays performed on monolysogens of the recombinant phage show that with transcription increasing over a 40-fold range, readthrough of rpoBa decreases from 61% to 19%. In contrast, two other well-characterized terminators show nearly constant efficiencies over a similar range of transcription frequencies. Using a set of phage P22 ant promoter variants with single-nucleotide changes in the promoter consensus sequences also demonstrates that the modulation of rpoBa function appears to be unrelated to the phenomenon of 'factor-independent antitermination' reported by others. The implications for autogenous control of RNA polymerase synthesis are discussed.

Autogenous regulation of the RNA polymerase beta subunit of Escherichia coli occurs at the translational level in vivo

A series of transcriptional and translational fusions of the gene for the beta subunit of RNA polymerase (rpoB) to the lacZ reporter gene have been constructed on lambda vectors. Both transcriptional and translational fusions carry the upstream rplKAJL ribosomal protein gene region, which contains the two strong promoters rplKp and rplJp responsible for the transcription of rpoBC. Monolysogens carrying either the transcriptional translational fusion were assayed for beta-galactosidase, providing a measure of the transcription or of both transcription and translation of rpoB, respectively. Translational fusion monolysogens which also carried a multicopy plasmid containing the beta and beta' genes (rpoBC) under the control of a regulatable promoter, exhibited a substantial decrease in the beta-galactosidase levels upon overproduction of beta and beta'. No significant effect was seen in comparable experiments with the transcriptional fusions. These results argue that in vivo, the synthesis of the RNA polymerase beta subunit is autogenously regulated by a translational mechanism. Furthermore, experiments with the overexpressing plasmids confirm the requirement for a portion of the rplL-rpoB intercistronic region in the vicinity of the RNaseIII processing site for the efficient translation of the beta subunit mRNA.

The protein synthesis initiation factor 2 G-domain. Study of a functionally active C-terminal 65-kilodalton fragment of IF2 from Escherichia coli

Protein synthesis initiation factor 2 (IF2) is present in Escherichia coli cells as two forms which are expressed from the same gene: IF2 alpha [97.3 kilodaltons (kDa)] and IF2 beta (79.7 kDa). During isolation, a smaller form, IF2 gamma, is generated, presumably by partial proteolysis. It has been purified to homogeneity and has an apparent mass of 70 kDa, as determined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Immunoelectrophoresis of IF2 alpha and IF2 gamma shows that IF2 gamma is immunologically partially identical with IF2 alpha. The sequence of the 15 N-terminal amino acid residues of IF2 gamma was determined and compared with that of IF2 alpha. The N-terminal amino acid of IF2 gamma corresponds to Arg-290 of IF2 alpha, suggesting that IF2 gamma is generated by proteolytic cleavage of the Lys-289-Arg-290 bond of IF2. Assuming a C terminus identical with IF2 alpha, we calculate that IF2 gamma comprises 601 amino acid residues and has a mass of 64.8 kDa. The truncated protein was tested for activities characteristic of IF2 in three in vitro assays: fMet-tRNA(fMet) binding to 70S ribosomes, N-terminal dipeptide synthesis in a DNA-dependent transcription/translation system, and ribosome-dependent GTP hydroly97-7. The specific activities of IF2 gamma were comparable with, or only slightly less than, those for IF2 alpha, indicating that IF2 gamma contains the active centers for interaction with fMet-tRNA(fMet), ribosomes, and GTP. A central region in the primary structure of IF2 shows extensive sequence homology with a number of GDP-binding proteins and especially with the G-domain of elongation factor Tu (EF-Tu).(ABSTRACT TRUNCATED AT 250 WORDS)

Feedback regulation of RNA polymerase subunit synthesis after the conditional overproduction of RNA polymerase in Escherichia coli

The beta and beta' subunits of RNA polymerase are thought to be controlled by a translational feedback mechanism regulated by the concentration of RNA polymerase holoenzyme. To study this regulation in vivo, an inducible RNA polymerase overproduction system was developed. This system utilizes plasmids from two incompatibility groups that carry RNA polymerase subunit genes under lac promoter/operator control. When the structural genes encoding the components of core RNA polymerase (alpha, beta and beta') or holoenzyme (alpha, beta, beta' and sigma 70) are present on the plasmids, induction of the lac promoter results in a two fold increase in the concentration of functional RNA polymerase. The induction of RNA polymerase overproduction is characterized by an initial large burst of beta beta' synthesis followed by a gradual decrease as the concentration of RNA polymerase increases. Overproduction of RNA polymerase in a strain carrying an electrophoretic mobility mutation in the rpoB gene results in the specific repression of beta beta' synthesis off the chromosome. These results indicate that RNA polymerase feedback regulation controls beta beta' synthesis in vivo.

Growth rate-dependent regulation of RNA polymerase synthesis in Escherichia coli

The rate of synthesis of the beta and beta' subunits of RNA polymerase relative to the rate of synthesis of total protein was found to remain constant with increasing steady state growth rate. This is in contrast to the relative synthesis rates of ribosomal proteins which are known to increase with growth rate. Yet the ratio of the rate of transcription of the ribosomal protein (rplJL) and RNA polymerase (rpoBC) domains of the rplKAJLrpoBC gene cluster was found to be invariant. Fusions to lacZ were used to relate the rate of transcription of the rplKAJL genes to the rate of synthesis of total protein. No change was seen at growth rates above 0.8 doublings per hour. This indicates that the growth rate-dependent expression of these ribosomal proteins is regulated at the post-transcriptional level. However because both the relative rate of transcription of rpoBC and rate of synthesis of beta and beta' were found to remain invariant over this growth range it suggests the expression of these RNA polymerase subunits is regulated at the transcriptional level.

An in vitro system to measure gene expression based on dipeptide synthesis

A simplified E. coli in vitro system has been developed to study gene expression based on the synthesis of the first di- or tripeptide of the gene product. Plasmids containing bacterial and chloroplast genes have been used as templates in this system. The expression of the E. coli L10 operon, which is under both transcriptional and translational control, has been investigated in some detail using the dipeptide system. A similar system has been developed, using eukaryotic translation components, to measure the expression of eukaryotic mRNA based on dipeptide formation.

Sequence of the initiation factor IF2 gene: unusual protein features and homologies with elongation factors

The gene for protein synthesis initiation factor IF2 in Escherichia coli, infB, is located downstream from nusA on the same operon. We sequenced about 3 kilobases of DNA beginning within nusA and including the entire infB structural gene plus another 392 bases downstream. This region contains no obvious strong promoter signals, but a possible transcriptional termination or pausing site occurs downstream from infB. The putative initiator codon for IF2 alpha (97,300 daltons) is AUG; that for IF2 beta (79,700 daltons) is GUG, located 471 bases downstream in the same reading frame. The codon usage for IF2 is typical of other highly expressed proteins in E. coli and suggests that IF2 mRNA is efficiently translated. IF2 alpha contains two adjacent regions (residues 104-155 and 167-214) that are rich in alanine and charged amino acids and that show striking periodicities in their sequences. These regions may alternate between flexible and helical conformations, thereby drawing together the NH2-terminal and COOH-terminal globular domains of the factor as IF2 interacts with ribosomes or tRNA. Certain regions of the DNA and protein sequences of IF2 share strong homologies with elongation factor EF-Tu and lesser homology with EF-G. In particular, a region of EF-Tu implicated in GTP binding contains sequences and secondary structure that are conserved in IF2. The homologies indicate that the genes for IF2 and the elongation factors are derived at least in part from a common ancestor.

Determination of the translation start site of the large subunit of ribulose-1,5-bisphosphate carboxylase from maize

Sequence studies of the gene for the large subunit of ribulose-1,5-bisphosphate carboxylase from maize indicate the presence of two translation start sites, 18 bp apart. Each site is preceded by a suitable ribosome binding region. By using a simplified E. coli-based in vitro system which measures fromation of the first dipeptide of the gene product, we have determined that only the second methionine initiates translation.

In vitro expression and characterization of the translation start site of the psbA gene product (QB protein) from higher plants

The psbA gene from higher plants, which codes for the atrazine herbicide binding protein of photosystem II (QB protein), has been recently sequenced by various laboratories. From these data there are two potential translation sites, one yielding a protein of 38,500 kd and another a protein of 34,500 kd. In the present study, cloned psbA gene sequences from maize, tobacco, and pea have been expressed in a highly defined E. coli in vitro transcription/translation system. In order to determine the start site of translation, we also have employed a simplified E. coli system designed to synthesize the first di- or tripeptide of the gene product. From these results, it is clear that the first ATG of the longest open reading frame of the psbA gene, that begins fMet-Thr, is not recognized in vitro. Instead, the next downstream Met at position 37 is the initiation site, since the expected dipeptide fMet-Ile is synthesized from all psbA clones. These data are in accord with the in vivo results that the gene product is a precursor protein of 34,500 kd.

Two initiation sites detected in the small s1 species of reovirus mRNA by dipeptide synthesis in vitro

Reovirus mRNAs directed the synthesis of fMet dipeptides in a translation initiation system reconstituted from rabbit reticulocyte initiation and elongation factors, Artemia salina 80S ribosomes, yeast fMet-tRNAiMet and Escherichia coli3H-labeled aminoacyl tRNAs. As predicted from the GC(U,G) codon that follows the 5'-proximal AUG in half of the viral mRNA species, fMet-Ala was the predominant dipeptide product obtained in response to a mixture of mRNAs or to the separated size classes of medium (m) and small (s) mRNA. The four individual small mRNA species each directed the synthesis of an fMet dipeptide that was consistent with the utilization of the 5'-proximal AUG for initiation. In addition to fMet-Asp, the s1 mRNA also directed fMet-Glu synthesis indicative of initiation in a second reading frame at the 5'-penultimate AUG. The tripeptide fMet-Glu-Tyr was also synthesized from s1 mRNA, which further verified this second initiation site. mRNAs containing 5'-terminal GpppG were 10-15% as active as the corresponding m7G-capped templates. The dipeptide assay provides a rapid method for determining initiation sites in individual mRNAs or in mixtures of mRNAs.

Simplified in vitro system for study of eukaryotic mRNA translation by measuring di- and tripeptide formation

An in vitro system for measurement of rabbit globin mRNA translation has been developed based on the formation of the NH2-terminal dipeptide, fMet-Val. The basic components include a partially purified initiation factor preparation from rabbit reticulocytes supplemented with eukaryotic initiation factor 4A, purified and formylated yeast Met-tRNAi, and rabbit liver or Escherichia coli Val-tRNA1Val. Picomole quantities of fMet-Val are synthesized, dependent on mRNA, and the dipeptide is readily assayed by a simple extraction procedure. In the presence of Leu-tRNA or His-tRNA, the tripeptides fMet-Val-Leu and fMet-Val-His are synthesized, corresponding to the NH2-terminal sequence of alpha- and beta-globin, respectively. Therefore, tripeptide synthesis provides a simple means to distinguish between the expression of the alpha- and beta-globin mRNA species.

In vitro synthesis of the tryptophan operon leader peptides of Escherichia coli, Serratia marcescens, and Salmonella typhimurium

We used an in vitro DNA-dependent protein-synthesizing system to demonstrate de novo synthesis of the leader peptide specified by the tryptophan (trp) operons of several bacterial species. Peptide synthesis was directed by self-ligated short restriction fragments containing the trp promoter and leader regions. Synthesis of leader peptides was established by demonstrating that they were labeled in vitro only by those amino acids predicted to be present in the peptides. Leader peptide synthesis was abolished by the addition of the Escherichia coli trp repressor. The E. coli trp leader peptide was found to be extremely labile in vitro; it had a half-life of 3-4 min. In a highly purified DNA-dependent peptide-synthesizing system, synthesis of the di- and tripeptides predicted from the Salmonella typhimurium trp operon leader sequence, fMet-Ala and fMet-Ala-Ala, also was observed. Using this dipeptide synthesis system, we demonstrated that translation initiation at the ribosome binding site used for trp leader peptide synthesis was reduced 10-fold when the transcript contained a segment complementary to the ribosome binding site.