Escherichia coli lac operator mRNA affects translation initiation of beta-galactosidase mRNA

Messenger RNA Decay

This chapter discusses several topics relating to the mechanisms of mRNA decay. These topics include the following: important physical properties of mRNA molecules that can alter their stability; methods for determining mRNA half-lives; the genetics and biochemistry of proteins and enzymes involved in mRNA decay; posttranscriptional modification of mRNAs; the cellular location of the mRNA decay apparatus; regulation of mRNA decay; the relationships among mRNA decay, tRNA maturation, and ribosomal RNA processing; and biochemical models for mRNA decay. Escherichia coli has multiple pathways for ensuring the effective decay of mRNAs and mRNA decay is closely linked to the cell's overall RNA metabolism. Finally, the chapter highlights important unanswered questions regarding both the mechanism and importance of mRNA decay.

An efficient Shine-Dalgarno sequence but not translation is necessary for lacZ mRNA stability in Escherichia coli

The 5' ends of many bacterial transcripts are important in determining mRNA stability. A series of Shine-Dalgarno (SD) sequence changes showed that the complementarity of the SD sequence to the anti-SD sequence of 16S rRNA correlates with lacZ mRNA stability in Escherichia coli. Several initiation codon changes showed that an efficient initiation codon is not necessary to maintain lacZ mRNA stability. A stop codon in the 10th codon of lacZ increased mRNA stability. Therefore, ribosomal binding via the SD sequence but not translation of the coding region is necessary to maintain lacZ mRNA stability.

The 5' ends of RNA oligonucleotides in Escherichia coli and mRNA degradation

The 5' ends of RNA oligonucleotides in Escherichia coli were identified to assess the contributions of specific endoribonucleases to the cleaving of bulk mRNA. About 60% of the total 5' ends have a 5' OH, and 40% a phosphate. Of those oligonucleotides with a 5'-OH end, 55% of the larger-sized molecules started with 5'-OH-A. With decreasing size there was a progressive decrease in its relative abundance, reaching 33% for the mononucleotide pool, close to its content in E. coli mRNA. In a mutant lacking RNase I* (a form of RNase I), the fraction starting with 5'-OH-A was even higher; 65-70% for oligonucleotides of any size, as well as the mononucleotides, whereas only 3-5% started with 5'-OH-U. Oligonucleotides with a 5'-P end were analyzed after pulse-labeling growing cells with 32Pi. Virtually all of them had a 5'-ppp-purine end which would result from transcription initiations, and there were four-times more G than A starts. The fraction of 5' ends with a monophosphate (5'-pN) was too low to measure. The known degradative enzymes of E. coli (RNases I, I*, M and R) release a 5'-OH oligonucleotide upon cleavage, whereas known processing endoribonucleases, e.g. RNases E, H, P and III, generate 5'-P oligonucleotides. Among these enzymes, RNase M is the only one known to enrich for 5'-OH-A ends, since its preference is for pyrimidine-A bonds [Cannistraro, V. J. & Kennell, D. (1989) Eur. J. Biochem. 181, 363-370]. It also gives a very low level of 5'-OH-U ends. These results are consistent with generalizations derived from our previous studies [Cannistraro, V. J., Subbaro, M. N. & Kennell, D. (1986) J. Mol. Biol. 192, 257-274] and suggest that RNase M is a primary endoribonuclease for mRNA degradation in E. coli. The results also indicate that RNase I* contributes a smaller fraction of cleavages to larger RNA oligonucleotides and accounts for most of the degradation of the very small oligonucleotides and almost all degradation of dinucleotide to mononucleotide.

Interdependence of translation, transcription and mRNA degradation in the lacZ gene

We have constructed a collection of Escherichia coli strains which differ by point mutations in the ribosome binding site (RBS) that drives the translation of the lacZ gene. These mutations affect the Shine-Dalgarno sequence or the initiation codon, or create secondary structures that sequester these elements, and result in a 200-fold variation in beta-galactosidase expression. Surprisingly, these variations of expression are paralleled by nearly equivalent changes in the lacZ mRNA level. The ratio of the beta-galactosidase expression to the mRNA level reflects the average spacing between translating ribosomes: hence, paradoxically, mutations that affect translation initiation do not correspondingly change this spacing. Further analysis of the mRNA level variations shows that they originate from two independent mechanisms. When beta-galactosidase expression exceeds a threshold corresponding roughly to one translation event per transcript, the variations in the efficiency of translation initiation affect largely the chemical and functional lifetimes of the mRNA. We further show that the rate-limiting step in the chemical decay process is an RNase E-dependent cleavage, which is outcompeted by translation initiation. Below this expression threshold, the mRNA lifetime levels out and strain-to-strain variations in mRNA level arise solely from polarity effects. We suggest that, in this activity range, most mRNA molecules that escape polarity are crossed by a single ribosome, and hence are identical from the viewpoint of degradation. Altogether, the tight couplings between translation initiation on one hand, polarity and/or mRNA degradation on the other, result in translation initiation events being closely spaced in time even from inefficient RBS, at the expense of the mRNA level. Finally, we evocate the possible beneficial consequences of a coupling between translation, transcription and mRNA degradation, for the management of cellular resources.

In the Escherichia coli lacZ gene the spacing between the translating ribosomes is insensitive to the efficiency of translation initiation

We have constructed a series of 44 Escherichia coli strains in which the chromosomal region corresponding to the Ribosome Binding Site (RBS) of the lacZ gene, has been replaced by small DNA fragments harboring either RBSs from other genes, or artificial RBSs. The beta-galactosidase expression from these strains ranges from 1 to 130 per cent of that of the parental strain. Using this collection, we demonstrate here that strain-to-strain variations in expression are paralleled by nearly equivalent variations in lacZ mRNA content. We propose that, in this system, polarity and mRNA stability are tightly coupled to translation initiation, so that changes in RBS efficiency are detected mainly as changes in mRNA concentration rather than in the spacing between translating ribosomes. In addition, we show that the mRNA sequence immediately downstream from the initiator codon influences per se the lifetime of the lacZ mRNA. We discuss the mechanism of the interdependence between translation, transcription and degradation in this gene, and speculate about the general role of this interdependence in determining the expression of bacterial genes.

Cloning and sequencing the gene encoding Escherichia coli ribonuclease I: exact physical mapping using the genome library

The amino acid (aa) sequence of the N terminus of Escherichia coli RNase I was determined. A mixed oligodeoxynucleotide coding for that sequence was used to probe the 476 lambda clones of Kohara et al. [Cell 50 (1987) 495-508]. DNA from these clones carry almost the entire E. coli chromosome in overlapping segments. Two overlapping clones hybridized to the probe sequence. From one of them DNA containing the rna gene was subcloned and sequenced. The inferred protein contains 245 aa residues and has an Mr of 27,156, which agrees with earlier estimates from sodium dodecyl sulfate-polyacrylamide-gel electrophoresis. RNase I is close to twice the size of pancreatic RNase A, but both enzymes contain eight Cys and four His; those aa are important for structure and function of RNase A. Proximal to the rna gene is a sequence that would code for a 23-aa peptide which conforms to consensus rules for signal peptides, and thus should transport this periplasmic enzyme. Sites for eight restriction enzymes had been mapped on each lambda clone. By relating to the map for that specific region, it was possible to position the rna gene exactly at 659 kb from the thr locus (time zero on a time scale of 100 min). This physical mapping gave a more precise (exact) map position based on distance than was possible using genetic mapping based on a time scale derived from conjugation, and should be applicable for mapping many other E. coli genes.

In vitro secondary structure analysis of mRNA from lacZ translation initiation mutants

mRNA secondary structure can be an important determinant of the efficiency of translation initiation. To study the effect of secondary structure on translation initiation, in vitro secondary structure analysis was performed on 32 lacZ RNA transcripts that differ in their in vivo translation initiation efficiencies because of mutations. We have shown that well-translated RNA has a relatively unstructured translation initiation region in vitro. In contrast, the translation initiation region of many of the poorly translated RNA transcripts is involved in a stem-loop structure. Mutations that decrease the in vitro stability of the stem-loop increase the frequency of translation initiation. The sequences responsible for forming this stem-loop structure were localized to a small region of RNA. The results confirm some of the previous predictions of the RNA secondary structure of the mutant RNAs based on computer modeling, but they disagree with some of the predicted long-range interactions.

Purification and characterization of ribonuclease M and mRNA degradation in Escherichia coli

A previously unreported endoribonuclease has been identified in Escherichia coli, which has a preference for hydrolysis of pyrimidine-adenosine (Pyd-Ado) bonds in RNA. It was purified about 7000-fold to give a single band after SDS/polyacrylamide gel electrophoresis; the eluted protein gave the same RNase specificity. The sizes of the native and denatured enzymes agreed suggesting that the enzyme exists as a monomer of approximately 26 kDa. It is called RNase M. The only other reported broadly specific endoribonuclease in E. coli is RNase I, a periplasmic enzyme. Based on differences in charge, heat stability and substrate specificity, it was clear that RNase M is not RNase I. The specificity of RNase M was remarkably similar to that of pancreatic RNase A even though the two enzymes differ in charge characteristics and size. Earlier studies had shown that mRNA from the lactose operon of E. coli is hydrolyzed in vivo primarily between Pyd-Ado bonds [Cannistraro et al. (1986) J. Mol. Biol. 192, 257-274] We propose that this major RNase activity accounts for these cleavages observed in vivo and that it is the endonuclease for mRNA degradation in E. coli.

Terminal sequences do not contain the rate-limiting decay determinants of E. coli cat mRNA

The mechanism of E. coli chloramphenicol acetyltransferase (cat) mRNA decay was investigated. Alteration of the 5' untranslated terminus does not appear to have an effect on the turnover rate of the mRNA. Similarly, changes at the 3' terminus of the message, including the addition of a stable stem and loop structure, do not affect the half-life of the message. The data suggest that 5' and 3' terminal untranslated sequences do not contain the rate-limiting determinants for cat message decay. Decay rates for various segments of the cat mRNA were measured and indicate that all regions of the message have similar stabilities. The current model of cat mRNA degradation involves a rate-limiting endonucleolytic decay event that occurs internal to the message followed by degradation of the cleavage products.

Sequence changes preceding a Shine-Dalgarno region influence trpE mRNA translation and decay

In studies with a trpE promoter-strength measuring system we observed that constructs containing the Escherichia coli trp promoter and its adjacent transcribed region yielded lower levels of trpE protein than were expected. To analyze this observation we introduced mutational changes in the nucleotide sequence preceding the trpE Shine-Dalgarno region and examined their effects on trpE mRNA synthesis, translation and decay. We found that certain deletion, insertion and substitution mutations in the pre-Shine-Dalgarno region caused a two- to fivefold increase in trpE enzyme activity. These increases were accompanied by increases in steady-state levels of trpE mRNA. Pulse-chase analyses of trpE mRNA degradation revealed that the observed steady-state trpE mRNA levels correlated with changes in trpE mRNA stability. These findings are interpreted in terms of alternative models in which the primary effect of mutational changes that elevate trpE expression is to increase trpE mRNA translation, versus increasing trpE mRNA stability.

Role of the ribosome in suppressing transcriptional termination at the pyrBI attenuator of Escherichia coli K-12

Pyrimidine-mediated regulation of pyrBI operon expression in Escherichia coli K-12 occurs primarily by an attenuation control mechanism. Previous studies have suggested a model for attenuation control in which low intracellular levels of UTP cause close coupling of transcription and translation within the pyrBI leader region. This close coupling apparently prevents transcriptional termination at an attenuator (a rho-independent transcriptional terminator) located 23 base pairs before the pyrBI structural genes within an open reading frame for a 44-amino acid leader polypeptide. Presumably, a ribosome involved in the synthesis of the leader polypeptide disrupts or precludes the formation of the attenuator-encoded RNA hairpin, which is required for transcriptional termination. In this study, we examined the role of the ribosome in inhibiting transcriptional termination at the pyrBI attenuator. Using oligonucleotide-directed mutagenesis, we systematically introduced termination codons into the reading frame for the leader polypeptide to determine the distance a ribosome must translate to suppress transcriptional termination. These mutations were incorporated individually into a pyrB::lacZ gene fusion, which was then introduced into the E. coli chromosome. The resulting fusion strains were used to measure the effect of each mutation on pyrB::lacZ expression. The results show that a ribosome must translate to within 14-16 nucleotides of the attenuator-encoded RNA hairpin to inhibit transcriptional termination efficiently, which indicates a direct interaction between the ribosome and the termination hairpin sequence as proposed in the present model. Additional results indicate that factors not included in the present model for attenuation control contribute to the expression and regulation of the pyrBI operon.

Relationship between size of mRNA ribosomal binding site and initiation factor function

The rate and the extent of the binding of initiator fMet-tRNA(fMet) to 30S ribosomal subunits in the presence of IF1, IF2 and GTP is either inhibited or slightly stimulated by the presence of IF3 depending on whether the initiation triplet AUG or the polynucleotide poly(AUG) is used as template. To determine the length of the template required for the transition from the AUG- to the poly(AUG)-type of behavior in the presence of IF3, the ribosomal binding of fMet-tRNA was studied in response to AUG triplets extended on either the 5'- or the 3'-side by stretches of homo-oligonucleotides of different lengths. When the binding of fMet-tRNA was studied at equilibrium it was found that IF3 no longer inhibits the amount of ternary complex formed if AUG is extended either 10 nucleotides on the 5'- or 35-40 nucleotides on the 3'-side. When the initial rate of ternary complex formation is considered, shorter extensions (4 nucleotides on the 5'-side or 20-30 nucleotides on the 3'-side) are sufficient to elicit a substantial stimulation by IF3. These results are discussed in relation to the mechanism of action of the initiation factors in the selection of the initiation region of the mRNA by ribosomes.

Mutational alterations of translational coupling in the L11 ribosomal protein operon of Escherichia coli

The L11 operon in Escherichia coli consists of the genes coding for ribosomal proteins L11 and L1. It is known that translation of L1 does not take place unless the preceding L11 cistron is translated, that is, the two cistrons are translationally coupled, and this is the basis of coregulation of the translation of the two cistrons by a single repressor, L1. Several mutational analyses were carried out to define the region responsible for coupling L1 translation with L11 translation. First, by introducing several amber mutations into the L11 gene by a site-directed mutagenesis technique, it was shown that translation by ribosomes down to a position 21 nucleotides upstream, but not to a position 45 nucleotides upstream, from the end of the L11 cistron allowed the initiation of L11 translation. Second, deletion analysis indicated that a region located 23 to 20 nucleotides from the end of the L11 gene was involved in preventing independent initiation from L1 translation. Third, five different mutations obtained by screening for activation of the masked L1 initiation site were found to be clustered in a small region immediately upstream from the Shine-Dalgarno sequence of L1, and all of them were G-to-A transitions. These results, together with some additional experiments with oligonucleotide-directed mutagenesis, defined the region involved in the coupling and suggest that some special feature of this region, probably different from simple masking of the initiation site by base pairing, is responsible for translational coupling. The present results also suggest that there might be specific differences in the primary nucleotide sequence that distinguish independent translational initiation sites from translationally coupled (i.e., masked) initiation sites.

The functional stability of the lacZ transcript is sensitive towards sequence alterations immediately downstream of the ribosome binding site

Various synthetic DNA sequences were inserted downstream of the fourth codon of the Escherichia coli lacZ gene on plasmids containing a hybrid lacZ-galK operon. Several different sequences, one as short as 10 bp, reduced the functional stability of the lacZ message three- to fourfold, whereas others had little or no effect. Introduction of synthetic sequences into a plasmid containing the intact lac operon resulted in similar reductions of mRNA stability. The sequence alterations also reduced the translational efficiency and transcription through lacZ as monitored by measurements of galactokinase synthesis from the downstream galK gene. There was no correlation between the average translational frequency and the stability of the lacZ message indicating that some of the inserted sequences reduced mRNA stability directly and not as a consequence of their effect on translation. The reduction of transcription through the lacZ gene correlated with the reduction of translation in agreement with current models of transcriptional polarity.

Isolating and sequencing the infrequent 3'-ends of a specific mRNA

Procedures are described for identification of very infrequent in vivo 3'-ends of RNA. After purification by filter hybridization, the 3'-ends were labeled with [5'-32P] cytosine-3'-P in the RNA ligase reaction. Significantly fewer counts were incorporated in the ligase reaction than in the polynucleotide kinase reaction to label 5'-ends. The incorporation was increased by increasing the RNA concentration 5-10 fold by using only one round of filter hybridization. Non-specific RNA binding could be eliminated by RNase A treatment of the filter if a great excess of denatured heterologous DNA was immobilized along with the DNA probe. Significant amounts of DNA were released when eluting the hybrid RNA from such filters. DNA inhibited the ligase reaction, while its DNase products were even more inhibitory. Treatment of the DNase products with alkaline phosphatase completely eliminated the inhibition. We detected no spurious 5'- or 3'-ends generated in the hybrid RNA by RNase A activity used to reduce the non-specific RNA. Also, RNase T1 could be used in place of RNase A to eliminate non-specific RNA binding, but about 25 times more RNase T1 (microgram/microgram) was needed. We used partial alkali digestion to sequence 3'-ends. A major (one hit) and minor (two hit) set of products were produced which could be distinguished from each other by alkaline phosphatase treatment and homochromatography of the products.

Specific endonucleolytic cleavage sites for decay of Escherichia coli mRNA

The polycistronic lac mRNA of Escherichia coli contains three messages. The rate of degradation of the second (lacY) message was observed to be equal to that of the third (lacA), and each decayed twice as fast as did the first (lacZ). Specific 5'- and 3'-ended lacY mRNA molecules could be recovered from cells; most likely, they are generated from endonucleolytic cleavages that are a part of the degradative process. They were observed by S1 nuclease mapping, and the exact 5'- and 3'-end oligonucleotides of many of them were identified by direct sequencing. Almost all of the molecules started with a 5' adenosine that would be preceded by a pyrimidine. The specificity was further restricted by neighboring nucleotides, and analysis of the data suggested that 5'-U-U decreases-A-U- is especially vulnerable. Also, computer analyses predicted the most stable secondary structures of selected segments of the mRNA and suggested that cleavages may only occur in regions of single strandedness. A model of mRNA degradation is proposed based on these observations and earlier ones. There is no unique target on a message for the initial inactivating attack: any region free of ribosomes is vulnerable, but for statistical reasons the initial attack of most molecules is near the ribosome-loading site. With no further ribosome loading, the newly unprotected 5' ends are "chopped off" at one of the next preferred target sites almost as fast as the last ribosomes moves down the mRNA.

Secondary structure as primary determinant of the efficiency of ribosomal binding sites in Escherichia coli

Using a previously described vector (pKL203) we fused several heterologous ribosomal binding sites (RBSs) to the lacZ gene of E. coli and then studied the variation in expression of the fusions. The RBSs originated from bacteriophage Q beta and MS2 genes and the E. coli genes for elongation factor EF-Tu A and B and ribosomal protein L11 (rplK). The synthesis of the lacZ fusion proteins was measured by an immuno precipitation method and found to vary at least 100-fold. Lac-specific mRNA synthesis follows the variation in protein production. It appears that there is a correlation between the efficiency of an RBS to function in the expression of the fused gene and the lack of secondary structure, involving the Shine and Dalgarno nucleotides (SDnts) and/or the initiation codon. This efficiency is context dependent. The sequence of the SD nts and the length and sequence of the spacer region up to the initiation codon alone are not able to explain our results. Deletion mutations, created in the phage Q beta replicase RBS, reveal a complex pattern of control of expression, probably involving the use of a "false" initiation site.

Initiation, attenuation and RNase III processing of transcripts from the Escherichia coli operon encoding ribosomal protein S15 and polynucleotide phosphorylase

The rpsO gene of Escherichia coli, which encodes ribosomal protein S15 is located at 69 minutes on the chromosome. It is adjacent to the pnp gene, which encodes polynucleotide phosphorylase. The two genes are separated by 249 nucleotides and are transcribed in the same direction. We report here in vivo S1 nuclease mapping and in vitro transcription experiments that demonstrate that rpsO and pnp are cotranscribed from a promoter P1, located 108 nucleotides upstream from rpsO, and that another promoter P2, located between the two genes 158 nucleotides upstream from pnp, also directs the transcription of pnp. Transcription from P1 can either terminate at the terminator t1 identified in vivo and in vitro, 18 nucleotides downstream from rpsO, or transcribe through t1 and into pnp. Comparison of the transcripts synthesized in wild-type and RNase III-deficient strains of E. coli shows that all the P1 readthrough transcripts and P2 transcripts are cleaved by RNase III. Two specific cuts are made by RNase III in a double-stranded structure about 100 nucleotides upstream rpsO. We also found that some transcripts of this operon start 47 nucleotides downstream from rpsO, in the region of t1. No promoter has been identified in this region. This mRNA is attributed to an endonucleolytic cleavage of the polycistronic transcripts and the location of the cut is named M. The order of the transcription signals and of the maturation sites in relation to rpsO and pnp can be summarized as follows: P1, rpsO, t1, M, P2, RNase III-processing sites, pnp. The possible roles of mRNA processing events in the expression of rpsO-pnp operon are discussed.

Isolating and sequencing the predominant 5'-ends of a specific mRNA in cells. I. Purification by filter hybridization

Procedures are considered for purification of a specific procaryotic RNA by successive hybridizations to DNA immobilized to nitrocellulose with special consideration of problems associated with subsequent end-labeling in the T4 polynucleotide kinase reaction. (1) Inhibitors of the kinase can be associated with the plasmid but were removed by electrophoresis of the DNA fragment through polyacrylamide. (2) Residual soluble acrylamide, contaminating the DNA and preventing its efficient retention to nitrocellulose, could be removed by DE52 chromatography. (3) Short denatured DNA required high salt (0.9 M) to bind to nitrocellulose but reannealed quickly at those salt concentrations unless applied at less than or equal to 0.3 micrograms/ml at 4 degrees C with a flow rate of 1 ml/min. (4) The kinetics of the hybrid reaction were a function of DNA length, concentration, and temperature. (5) Formamide was a more effective denaturing agent to remove hybrid RNA from the filter than either 12 M urea or 8 M guanidine-HCl, but caused significant release of DNA from the nitrocellulose as well as another potent inhibitor of the kinase reaction. The release of DNA and other kinase inhibitors was greatly reduced by eluting in boiling water.

Point mutations that affect translation initiation in the Escherichia coli gal E gene

This paper describes the selection and characterization of several mutations in the Escherichia coli galactose operon that affect translation initiation of the galE gene but are located outside of the Shine-Dalgarno sequence and the initiator codon. One mutation lies in the gal promoter region and shifts transcription initiation from the galP1 to the galP2 promoter. This results in a gal messenger that is five nucleotides longer and that is translated threefold more efficiently in vivo. This accords with previous observations from in vitro experiments which showed that the longer gal messenger was better translated (Queen & Rosenberg, 1981). The other mutations that affect galE translation are located in the coding sequence immediately downstream from the initiator codon. In contrast to the promoter mutation, these cause alterations in galE expression only when the gene carries a mutated initiator codon or Shine-Dalgarno sequence and have no effect on the wild-type galE gene. These findings are discussed with respect to our present knowledge of translation initiation mechanisms.

The 5' ends of Escherichia coli lac mRNA

We identified the predominant 5' ends of an mRNA in Escherichia coli to the exact nucleotides. There are four such ends of lac mRNA in fully induced cells. About 70% of the molecules have the reported major in vitro end, A-A-U-U-G (at +1), which is located 38 nucleotides before the A-U-G translation start. Another 15% start with A-U-U-G at +2, and about 8% start with A-U-U-A-G at -52. A fourth class of molecules begin with either A-G, C-A-G, A-C-A-G, or a weak A-C-A-C-A-G (at +24), observed only once. The origins of this latter set (less than or equal to 10% of the total) are not known, but they could represent "ragged" ends of the mRNA when it is degraded to the beginning of the ribosome-protected region of the message. The A-U-U-A-G molecules are probably initiated from an upstream promoter whose position would coincide with the cAMP-CRP DNA binding site for the major promoter.

Evidence that the 5' end of lac mRNA starts to decay as soon as it is synthesized

By monitoring the decay of the first 16% of the beta-galactosidase message, we showed that the 5' end started to decay before the 3' end was completed and at a rate equivalent to that of the whole molecule. Thus, decay was neither from 3' to 5' nor from random internal fragmentation but rather proceeded in a net 5' to 3' direction.

lacZ translation initiation mutations

Sixteen single point mutations near the beginning of the lacZ gene have been isolated and their effect on lacZ expression has been measured. Five mutations were obtained that alter a potential stem-and-loop structure in the messenger RNA that masks the initiation codons. Formation of this stem-and-loop is a result of transcription of DNA sequences introduced during the cloning of the lac regulatory region. The mutations isolated were then moved into a background that deleted this structure. Analysis of these mutations indicated that the secondary structure inhibited lacZ expression 5.8-fold and that either single point mutations or a 9 base-pair deletion could relieve this inhibition completely. In addition, it was found that an A to C transversion in the first base following the initiation codon (in the absence of the inhibitory secondary structure) decreases lacZ expression almost twofold, whereas C to U transitions in the next two positions have negligible effects. Mutations were also obtained that either increase or decrease the length of the Shine-Dalgarno sequence. The effects of these mutations were studied in the presence or absence of the secondary structure that involves the two initiation codons. It was found that when translation initiation was inhibited by the secondary structure, increasing the length of the Shine-Dalgarno sequence increased lacZ expression 2.8-fold and decreasing the length of this sequence reduced lacZ expression 12-fold. When translation initiation was not inhibited by the secondary structure, increasing the length of the Shine-Dalgarno sequence had no effect and decreasing the length of this sequence only reduced lacZ expression sixfold. The mechanistic implications of these results are discussed. Two initiation codons are located in the beginning of the lacZ gene, 7 and 13 bases from the Shine-Dalgarno sequence. NH2-terminal sequence analysis indicated that the majority of the protein synthesized initiate at the first initiation codon in the wild-type lacZ gene (in agreement with results reported previously by J. L. Brown and his colleagues). Upon introduction of sequences that result in a change in the mRNA secondary structure, both initiation codons are used in almost equal amounts. Three mutations and two pseudorevertants were obtained, which are located in the first initiation codon. It was found that when the first initiation codon is changed from AUG to GUG, translation initiation is decreased tenfold at that codon.(ABSTRACT TRUNCATED AT 400 WORDS)

Effects of alterations in the translation control region on bacterial gene expression: use of cat gene constructs transcribed from the lac promoter as a model system

The region controlling translation of the cat gene, which codes for chloramphenicol acetyltransferase, has been varied structurally in a series of plasmids that place the gene under control of the lac promoter. These plasmid constructs have enabled study of the structural features that affect the efficiency of mRNA translation. Altering the potential for secondary structure formation within the translation control region caused a tenfold variation in the synthesis of CAT enzyme, whereas varying the distance between the Shine-Dalgarno sequence (SD) and the translation start codon from 7 to 13 bases did not significantly affect the yield of CAT. If the SD was situated in a region of mRNA that is capable of base pairing, the efficiency of translation was decreased; however, the translation start codon, AUG, can initiate translation efficiently even when located in a segment capable of duplex formation. Overlapping of the cat translation control region by translation initiated upstream markedly affected initiation of translation within the cat gene: out-to-frame overlapping translation reduced CAT production by 90%; in-frame overlapping translation prevented detectable initiation of protein synthesis at the cat gene translation start codon, and yielded only fusion proteins. The enzymatic activity of such proteins was influenced by the length of the adventitious peptide segment added to the amino-terminus of the CAT polypeptide.

DNA sequence of the Escherichia coli gene, gnd, for 6-phosphogluconate dehydrogenase

Expression of gnd of Escherichia coli, which encodes 6-phosphogluconate dehydrogenase, an enzyme of the hexose monophosphate shunt, is subject to growth rate-dependent regulation and is gene dosage-dependent: the level of the enzyme increases in direct proportion to the cellular growth rate at both low and high gene copy numbers. We have determined the nucleotide sequence of gnd and flanking control regions, the 5'-end of in vivo gnd mRNA, and the start codon of the structural gene. Analysis of the sequence indicated that: (i) the gnd promoter is typical of other E. coli promoters and the structural gene is followed by a rho-independent transcription termination signal; (ii) the 56-nucleotide leader of gnd mRNA does not contain a rho-independent transcription termination signal, so growth rate-dependent regulation of 6-phosphogluconate dehydrogenase level is not carried out by an attenuation mechanism analogous to the one that controls expression of the E. coli ampC gene; (iii) the codon composition of the structural gene resembles that of other highly expressed E. coli genes and thus is not responsible for the regulation either; (iv) the structural gene is preceded at an optimal distance by a strong Shine-Dalgarno (SD) sequence, AGGAG ; (v) the leader region of the mRNA contains regions of dyad symmetry that have the potential to sequester the SD sequence and the start codon. This latter feature of the gene suggests that growth rate-dependent regulation may involve regulation of translation initiation frequency.

Cloning and sequencing of the ribosomal RNA genes in maize: the 17S region

The maize genes for the 17S, 5.8S, and 26S ribosomal RNAs (rRNAs) are located on chromosome 6 and consist of 9-kb sequences repeated about 5,000-10,000 times per 2C. One of these sequences was isolated from a lambda library containing maize Eco RI genomic segments. The sequence of the small-subunit (17S) RNA was determined using the M13 shotgun-dideoxy sequencing approach. The maize sequence was compared with nuclear rRNAs from yeast, Xenopus, and rat. Using these sequences, it is possible to identify tentatively the start and the end points of the sequence of the maize nuclear small subunit rRNA. This RNA has a length of 1809 nucleotides. The alignment of all four sequences for maximal homology allows us to identify regions within the rRNA that have been conserved during eukaryotic evolution.

Recognition of messenger RNA during translational initiation in Escherichia coli

The structural aspects of recognition by E. coli ribosomes of translational initiation regions on homologous messenger RNAs have been reviewed. Also discussed is the location of initiation region on mRNA, its confines, typical nucleotide sequences responsible for initiation signal, and the influence of RNA macrostructure on protein synthesis initiation. Most of the published DNA nucleotide sequences surrounding the start of various E. coli genes and those of its phages have been collected.

Increased expression of a cloned gene by local mutagenesis of its promoter and ribosome binding site

A strategy for local mutagenesis of DNA has been developed. The lac promoter in phage M13mp9 was replaced with the E. coli trp promoter. A restriction fragment bearing only the trp promoter region was mutagenized with nitrous acid, religated to the unmutagenized vector and transfected into E.coli. Several clones which give darker blue plaques on indicator media, suggesting increased beta-galactosidase synthesis, were selected for DNA sequencing. One clone has a G leads to A transition on the 3' side of the 'Pribnow box' which results in a constitutive promoter. Two clones have different point mutations (C leads to T and T leads to C) between the Shine-Dalgarno sequence and initiation codon which raise expression of beta-galactosidase two-fold. A secondary structure model suggests that the latter two mutations could exert their effect by destabilizing base-pairing of the lac Z coding region with the ribosome binding site (RBS), thereby allowing easier access to ribosomes. Support for the model comes from the finding that neither of the RBS mutations increase expression of a different downstream gene which forms no obvious secondary structure with the RBS region, whether or not the mutations are present. These results strengthen the hypothesis that secondary structure masking is a major determinant of RBS strength.

Possible role of flanking nucleotides in recognition of the AUG initiator codon by eukaryotic ribosomes

Sequences flanking the initiator codon in eukaryotic mRNAs are not random. Out of 153 messages examined, 151 have either a purine in position -3, or a G in position +4, or both. Thus, [A/G]XXAUGG emerges as the favored sequence for eukaryotic initiation sites. Nucleotides flanking nonfunctional AUG triplets, which occur in the 5'-noncoding region of a few eukaryotic messages, are different from those found at most functional sites. Whereas most authentic initiator codons are preceded by a purine (usually A) in position -3, most nonfunctional AUGs have a pyrimidine in that position. The observed asymmetry suggests that purines in positions -3 and +4 might facilitate recognition of the AUG condon during formation of initiation complexes. To test this idea, in vitro binding studies were carried out with 32P-labeled oligonucleotides. Binding of AUG-containing oligonucleotides to wheat germ ribosomes was significantly enhanced by placing a purine in position -3 or +4. The scanning model, which postulates that 40S ribosomal subunits attach at the 5'-end of a message and migrate down to the AUG codon, is discussed in light of these new observations. A modified version of the scanning mechanism is proposed.

Escherichia coli gal operon proteins made after prophage lambda induction

Expression of the EScherichia coli gal operon under the control of the prophage lambda promoter pL leads to gross discoordinacy of gal expression. Expression of the most promoter-distal cistron galK is much greater than expression of the promoter-proximal cistron galE. We had previously shown that transcription of the gal operon is coordinate after prophage induction. A survey of protein synthesized after prophage induction indicated that lack of expression of galE is due to a failure of translation of the galE sequence in the pL-gal transcript. This failure of translation of the galE sequence may be due to extensive dyad symmetry present in the vicinity of the gal promoter region of the pL-gal transcript. This symmetry could result in a ribonucleic acid stem-loop structure, blocking the attachment of ribosomes at the Shine-Dalgarno sequence of galE. To test this model, strains bearing the IS1 or IS2 insertion, deletion, or new promoter mutation within the symmetrical region were constructed. The restoration of some galE expression after such disruptions of the symmetrical region indicated that the ribonucleic acid stem-loop structure did play a role in the discoordinate expression of gal from pL. However, failure to obtain galE expression coordinated with high levels of galK expression suggested that other components were involved, perhaps other symmetries between galE and the pL transcript.

Cyclic AMP receptor proteins interacts with lactose operator DNA

The wildtype lac promoter-operator region of E. coli was reinvestigated for cyclic AMP receptor protein (CRP) binding sites using the 'footprinting' method. Two distinct interaction sites were found, one in the -60 base pair region, which has previously been described, and a second one covering the lac operator. These two sites are similar in extent, orientation and the characteristic pattern of CRP-induced DNaseI enhanced cutting sites.

The ribosome binding sites recognized by E. coli ribosomes have regions with signal character in both the leader and protein coding segments

Oligonucleotide analysis, by a novel computerized procedure, was first applied to determine the sequence of an ideal E. coli promoter (Scherer et al., Nucl. Acids Res. 1978, 5:3759-3773) and has now been used to obtain the sequence of nucleotides that should be present in a messenger RNA for optimum binding to the E. coli ribosome. This sequence is: UU.UUAAAAAUUAAGGAGGUAUAUUAUGAAAAAAAUUAAAAAACUCAA AA U A AUA A CUC G. Comparison of this sequence with each of the 68 ribosome binding site sequences used to generate it shows a preference rather than an absolute requirement for a specific base in any given position. The preference for certain bases persists along the whole length of the RNA within the ribosome binding domain even though nearly half of that length includes translated codons. Thus messages without leader sequences (like lambda CI mRNA) can still have some affinity for the ribosome. Part of the model sequence is complementary to the 3'end of 16S rRNA.

The effect of urea on catabolite sensitive operons in Escherichia coli K 12

Low concentrations of urea specifically inhibit the expression of catabolite sensitive genes (the lactose, galactose and maltose operons and the tryptophanase gene). This inhibition depends upon growth conditions, i.e. carbon source and temperature. The main effect of urea is exerted at the level of transcription initiation. However an additional inhibitory effect is observed on the decay and expression of the beta-galactosidase messenger. In a strain harboring the UV5 mutation in the lactose promoter, the effect at the level of transcription is relieved while the effect on the decay and the expression of the beta-galactosidase messenger remains the same. Just like the extreme physiological catabolite repression, the urea effect occurs even in a cya delta strain and is not antagonized by addition of adenosine 3'-5' cyclic monophosphate.

Secondary structure of mRNA and efficiency of translation initiation

A series of recombinant plasmids, containing the cro gene of phage lambda, exhibit strikingly different levels of expression depending apparently only on the nucleotide sequence of the untranslated 5' mRNA (Roberts et al., 1979). We postulate that initiation of translation involves interaction between an activated 30S ribosomal subunit and the 5'-terminal region of a messenger RNA already folded in a specific secondary structure. The observed variation in cro synthesis can then adequately be explained by secondary structure models which were derived for the different mRNAs. To maximize expression, it appears necessary that the initiation codon and, although less important, the ribosome interaction site are accessible.