Models for decay of Escherichia coli lac messenger RNA and evidence for inactivating cleavages between its messages

Re-defining how mRNA degradation is coordinated with transcription and translation in bacteria

In eukaryotic cells, transcription, translation, and mRNA degradation occur in distinct subcellular regions. How these mRNA processes are organized in bacteria, without employing membrane-bound compartments, remains unclear. Here, we present generalizable principles underlying coordination between these processes in bacteria. In Escherichia coli, we found that co-transcriptional degradation is rare for mRNAs except for those encoding inner membrane proteins, due to membrane localization of the main ribonuclease, RNase E. We further found, by varying ribosome binding sequences, that translation affects mRNA stability not because ribosomes protect mRNA from degradation, but because low translation leads to premature transcription termination in the absence of transcription-translation coupling. Extending our analyses to Bacillus subtilis and Caulobacter crescentus, we established subcellular localization of RNase E (or its homolog) and premature transcription termination in the absence of transcription-translation coupling as key determinants that explain differences in transcriptional and translational coupling to mRNA degradation across genes and species.

Post-transcriptional control of gene expression: bacterial mRNA degradation

Many biological processes cannot be fully understood without detailed knowledge of RNA metabolism. The continuous breakdown and resynthesis of prokaryotic mRNA permit rapid production of new kinds of proteins. In this way, mRNA levels can regulate protein synthesis and cellular growth. Analysing mRNA degradation in prokaryotes has been particularly difficult because most mRNA undergo rapid exponential decay. Prokaryotic mRNAs differ in their susceptibility to degradation by endonucleases and exonucleases, possibly because of variation in their sequencing and structure. In spite of numerous studies, details of mRNA degradation are still largely unknown. This review highlights those aspects of mRNA metabolism which seem most influential in the regulation of gene expression.

Structured model of genetic control via the lac promoter in Escherichia coli

A model that describes induction of protein synthesis from lac-based promoters has been developed and incorporated into the single-cell model of Escherichia coli with transcriptional and translational modifications. Unlike previous models of lac-based promoters, this model allows a priori prediction of the intracellular parameters controlling transcription from lac-based promoters with only the extracellular levels of substrate and inducer as inputs. Because of the structural detail of the model, it is possible to simulate different genetic constructions for comparison, such as Lacl(q) strains versus wild-type cells, or including lacl on a multicopy plasmid. Expression from lac to tac promoters is predicted to yield 5% and 30% of the total cellular protein, respectively, with a pBR322-type plasmid. The model predicts the experimental observation that the Lacl(q) strain is not as fully induced as the wild-type strains, even at higher inducer concentrations. Additionally, the model predicts the right order of magnitude of protein production from lac and tac promoters when mechanisms for attenuation of transcription at lower translational efficiency are considered. Finally, the model predicts that for high copy number systems ribosomes become limiting in the synthesis of plasmid-encoded proteins. (c) 1994 John Wiley & Sons, Inc.

Model-based inference of gene expression dynamics from sequence information

A dynamic model of prokaryotic gene expression is developed that makes considerable use of gene sequence information. The main contribution arises from the fact that the combined gene expression model allows us to access the impact of altering a nucleotide sequence on the dynamics of gene expression rates mechanistically. The high level of detail of the mathematical model is considered as an important step towards bringing together the tremendous amount of biological in-depth knowledge that has been accumulated at the molecular level, using a systems level analysis (in the sense of a bottom-up, inductive approach). This enables to the model to provide highly detailed insights into the various steps of the protein expression process and it allows us to access possible targets for model-based design. Taken as a whole, the mathematical gene expression model presented in this study provides a comprehensive framework for a thorough analysis of sequence-related effects on the stages of mRNA synthesis, mRNA degradation and ribosomal translation, as well as their nonlinear interconnectedness. Therefore, it may be useful in the rational design of recombinant bacterial protein synthesis systems, the modulation of enzyme activities in pathway design, in vitro protein biosynthesis, and RNA-based vaccination.

Polarity Effects in the Lactose Operon of Escherichia coli

An intergenic RNA segment between lacY and lacA of the lactose operon in Escherichia coli is cleaved by RNase P, an endoribonuclease. The cleavage of the intergenic RNA was ten times less efficient than cleavage of a tRNA precursor in vitro. Fragments of the RNase P cleavage product are detectable in vivo in the wild-type strain but not in a mutant strain at the restrictive temperature. The cleavage product that contains lacA in the wild-type strain was quickly degraded. When this intergenic segment was cloned upstream of a reporter gene, the expression of the reporter gene was also inhibited substantially in wild-type E.coli, but not in a temperature sensitive mutant strain in RNase P at the restrictive temperature. These results support data regarding the natural polarity between lacZ versus lacA, the downstream gene.

Direct evidence for selective modulation of psbA, rpoA, rbcL and 16S RNA stability during barley chloroplast development

The turnover of RNAs encoded by seven different barley chloroplast genes was analyzed after treatment of barley shoots with tagetitoxin, a selective inhibitor of chloroplast transcription. Changes in RNA stability were examined during chloroplast development using basal and apical leaf sections of 4.5-day-old dark-grown seedlings and apical leaf sections of 4.0-day-old dark-grown seedlings which had been illuminated for 12 h. Of the RNAs examined, a 2.6 kb unspliced precursor of tRNA(lys) exhibited the shortest half-life, which was estimated to be 3 h. The 16S rRNA and psbA mRNA had the longest estimated half-lives, which were greater than 40 h. Among mRNAs, half-lives were estimated to range from 6 h for psaA mRNA, to over 40 h for psbA mRNA. Therefore, barley chloroplast mRNAs have long half-lives relative to bacterial mRNAs. The stability of atpB mRNA and the unspliced precursor of tRNA-lys was not altered during chloroplast development, while the stability of psaA mRNA decreased 2-fold. In contrast, the stability of the 16S rRNA and mRNAs for rpoA, psbA and rbcL increased during chloroplast development. The stability of 16S rRNA increased markedly during chloroplast development in the dark and this increase was maintained in illuminated seedlings. The stability of rbcL mRNA increased 2.5-fold during chloroplast development in the dark, and then decreased 2-fold in chloroplasts of light-grown plants. The initial increase in rpoA and psbA mRNA stability was also light-independent, with total increases in stability of at least 5-fold. In the case of rpoA, the stability of 2 of the 13 polycistronic rpoA transcripts that were detected in dark-grown plants was selectively increased during chloroplast development. In conclusion, the stability of some transcripts is selectively increased and further modulated during chloroplast development in barley. We propose that the selective stabilization of chloroplast mRNA, which occurred independent of light, is an indication that non-light regulated developmental signals are involved in barley chloroplast mRNA stability.

Lack of a 5' non-coding region in Tn1721 encoded tetR mRNA is associated with a low efficiency of translation and a short half-life in Escherichia coli

The repressor-encoding tetR gene from Tn1721 is expressed with a very low efficiency. Its mRNA lacks an untranslated leader sequence. We have constructed protein fusions with the lacZ gene which contain between 14 and 157 5' nucleotides from the tetR gene. Since they are all expressed with similar efficiencies we conclude that the sequence information for initiation of translation is contained within the first 14 bases of the tetR coding region. These fusion transcripts are about 20-fold less efficiently translated than the wild type lacZ transcript. A toeprint analysis confirms that the initiation complex is indistinguishable from those formed by regular transcripts with 5' untranslated regions but occurs in a very low amount in vitro. Thus, the absence of a 5' leader causes a poor rate of translation initiation. The half-lives of tetR and tetR-lacZ mRNAs are about 30 seconds, which is 3-times lower than that of the wt lacZ mRNA. Inactivation of the ams/rne locus in E. coli stabilizes the tetR transcript more than ten-fold. The influence of translation on the tetR half-life is discussed.

Intermediates in the degradation of mRNA from the lactose operon of Escherichia coli

We have analyzed the processing of mRNA from the lac operon in an Escherichia coli strain carrying the lac on a multicopy plasmid. Messenger RNA was analyzed by hybridization and nuclease protection of pulse-labeled RNA and precursor-product relationships were determined by quantitating radioactivity in primary and processed transcripts at various times after induction of the lac promoter or inhibition of transcription with rifampicin. Our results support the existence of two types of processed transcripts with endpoints in the lacZ-lacY intercistronic region. One of these carries lacZ sequences and has a 3' endpoint about 30 bases downstream of this gene. The other carries lacY sequences and has a 5' end in the translation termination region of the lacZ gene. Finally, we have found evidence that transcription is continued at least 268 bases beyond the last gene (lacA) and that this 3' non-translated region is shortened by post-transcriptional processing.

Multiple determinants of functional mRNA stability: sequence alterations at either end of the lacZ gene affect the rate of mRNA inactivation

The Escherichia coli lacZ gene was used as a model system to identify specific sequence elements affecting mRNA stability. Various insertions and substitutions at the ribosome-binding site increased or decreased the rate of mRNA inactivation by up to fourfold. Deletion of a dyad symmetry, which may give rise to a very stable secondary structure in the mRNA immediately downstream of the gene, decreased the functional stability of the lacZ message. The magnitude of the latter effect was strongly dependent on the sequences at the ribosome-binding site, ranging from practically no effect for the most labile transcripts to a threefold decrease in stability for the most stable one. The results suggest that the wild-type lacZ message is inactivated predominantly by attacks near the ribosome-binding site, presumably in part because the putative secondary structure downstream of the gene protects against 3'-exonucleolytic attack. Taken together, the data for all of the modified variants of lacZ were shown to be quantitatively compatible with a general model of mRNA inactivation involving multiple independent target sites.

Transcription and decay of the lac messenger: role of an intergenic terminator

Prior work has indicated that the polycistronic lacZYA mRNA of Escherichia coli is cleaved during decay at approximately intergenic sites (L. W. Lim and D. Kennell, J. Mol. Biol. 135: 369-390, 1979). In this work, we characterized the products by using probes specific for the different cistrons. This analysis indicated that six lac mRNA species are present in the following order of decreasing abundance: lacZ, -A, -ZYA, -ZY, -YA, and -Y. Very little lacYA and lacY mRNAs were present, whereas in cells induced to steady state, there was 10 times more lacZ than lacZYA mRNA. The lacZ mRNA appeared as a discrete species extending to a site in the lacZ-Y intergenic space (ca. residue 3150). This site is just distal to a potential rho-independent termination sequence. We examined the function of this sequence to determine whether it contributes to the distribution of the mRNAs. Although the termination sequence was shown to function in vitro, when it was recloned into an expression vector, no termination was seen in vivo. Moreover, direct examination of the kinetics of lac messenger synthesis revealed that after initiation, most transcription continued to the end of the operon. We conclude that during normal growth, the operon is transcribed in its entirety and that the individual lac mRNAs are formed by cleavage. These results confirm earlier work implying that the lac operon is transcribed in its entirety but are in conflict with several recent reports suggesting that internal termination occurs. Our findings indicate that the natural polarity of the operon (lacZ is expressed sixfold more strongly than lacA) is based on posttranslational effects and not on polarity of transcription.

The importance of the 5'-region in regulating the stability of sdh mRNA in Bacillus subtilis

The decay of the polycistronic Bacillus subtilis sdh mRNA was analysed using probes specific for each of the component cistrons, sdhC, sdhA and sdhB. In exponentially growing cells, the entire sdh mRNA seems to decay with an 'all or nothing' mechanism and with a uniform half-life of 2-3 min for all cistrons. In stationary-phase cells, the half-life of the 5'-part had dropped to about 0.6 min whereas that of the 3'-part was about 1.2 min. Decay of sdh mRNA was also measured in exponentially growing cells containing a 'down-mutation' in the ribosomal binding site preceding sdhC which decreases the expression of sdhC by about 90%. The mutation has a moderate effect on expression of the downstream cistron sdhA. In this mutant, the half-life of the 5'-part of sdh mRNA was about 0.5 min (i.e. the same as in stationary phase wild-type cells) and the half-life of the 3'-part about 1.3 min. Also, analysis of the decay of an sdh-cat fusion transcript revealed that the sdh (5') part decayed more rapidly than the cat part and this difference was more pronounced in stationary-phase cells compared to exponentially growing cells. The results of these experiments demonstrate the importance of the 5'-segment of sdh mRNA in controlling the stability of the transcript under different growth conditions.

Differential mRNA stability controls relative gene expression within the plasmid-encoded arsenical resistance operon

The arsenical resistance (ars) operon of the conjugative plasmid R773 encodes an ATP-driven anion extrusion pump, conferring bacterial resistance to arsenicals. The operon contains a regulatory gene, arsR, and three structural genes, arsA, arsB, and arsC. The hydrophilic ArsA and ArsC proteins are produced in large amounts, but the hydrophobic ArsB protein, an integral membrane polypeptide, is synthesized in limited quantities. Northern (RNA-DNA) hybridizations provide evidence that the inducible operon is regulated at the level of transcription. The genes were transcribed in the presence of an inducer (arsenite) as a single polycistronic mRNA with an approximate size of 4.4 kilobases (kb). This transcript was processed to generate relatively stable mRNA species: one of 2.7 kb, encoding the ArsR and ArsA proteins, and a second of 0.5 kb, encoding the ArsC protein. Segmental differences in stability within the polycistronic transcript are proposed to account for the differential expression of the ars genes. In addition, analysis of the mRNA structure at the 5' end of arsB suggests a potential translational block to the synthesis of this membrane protein.

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.

Distribution of 5'-triphosphate termini on the mRNA of Escherichia coli

We have determined the distribution of 5'-nucleoside triphosphates on the RNA in Escherichia coli. These groups represent the initial nucleoside triphosphate incorporated when RNA polymerase initiates transcription. It was estimated that at least 15% of polysome-associated messengers had triphosphates. This was interpreted to mean that removal of the triphosphate or messenger leader is not necessary for the functioning of most mRNAs but that a substantial amount of messenger processing occurs in the polysome pool. We found that the ratio of GTP- to ATP-initiated messengers was about 2 to 1. Since prior work has indicated that G- and A-initiated RNAs decay at the same rate and since a compilation of messenger start sites shows an A preference, this value implies that there is a significant physiological selection of G-initiated transcripts. We also characterized the 5'-terminal groups on RNAs in other fractions. A small amount was found associated with 30S ribosomes, presumably in initiation complexes; such complexes have not previously been detected in situ. In addition, it was concluded that the 5' terminus of rRNA precursors is processed more rapidly than is implied by the current literature.

Coliphage lambda to terminator lowers the stability of messenger RNA in Escherichia coli hosts

The effects of the transcription terminators to and tfd on the overall high-level expression of a human interferon-beta gene (IFN-beta) in Escherichia coli hosts were compared. Deletion mapping shows that mRNA lability is caused by sequences at or near the lambda terminator to stem-loop structure. Extensive RNA secondary structure in this region indicates a potential RNase III cleavage/binding site. In RNase III- E. coli hosts, IFN-beta synthesis is indeed considerably enhanced. The bacteriophage tfd terminator does not confer this mRNA labilization phenomenon. In all cases, RNA level and stability correlate with the level of IFN-beta synthesized in the cell. In the system described, ongoing translation stabilizes mRNA only moderately.

Mechanisms of mRNA decay in bacteria: a perspective

Messenger RNA decay plays an important role in prokaryotic gene expression. The disparate stabilities of bacterial messages in vivo are a consequence of their differential susceptibility to degradation by cellular endoribonucleases and 3' -exoribonucleases, which in turn results from differences in mRNA sequence and structure. RNase II and polynucleotide phosphorylase, the major bacterial exonucleases involved in mRNA turnover, rapidly degrade single-stranded RNA from the 3' end, but are impeded by 3' stem-loop structures. At present, the identify and substrate specificity of the endonucleases that control mRNA decay rates are relatively poorly defined. Ribosomes and antisense RNA also can influence the stability of transcripts with which they associate. Differences in mRNA stability can contribute to differential expression of genes within polycistronic operons and to modulation of gene expression in response to changes in bacterial growth conditions.

Evidence for endonucleolytic cleavages in decay of lacZ and lacI mRNAs

S1 nuclease mapping revealed lacZ mRNA molecules whose 5' and 3' ends were internal to the transcription start and consistent with cleavages at pyrimidine-adenosine bonds 20 to 50 nucleotides apart. With the net 5'-to-3' direction known, lacZ mRNA is probably degraded by sequential cleavages of naked mRNA at vulnerable sites exposed by transit of the last translating ribosome.

Differential mRNA stability controls relative gene expression within a polycistronic operon

In this paper we demonstrate a role for mRNA stability in controlling relative gene expression within a polycistronic operon. The polycistronic malEFG operon of E. coli contains two REP sequences (highly conserved inverted repeats) within the malE-malF intercistronic region. Deletion of these REP sequences from the chromosomal operon not only destabilizes upstream malE mRNA, but also results in a 9-fold reduction in the synthesis of MalE protein. A single REP sequence seems to be as efficient as the two normally found in this intergenic region at stabilizing translationally active upstream mRNA. The widespread occurrence of REP sequences and other sequences that could potentially stabilize upstream mRNA suggests that this mechanism of control of gene expression may be rather common.

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.

The mRNA for an inducible chloramphenicol acetyltransferase gene is cleaved into discrete fragments in Bacillus subtilis

cat-86 is a promoter-deficient plasmid gene that encodes chloramphenicol acetyltransferase (CAT). Insertion of a promoter at a site 144 base pairs 5' to the cat-86 coding sequence activates transcription of the gene and allows cat-86 to specify chloramphenicol-inducible CAT activity in Bacillus subtilis. Induction of cat-86 by chloramphenicol has been shown to result from a regulatory event that activates translation of cat-86 mRNA that is present in cells before the addition of inducer (E. J. Duvall and P. S. Lovett, Proc. Natl. Acad. Sci. USA 83:3939-3943, 1986). In the present study we show an unusual property of cat-86 mRNA. Full-length cat-86 transcripts, consisting of 920 nucleotides (nt), are cleaved in B. subtilis to yield two predominant fragmentation products: an 810-nt species that lacks sequences present at the 5' end of the 920-nt species and a 720-nt species that lacks sequences present at the 3' end of the 920-nt species. A third fragmentation product consisting of 620 nt may result from the cleavage of a single 920-nt transcript at both the 5' and 3' ends. The sequences which are missing from the 720- and 620-nt species suggest that these transcripts cannot be translated into functional CAT. The 810-nt species lacks sequences from the 5' regulatory region, and it is not yet certain whether or not translation of this species can be induced by chloramphenicol. The ratio of 920-nt molecules/720-nt molecules in rifampin-treated cells is increased when the cells are grown in chloramphenicol. Therefore, induction may partially stabilize full-length cat-86 transcripts against inactivation by a novel processing-like system.

Stabilization of translationally active mRNA by prokaryotic REP sequences

The REP sequence is a highly conserved inverted repeat that is present in about 25% of all E. coli transcription units. We show that the REP sequence can stabilize upstream RNA, independently of any other sequences, by protection from 3'-5' exonuclease attack. The REP sequence is frequently responsible for the differential stability of different segments of mRNA within an operon. We demonstrate that REP-stabilized mRNA can be translated in vivo and that cloning the REP sequence downstream of a gene can increase protein synthesis. This provides direct evidence that alterations in mRNA stability can play a role in determining bacterial gene expression. The implications of these findings for the mechanisms of mRNA degradation and for the role of RNA stability in the regulation of gene expression are discussed.

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.

Nucleotide sequence of the transcription unit containing the aroL and aroM genes from Escherichia coli K-12

The nucleotide sequence of 2,021 base pairs (bp) of DNA containing the Escherichia coli aroLM operon was determined, and the coding regions of both aroL and aroM were identified. The 501-bp intercistronic region between aroL and aroM contains an open reading frame which might encode a 63-residue protein. Northern blots with RNA from strains carrying multicopy aroL+ plasmids detected one longer (2,000-base) and two shorter (950- and 1,100-base) transcripts which contained aroL. It was concluded that the longest transcript, which was not abundant, spanned the entire operon and that the shorter transcripts resulted from either termination or posttranscriptional processing in the intercistronic region. The DNA upstream of aroL contains a number of imperfect palindromes which are closely homologous to known sites of regulation by the TyrR protein in other operons.

The relationship between translational initiation and messenger RNA inactivation in down-shifted Escherichia coli

The parameters of protein synthesis and functional inactivation of global messenger RNA (mRNA) were examined in a Tic+ strain of Escherichia coli during the 30-min period following a shift-down from glucose-minimal to succinate-minimal medium. The rate of mRNA inactivation and the relative translational initiation frequency were both most severely depressed immediately after the shift-down and increased slowly thereafter. If glucose was restored to the medium at any time after shift-down, mRNA inactivation immediately resumed its normal (preshift) rate and the protein-forming capacity was increased. These changes in mRNA inactivation rate do not reflect an altered mRNA composition in the down-shifted cells. The relative rate of mRNA inactivation was linearly proportional to the relative translational initiation frequency over a 10-fold range of initiation frequencies. Low initiation frequencies represent increased "dwell" of the ribosomes at the initiation site before the commencement of polypeptide chain initiation. We propose that initiating ribosomes protect mRNA from an inactivating endonucleolytic cleavage at or near the ribosome binding site.

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.

Posttranscriptional modulation of bacteriophage P22 scaffolding protein gene expression

The bacteriophage P22 late operon contains 2 genes whose products are required for cell lysis and 13 genes whose products are involved in the morphogenesis of the phage particle. This operon is under the positive control of the phage gene 23 product and is thought to have a single promoter. The expression of one of these late genes, the scaffolding protein gene, is autogenously modulated independently from the remainder of the late genes. When unassembled, scaffolding protein turns down the rate of synthesis of additional scaffolding protein, and when it is assembled into phage precursor structures, it does not. Experiments presented here show (i) that the mRNA from the scaffolding protein gene is functionally threefold more stable when most of the scaffolding protein is assembled than when it is unassembled and (ii) that no new promoter near the scaffolding protein gene is activated at the high level of synthesis. These data support the model that this autogenous modulation occurs at a posttranscriptional level. We also observed that another message, that of coat protein, appears to become increasingly stable with time after phage infection.

A mathematical model that applies to protein degradation and post-translational processing of proteins and to analogous processes for other molecules in non-growing and exponentially growing cells

A mathematical model is presented that describes first order degradation and post-translational processing of proteins in non-growing and exponentially growing cells. The model applies to proteins that are substrates or products of processing. General equations are presented that can be applied to many different experimental protocols. Application of the model to pulse-chase and continuous labeling experiments is illustrated. The mathematical expressions apply to any cellular component that is synthesized in proportion to cellular mass and is degraded or processed by reactions that follow first order kinetics. However, in this paper, the model is discussed solely as it applies to protein metabolism.

Characterization of the mRNA coding for ribonucleoside diphosphate reductase in Escherichia coli

Total Escherichia coli RNA was separated by electrophoresis on methyl mercury agarose gels, transferred to diazobenzyloxymethyl-paper, and hybridized to various DNA probes containing different segments of the nrd genes to determine the organization of these genes. A 3.2-kilobase polycistronic mRNA transcript which hybridizes to both the nrdA and nrdB genes indicated that the nrdA and nrdB genes are organized in an operon. The polycistronic transcript contained the nrdA gene at the 5' end and the nrdB gene at the 3' end. The size of the polycistronic mRNA was sufficient to code for the 80,000-molecular-weight B1 protein and the 40,000-molecular-weight B2 protein. The results also indicated that the nrdA and nrdB genes are the only genes in E. coli that code for ribonucleoside diphosphate reductase. Two smaller RNA species that hybridized to nrd DNA were observed and probably overlap with the 3.2-kilobase nrd mRNA.

Amplification of ribonuclease II (rnb) activity in Escherichia coli K-12

A 7.1 kb HindIII-XhoI fragment of E. coli DNA which contains the structural gene for ribonuclease II (rnb) has been cloned in the recombinant plasmid pDK24. At least two constitutively expressed genes are encoded on the fragment as shown by maxicell analysis. On denaturing polyacrylamide gels RNase II appears as a single 72,000 dalton species. The approximate site of transcription initiation of the rnb gene has been mapped. Although derivatives of E. coli harboring pDK24 contained 10-fold more RNase II activity that wild type strains without the plasmid, the degradation rate of mRNA was similar in all strains tested. Strains deficient in both RNase II and polynucleotide phosphorylase appear inviable.

lac Transcription in Escherichia coli cells treated with chloramphenicol

When protein synthesis was blocked by chloramphenicol in vivo, transcription initiation of lac mRNA was severely inhibited. In a promoter mutant (L8-UV5) or in wild-type cells supplemented with adenosine 3',5'-phosphate (greater than or equal to 5 mM), nearly normal initiation could be achieved, and when the mRNA chains formed were extracted, they coded for the 5'-terminal alpha-peptide of the lacZ gene in vitro. However, even under such conditions, only a fraction of RNA polymerases proceeded to the end of the Z gene in the presence of chloramphenicol; as a consequence, a wide range of sizes of mRNA was produced, and very few transcripts were formed all the way to the natural termination site of the operon. In other words, premature transcription termination occurred in chloramphenicol-treated cells, as current models predict, but terminations occurred to variable extents at several intragenic sites and apparently at least one intergenic site. Termination at intragenic sites occurred far less in cells bearing a mutation in the transcription termination factor rho.

Dual function transcripts specifying tRNA and mRNA

A cluster of four tRNA genes in Escherichia coli is co-transcribed with an adjacent gene encoding elongation factor Tu. The resultant transcript that specifies both structural (tRNA) and informational (mRNA) RNA may not be an uncommon occurrence and has interesting regulatory implications.

Lactose operon transcription from wild-type and L8-UV5 lac promoters in Escherichia coli treated with chloramphenicol

In cells treated with chloramphenicol and the inducer isopropyl-beta-D-thiogalacto-pyranoside, messenger ribonucleic acid transcription from the wild-type lac promoter was not detected. Transcription occurred from the mutant UV5-L8 promoter. The transcripts were of variable length; some included the whole Z gene. No major site of transcription arrest within the Z gene was apparent.