Contributions of RNA secondary structure and length of the thymidine tract to transcription termination at the thr operon attenuator

Role of the terminator hairpin in the biogenesis of functional Hfq-binding sRNAs

Rho-independent transcription terminators of the genes encoding bacterial Hfq-binding sRNAs possess a set of seven or more T residues at the 3' end, as noted in previous studies. Here, we have studied the role of the terminator hairpin in the biogenesis of sRNAs focusing on SgrS and RyhB in Escherichia coli. We constructed variant sRNA genes in which the GC-rich inverted repeat sequences are extended to stabilize the terminator hairpins. We demonstrate that the extension of the hairpin stem leads to generation of heterogeneous transcripts in which the poly(U) tail is shortened. The transcripts with shortened poly(U) tails no longer bind to Hfq and lose the ability to repress the target mRNAs. The shortened transcripts are generated in an in vitro transcription system with purified RNA polymerase, indicating that the generation of shortened transcripts is caused by premature transcription termination. We conclude that the terminator structure of sRNA genes is optimized to generate functional sRNAs. Thus, the Rho-independent terminators of sRNA genes possess two common features: a long T residue stretch that is a prerequisite for generation of functional sRNAs and a moderate strength of hairpin structure that ensures the termination at the seventh or longer position within the consecutive T stretch. The modulation of the termination position at the Rho-independent terminators is critical for biosynthesis of functional sRNAs.

Effects of cooperation between translating ribosome and RNA polymerase on termination efficiency of the Rho-independent terminator

An experimental system was designed to measure in vivo termination efficiency (TE) of the Rho-independent terminator and position–function relations were quantified for the terminator tR2 in Escherichia coli. The terminator function was almost completely repressed when tR2 was located several base pairs downstream from the gene, and TE gradually increased to maximum values with the increasing distance between the gene and terminator. This TE–distance relation reflected a stochastic coupling of the ribosome and RNA polymerase (RNAP). Terminators located in the first 100 bp of the coding region can function efficiently. However, functional repression was observed when the terminator was located in the latter part of the coding region, and the degree of repression was determined by transcriptional and translational dynamics. These results may help to elucidate mechanisms of Rho-independent termination and reveal genomic locations of terminators and functions of the sequence that precedes terminators. These observations may have important applications in synthetic biology.

Mycobacterial RNA polymerase requires a U-tract at intrinsic terminators and is aided by NusG at suboptimal terminators

Intrinsic terminators, which encode GC-rich RNA hairpins followed immediately by a 7-to-9-nucleotide (nt) U-rich “U-tract,” play principal roles of punctuating and regulating transcription in most bacteria. However, canonical intrinsic terminators with strong U-tracts are underrepresented in some bacterial lineages, notably mycobacteria, leading to proposals that their RNA polymerases stop at noncanonical intrinsic terminators encoding various RNA structures lacking U-tracts. We generated recombinant forms of mycobacterial RNA polymerase and its major elongation factors NusA and NusG to characterize mycobacterial intrinsic termination. Using in vitro transcription assays devoid of possible mycobacterial contaminants, we established that mycobacterial RNA polymerase terminates more efficiently than Escherichia coli RNA polymerase at canonical terminators with imperfect U-tracts but does not terminate at putative terminators lacking U-tracts even in the presence of mycobacterial NusA and NusG. However, mycobacterial NusG exhibits a novel termination-stimulating activity that may allow intrinsic terminators with suboptimal U-tracts to function efficiently.

Bacteria rely on transcription termination to define and regulate units of gene expression. In most bacteria, precise termination and much regulation by attenuation are accomplished by intrinsic terminators that encode GC-rich hairpins and U-tracts necessary to disrupt stable transcription elongation complexes. Thus, the apparent dearth of canonical intrinsic terminators with recognizable U-tracts in mycobacteria is of significant interest both because noncanonical intrinsic terminators could reveal novel routes to destabilize transcription complexes and because accurate understanding of termination is crucial for strategies to combat mycobacterial diseases and for computational bioinformatics generally. Our finding that mycobacterial RNA polymerase requires U-tracts for intrinsic termination, which can be aided by NusG, will guide future study of mycobacterial transcription and aid improvement of predictive algorithms to annotate bacterial genome sequences.

Sequences required for transcription termination at the intrinsic lambdatI terminator

The lambdatI terminator is located approximately 280 bp beyond the lambdaint gene, and it has a typical structure of an intrinsic terminator. To identify sequences required for lambdatI transcription termination a set of deletion mutants were generated, either from the 5' or the 3' end onto the lambdatI region. The termination efficiency was determined by measuring galactokinase (galK) levels by Northern blot assays and by in vitro transcription termination. The importance of the uridines and the stability of the stem structure in the termination were demonstrated. The nontranscribed DNA beyond the 3' end also affects termination. Additionally, sequences upstream have a small effect on transcription termination. The in vivo RNA termination sites at lambdatI were determined by S1 mapping and were located at 8 different positions. Processing of transcripts from the 3' end confirmed the importance of the hairpin stem in protection against exonuclease.

Occurrence, divergence and evolution of intrinsic terminators across eubacteria

In Escherichia coli, the canonical intrinsic terminator of transcription includes a palindrome followed by a U-trail on the transcript. The apparent underrepresentation of such terminators in eubacterial genomes led us to develop a rapid and accurate algorithm, GeSTer, to predict putative intrinsic terminators. Now, we have analyzed 378 genome sequences with an improved version of GeSTer. Our results indicate that the canonical E. coli type terminators are not overwhelmingly abundant in eubacteria. The atypical structures, having stem-loop structures but lacking 'U' trail, occur downstream of genes in all the analyzed genomes but different phyla show conserved preference for different types of terminators. This propensity correlates with genomic GC content and presence of the factor, Rho. 60-70% of identified terminators in all the genomes show "optimized" stem-length and DeltaG. These results provide evidence that eubacteria extensively rely on the mechanism of intrinsic termination, with a considerable divergence in their structure, positioning and prevalence. The software and detailed results for individual genomes are freely available on request.

Genome-wide analysis of the intrinsic terminators of transcription across the genus Mycobacterium

Termination of transcription in eubacteria is achieved by a region of the nascent transcript. In Escherichia coli, this intrinsic terminator consists of a hairpin followed by a U-stretch. Absence of the typical terminators in several genes of Mycobacterium tuberculosis led us to develop an accurate and efficient algorithm to identify putative terminators in all sequenced microbial genomes. In addition to the typical Escherichia coli type of terminators, several variant terminator structures were predicted by the algorithm and their existence was experimentally verified. We have now analysed 17 Mycobacterium genomes to obtain a comprehensive picture of the transcription terminators in mycobacteria. Our results show that the terminators that lack a U-trail, variant from the typical E. coli intrinsic terminators, are overwhelmingly predominant in all members of the genus. Most terminator structures are concentrated within 50 base pairs downstream of the stop codon. A large number of these terminators occur at the end of experimentally verified or predicted transcription units. We have observed inter-species variations in DeltaG and positioning of the terminators downstream of specific genes amongst closely related mycobacterial species suggesting differences in gene expression. The analysis would be useful in furthering our understanding of genome organization and gene expression in mycobacteria, in addition to the improvement in the annotation of the new genomes.

Modeling classic attenuation regulation of gene expression in bacteria

A model is proposed primarily for the classical RNA attenuation regulation of gene expression through premature transcription termination. The model is based on the concept of the RNA secondary structure macrostate within the regulatory region between the ribosome and RNA-polymerase, on hypothetical equation describing deceleration of RNA-polymerase by a macrostate and on views of transcription and translation initiation and elongation, under different values of the four basic model parameters which were varied. A special effort was made to select adequate model parameters. We first discuss kinetics of RNA folding and define the concept of the macrostate as a specific parentheses structure used to construct a conventional set of hairpins. The originally developed software that realizes the proposed model offers functionality to fully model RNA secondary folding kinetics. Its performance is compared to that of a public server described in Ref. 1. We then describe the delay in RNA-polymerase shifting to the next base or its premature termination caused by an RNA secondary structure or, herefrom, a macrostate. In this description, essential concepts are the basic and excited states of the polymerase first introduced in Ref. 2: the polymerase shifting to the next base can occur only in the basic state, and its detachment from DNA strand - only in excited state. As to the authors' knowledge, such a model incorporating the above-mentioned attenuation characteristics is not published elsewhere. The model was implemented in an application with command line interface for running in batch mode in Windows and Linux environments, as well as a public web server.(3) The model was tested with a conventional Monte Carlo procedure. In these simulations, the estimate of correlation between the premature transcription termination probability p and concentration c of charged amino acyl-tRNA was obtained as function p(c) for many regulatory regions in many bacterial genomes, as well as for local mutations in these regions.

On the interplay of gene positioning and the role of rho-independent terminators in Escherichia coli

The majority of intrinsic rho-independent terminator signals, reported to consist of stable hairpin structures followed by T-rich regions, possess the potential to operate bi-directionally and to induce transcription terminations on both strands of the DNA duplex in Escherichia coli. By using RNAMotif software, we investigated the distributions of termination motifs around the 3'-ends of overlapping and non-overlapping genes at the genomic level. We suggest that the positions of compactly encoded E. coli genes and rho-independent terminators are optimized to terminate the adjoining genes on their antisense strands efficiently, and not to mis-terminate overlapping transcripts, due to their bi-directional properties.

Gene order constrains adaptation in bacteriophage T7

The order of genes in the genome is commonly thought to have functional significance for gene regulation and fitness but has not heretofore been tested experimentally. We adapted a bacteriophage T7 variant harboring an ectopically positioned RNA polymerase gene to determine whether it could regain the fitness of the wild type. Two replicate lines maintained the starting gene order and showed only modest recovery of fitness, despite the accumulation of over a dozen mutations. In both lines, a mutation in the early terminator signal is responsible for the majority of the fitness recovery. In a third line, the phage evolved a new gene order, restoring the wild-type position of the RNA polymerase gene but also displacing several other genes to ectopic locations. Due to the recombination, the fitness of this replicate was the highest obtained but it falls short of the wild type adapted to the same growth conditions. The large benefits afforded by the terminator mutation and the recombination are explicable in terms of T7 biology, whereas several mutations with lesser benefits are not easily accounted for. These results support the premise that gene order is important to fitness and that wild-type fitness is not rapidly re-evolved in reorganized genomes.

Phospholipase D

Phospholipase D catalyses the hydrolysis of the phosphodiester bond of glycerophospholipids to generate phosphatidic acid and a free headgroup. Phospholipase D activities have been detected in simple to complex organisms from viruses and bacteria to yeast, plants, and mammals. Although enzymes with broader selectivity are found in some of the lower organisms, the plant, yeast, and mammalian enzymes are selective for phosphatidylcholine. The two mammalian phospholipase D isoforms are regulated by protein kinases and GTP binding proteins of the ADP-ribosylation and Rho families. Mammalian and yeast phospholipases D are also potently stimulated by phosphatidylinositol 4,5-bisphosphate. This review discusses the identification, characterization, structure, and regulation of phospholipase D. Genetic and pharmacological approaches implicate phospholipase D in a diverse range of cellular processes that include receptor signaling, control of intracellular membrane transport, and reorganization of the actin cytoskeleton. Most ideas about phospholipase D function consider that the phosphatidic acid product is an intracellular lipid messenger. Candidate targets for phospholipase-D-generated phosphatidic acid include phosphatidylinositol 4-phosphate 5-kinases and the raf protein kinase. Phosphatidic acid can also be converted to two other lipid mediators, diacylglycerol and lyso phosphatidic acid. Coordinated activation of these phospholipase-D-dependent pathways likely accounts for the pleitropic roles for these enzymes in many aspects of cell regulation.

Shortening of RNA:DNA hybrid in the elongation complex of RNA polymerase is a prerequisite for transcription termination

Passage of E. coli RNA polymerase through an intrinsic transcription terminator, which encodes an RNA hairpin followed by a stretch of uridine residues, results in quick dissociation of the elongation complex. We show that folding of the hairpin disrupts the three upstream base pairs of the 8 bp RNA:DNA hybrid, a major stability determinant in the complex. Shortening the weak rU:dA hybrid from 8 nt to 5 nt causes dissociation of the complex. During termination, the hairpin does not directly compete for base pairing with the 8 bp hybrid. Thus, melting of the hybrid seems to result from spatial restrictions in RNA polymerase that couple the hairpin formation with the disruption of the hybrid immediately downstream from the stem. Our results suggest that a similar mechanism disrupts elongation complexes of yeast RNA polymerase II in vitro.

Alternate paradigm for intrinsic transcription termination in eubacteria

Intrinsic transcription terminators are functionally defined as sites that bring about termination in vitro with purified RNA polymerase alone. Based on studies in Escherichia coli, intrinsic termination requires a palindromic stretch followed by a trail of T (or U) residues in the coding strand. We have developed a highly efficient algorithm to identify hairpin potential sequences in bacterial genomes in order to build a general model for intrinsic transcription termination. The algorithm was applied to analyze the Mycobacterium tuberculosis genome. We find that hairpin potential sequences are concentrated in the immediate downstream of stop codons. However, most of these structures either lack the U trail entirely or have a mixed A/U trail reflecting an evolutionarily relaxed requirement for the U trail in the mycobacterial genome. Predicted atypical structures were shown to work efficiently as terminators both inside the mycobacterial cell and in vitro with purified RNA polymerase. The results are discussed in light of the kinetic competition models for transcription termination. The algorithm identifies >90% of experimentally tested terminators in bacteria and is an invaluable tool in identifying transcription units in whole genomes.

Balanced branching in transcription termination

The theory of stochastic transcription termination based on free-energy competition [von Hippel, P. H. & Yager, T. D. (1992) Science 255, 809-812 and von Hippel, P. H. & Yager, T. D. (1991) Proc. Natl. Acad. Sci. USA 88, 2307-2311] requires two or more reaction rates to be delicately balanced over a wide range of physical conditions. A large body of work on glasses and large molecules suggests that this balancing should be impossible in such a large system in the absence of a new organizing principle of matter. We review the experimental literature of termination and find no evidence for such a principle, but do find many troubling inconsistencies, most notably, anomalous memory effects. These effects suggest that termination has a deterministic component and may conceivably not be stochastic at all. We find that a key experiment by Wilson and von Hippel [Wilson, K. S. & von Hippel, P. H. (1994) J. Mol. Biol. 244, 36-51] thought to demonstrate stochastic termination was an incorrectly analyzed regulatory effect of Mg(2+) binding.

Transcription elongation complex: structure and function

Our understanding of the mechanisms of transcription has been greatly advanced by recent determination of the X-ray structure of bacterial RNA polymerase. Using crosslinking approaches, extensive mapping of DNA and RNA contacts onto this structure allowed tracking of the path of nucleic acids through the transcription elongation complex. The resulting structural model of the transcription elongation complex is linked to the functional one, which is based on numerous data accumulated during previous studies of RNA synthesis. An integrated structure-function model allows the rational explanation of termination and pausing and provides new insights into the mechanisms of transcription.

RNA polymerases from Bacillus subtilis and Escherichia coli differ in recognition of regulatory signals in vitro

Adaptation of bacterial cells to diverse habitats relies on the ability of RNA polymerase to respond to various regulatory signals. Some of these signals are conserved throughout evolution, whereas others are species specific. In this study we present a comprehensive comparative analysis of RNA polymerases from two distantly related bacterial species, Escherichia coli and Bacillus subtilis, using a panel of in vitro transcription assays. We found substantial species-specific differences in the ability of these enzymes to escape from the promoter and to recognize certain types of elongation signals. Both enzymes responded similarly to other pause and termination signals and to the general E. coli elongation factors NusA and GreA. We also demonstrate that, although promoter recognition depends largely on the sigma subunit, promoter discrimination exhibited in species-specific fashion by both RNA polymerases resides in the core enzyme. We hypothesize that differences in signal recognition are due to the changes in contacts made between the beta and beta' subunits and the downstream DNA duplex.

A structural model of transcription elongation

The path of the nucleic acids through a transcription elongation complex was tracked by mapping cross-links between bacterial RNA polymerase (RNAP) and transcript RNA or template DNA onto the x-ray crystal structure. In the resulting model, the downstream duplex DNA is nestled in a trough formed by the beta' subunit and enclosed on top by the beta subunit. In the RNAP channel, the RNA/DNA hybrid extends from the enzyme active site, along a region of the beta subunit harboring rifampicin resistance mutations, to the beta' subunit "rudder." The single-stranded RNA is then extruded through another channel formed by the beta-subunit flap domain. The model provides insight into the functional properties of the transcription complex.

Regulation of intrinsic terminator by translation in Escherichia coli: transcription termination at a distance downstream

BACKGROUND

Rho-independent terminators in Escherichia coli are DNA sequences of 30-50 bp consisting of a GC-rich dyad symmetry sequence followed by a run of T residues in the nontemplate strand. The transcription termination at the Rho-independent terminator occurs within the T-tract in vitro. It has been believed that the transcription termination at the Rho-independent terminator occurs within the T-tract in vivo, as established in vitro, and therefore the 3' ends of mRNAs are mostly generated as a direct result of transcription termination. However, how the transcription termination occurs and how the 3' ends of mRNAs are formed in living cells remains to be studied.

RESULTS

We developed a double terminator system in which a second Rho-independent terminator was placed downstream of the crp terminator. This system made it possible to detect transcripts that pass through the crp terminator by Northern blotting. We found that most of the crp transcripts extend beyond the crp terminator. The transcriptional read-through at the crp terminator was reduced when the translation of crp mRNA was interrupted. The level of the read-through transcript decreased with distance between the two terminators, suggesting that transcription termination occurs at multiple positions beyond the crp terminator.

CONCLUSION

We conclude that most RNA polymerase reads through the crp terminator in the natural situation and terminates transcription over a wide region downstream of the crp terminator, resulting in heterogeneous primary transcripts that are subsequently processed back to the terminator hairpin. We propose that ribosome translation to the crp stop codon causes read-through of the terminator. The regulatory effect of translation on Rho-independent termination may be a general phenomenon at other operons.

Transcription of the trp operon in Lactococcus lactis is controlled by antitermination in the leader region

The regulatory functions of the leader region preceding the Lactococcus lactis trp operon have been studied by mutagenesis analysis. This leader presents striking similarity to 'T-box' leaders found upstream of many Gram-positive aminoacyl-tRNA synthetase genes and some amino acid biosynthesis operons, which are controlled by antitermination through interaction of the leader transcript with cognate uncharged tRNA. A region of the L. lactis leader transcript also contains a series of (G/U) AG repeats which, in Bacillus, are involved in the binding of the trp RNA-binding protein (TRAP) which controls trp transcription. A screen was developed for the isolation of regulatory mutants affected in the leader region. All spontaneous mutants contained deletions; point mutations were only obtained after UV-induced mutagenesis. All mutations affected the putative transcription terminator upstream of the trp operon, demonstrating that trp is indeed controlled by transcription antitermination.

Transcription termination by bacteriophage T3 and SP6 RNA polymerases at Rho-independent terminators

Transcription termination of T3 and SP6 DNA-dependent RNA polymerases have been studied on the DNA templates containing the threonine (thr) attenuator and its variants. The thr attenuator is from the regulatory region of the thr operon of Escherichia coli. The DNA template, encoding the thr attenuator, contains specific features of the rho-independent terminators. It comprises a dG + dC rich dyad symmetry, encoding a stem-and-loop RNA, which is followed by a poly(U) region at the 3'-end. Thirteen attenuator variants have been analyzed for their ability to terminate transcription and the results indicated that the structure as well as the sequence in the G + C rich region of RNA hairpin affect termination of both RNA polymerases. Also, a single base change in the A residues of the hairpin failed to influence termination, whereas changes in the poly(U) region significantly reduced the termination of both T3 and SP6 RNA polymerases. The requirement of a poly(U) region for termination by T3 and SP6 RNA polymerases was studied with nested deletion mutants in this region. The minimum number of U residues required for termination of SP6 and T3 RNA polymerases was five and three, respectively. However, both RNA polymerases needed at least eight U residues to reach a termination efficiency close to that achieved by wild-type thr attenuator encoding nine U residues. In addition, the orientation of the loop sequences of the RNA hairpin did not affect the transcription termination of either of the bacteriophage RNA polymerases.

Mutations that increase expression of the rpoS gene and decrease its dependence on hfq function in Salmonella typhimurium

The RpoS transcription factor (also called sigmaS or sigma38) is required for the expression of a number of stationary-phase and osmotically inducible genes in enteric bacteria. RpoS is also a virulence factor for several pathogenic species, including Salmonella typhimurium. The activity of RpoS is regulated in response to many different signals, at the levels of both synthesis and proteolysis. Previous work with rpoS-lac protein fusions has suggested that translation of rpoS requires hfq function. The product of the hfq gene, host factor I (HF-I), is a ribosome-associated, site-specific RNA-binding protein originally characterized for its role in replication of the RNA bacteriophage Qbeta of Escherichia coli. In this study, the role of HF-I was explored by isolating suppressor mutations that map to the region directly upstream of rpoS. These mutations increase rpoS-lac expression in the absence of HF-I and also confer substantial independence from HF-I. DNA sequence analysis of the mutants suggests a model in which the RNA secondary structure near the ribosome binding site of the rpoS mRNA plays an important role in limiting expression in the wild type. Genetic tests of the model confirm its predictions, at least in part. It seems likely that the mutations analyzed here activate a suppression pathway that bypasses the normal HF-I-dependent route of rpoS expression; however, it is also possible that some of them identify a sequence element with an inhibitory function that is directly counteracted by HF-I.

Point mutations in a transcription terminator, lambda tI, that affect both transcription termination and RNA stability

The terminator tI is located approx. 280 nucleotides beyond the int gene of bacteriophage lambda. Besides its role as a transcription terminator, tI may confer stability to the int message by protecting it from 3' exonucleolytic degradation. In order to study the role of the tI sequence in transcription termination and RNA stability, three different point mutations tI1, tI2, and tI3 were isolated and characterized. All the tI mutations map in the G + C-rich region of dyad symmetry in the terminator and decrease the transcriptional termination of tI in vivo from 99% for the wild type terminator to 81-93% as determined by galactokinase activity and in vitro from 80% for the wild type terminator to 8-12% using the E. coli RNA polymerase. Additionally, the tI mutations cause upstream transcript instability in vivo. This instability defect caused by tI mutations is compensated by the host mutant deficient in polynucleotide phosphorylase resulting in increased steady state levels of these mutant transcripts. The results show that the intact hairpin of tI is essential for efficient transcription termination and for maintaining mRNA stability by blocking the 3' to 5' exonucleolytic activity of polynucleotide phosphorylase.

Differential contributions of two elements of rho-independent terminator to transcription termination and mRNA stabilization

The hallmark features of rho-independent transcription terminators are a G(+)C-rich dyad symmetry sequence followed by a run of T residues on a sense strand. Both of these structural elements are required for efficient transcription termination. Besides its primary function, rho-independent terminators are also known to enhance expression of an upstream gene by stabilizing RNA in a few cases. The Escherichia coli crp gene encoding cAMP receptor protein (CRP) contains a typical rho-independent terminator. To gain further insight into the roles of the G(+)C-rich dyad symmetry sequence and the poly(T) tract both in transcription termination and mRNA stabilization, we constructed a series of variant crp terminators and analyzed their abilities regarding these two functions. Disruption of the G(+)C-rich dyad symmetry sequence almost completely eliminated terminator activity while disruption of the poly(T) tract reduced terminator activity significantly but not completely. Thus, the contribution of the G(+)C-rich dyad symmetry sequence to transcription termination is larger than that of the poly(T) tract. Disruption of the G(+)C-rich dyad symmetry region reduced expression of the upstream crp gene by accelerating the rate of mRNA degradation. However, disruption of the poly(T) sequence had no effect on the stability of the crp mRNA, indicating that the poly(T) tract plays no role in mRNA stabilization. When the crp terminator was replaced by terminators derived from other genes, the fusion genes expressed the crp mRNA at the same level as did the native crp gene, suggesting that the mRNA stabilization effect is probably a general nature of rho-independent terminators.

Transcription termination at the thr attenuator. Evidence that the adenine residues upstream of the stem and loop structure are not required for termination

The Escherichia coli thr operon attenuator has a structure similar to other Rho-independent terminators. The DNA sequence immediately 5' to the termination site is dG+dC-rich and contains a region of dyad symmetry that, when transcribed into RNA, encodes a hairpin structure in the transcript. It also contains a stretch of 9 consecutive dA-dT residues immediately distal to the region of dyad symmetry which encode uridine residues at the 3' end of the terminated transcript. In addition, the thr attenuator has a stretch of 6 dA-dT residues immediately upstream of the region of dyad symmetry which encode 6 adenines. These adenines could potentially pair with the distal uridines to form a hairpin structure extended by as much as 6 A-U base pairs. In this report we have examined the role of the upstream adenines in transcription termination. We used templates that specify mismatches or create new base pairs in the potential A-U secondary structure of the transcript as well as templates that delete segments of the A residues upstream of the hairpin. We conclude that A-U pairing is not required for efficient transcription termination at the thr attenuator. This conclusion is likely to apply to other Rho-independent terminators that contain hairpin-proximal dA-dT residues.

Transcription termination

Chromosomes are organized into units of expression that are bounded by sites where transcription of DNA sequences into RNA is initiated and terminated. To allow for efficient stepwise assembly of complete transcripts, the transcribing enzyme (RNA polymerase) makes a stable complex with the DNA template until it reaches the terminator. Three general mechanisms of transcription termination have been recognized: one is by a spontaneous dissociation of the RNA at a sequence segment where RNA polymerase does not maintain its usual stable interaction with the nascent chain; another involves the action of a protein (rho factor in bacteria) on the nascent RNA to mediate its dissociation; and a third involves an action triggered by a protein that binds to the DNA at a sequence that is just downstream of the termination stop point. Transcription termination is important in the regulation of gene expression both by modulating the relative levels of various genes within a single unit of expression and by controlling continuation of transcription in response to a metabolic or regulatory signal.

Parameters affecting transcription termination by Escherichia coli RNA. II. Construction and analysis of hybrid terminators

Rho-independent terminators are characterized by two major functional regions, one upstream from the termination site having a sequence capable of forming an RNA hairpin in the nascent transcript, the second extending, from the base of this hairpin, seven to nine nucleotides along the transcript to the actual sites of termination (3'-tail region). This latter region of the transcript is often rich in uridine residues. Both regions are postulated to play central roles in the termination process. We have constructed a series of hybrid rho-independent, transcription terminators in which sequences upstream and downstream from the RNA hairpin for the Escherichia coli trp attenuator (trpatt+) are interchanged with sequences from trpatt mutant (1419) or from the phage T7 early terminator (T7Te). Similar hybrids have been constructed for T7Te, replacing flanking sequences with trpatt regions. The effects of such changes on transcription termination have been tested in vitro with purified E. coli RNA polymerase to determine the intrinsic termination efficiency (%T) of each hybrid terminator. Both the trpatt+ terminator and T7Te are highly efficient rho-independent terminators in vitro. However, replacement of trpatt+ sequences upstream and downstream from the RNA-terminator hairpin with the comparable T7Te sequences reduces %T dramatically, suggesting that the RNA-terminator hairpin does not function independently from its flanking regions. Regions downstream from the actual termination/release site are shown to be of considerable importance in determining %T for terminators bearing the T7Te or trpatt1419 3'-tail region, but have little effect on terminators with the trpatt+ 3'-tail region. For terminators bearing the T7Te or trpatt1419 3'-tail region that are inefficient, efficient termination is restored by elevated concentrations of KCl in the reaction. The results do not fit well with models for termination in which %T is determined by a two-step process in which the terminator-RNA hairpin, and a seven to 12 base-pair DNA-RNA hybrid structure rich in uridine residues, act independently to cause the polymerase to pause, and to release the transcript, respectively. DNA sequences both upstream and downstream from these regions, as well as DNA sequences downstream from the transcript termination site, can significantly affect the termination process. Conversely, terminators lacking a 3'-tail region rich in uridine residues can be highly efficient, but only when joined with appropriate sequence immediately downstream from the termination site. This suggests that the 3'-tail region acts in some manner other than the formation of an unstable DNA-RNA hybrid that facilitates termination.

Parameters affecting transcription termination by Escherichia coli RNA polymerase

Escherichia coli RNA polymerase can terminate transcription efficiently at rho-independent terminators in a purified transcription system in the absence of accessory factors. This process of "intrinsic termination" involves direct recognition of the terminator by the core RNA polymerase, and provides an important model system for the study of the molecular interactions involved in the switch between elongation and termination. We have analyzed the intrinsic termination efficiency (%T) of 13 rho-independent terminators, under a variety of in vitro reaction conditions. Although all of these sites share the general sequence features of typical rho-independent terminators, we find a wide range of %T (2% to 90%) for the different sites under our standard transcription conditions. While %T for a particular site is characteristic of that site, the efficiency can be altered considerably by the nature and concentration of salts in the reaction, by alteration of the concentrations of the nucleoside triphosphate substrates, or by transcription from supercoiled rather than linear templates. Surprisingly, different conditions can alter %T to a different extent for different terminators. For neutral salts such as potassium chloride or potassium glutamate, changes in the range from 0.1 to 1 M affect %T for different terminators in a distinct manner, depending on the terminator and the anion involved. At some sites, %T is greatly increased by Cl- concentrations up to 1 M, while at other sites %T is reduced or unaffected by these conditions. At some sites K+ concentrations up to 1 M give a modest increase in %T, while at other sites %T is slightly reduced under the same conditions. Thus the actual values of %T, as well as the order of terminator sites ranked according to %T, can be altered greatly according to the choice of reaction conditions. Reduction of the Mg2+ concentration below 1 mM has a dramatic and quite different effect, enhancing termination to approximately 100% for all terminators tested. Transcription of supercoiled DNA templates gives somewhat reduced %T as compared with linear DNA templates. However, the effect is no greater than twofold. Our results are not consistent with those expected for models in which %T is determined by the differential stability of DNA, RNA and hybrid duplex structures at the melted region in the transcription complex. Thus, the Cl anion does not affect the stability of nucleic acid duplexes even at 1 M concentrations, but can enhance termination tenfold. Also, the alterations of monovalent cation concentration that affect %T are not expected to have a differential effect on Tm for DNA, RNA and hybrid duplexes.(ABSTRACT TRUNCATED AT 400 WORDS)

Functional importance of sequence in the stem-loop of a transcription terminator

Intrinsic transcription terminators of prokaryotes are distinguished by a common RNA motif: a stem-loop structure high in guanine and cytosine content, followed by multiple uridine residues. Models explaining intrinsic terminators postulate that the stem-loop sequence is necessary only to form structure. In the tR2 terminator of coliphage lambda, single-nucleotide changes reducing potential RNA stem stability eliminated tR2 activity, and a compensatory change that restored the stem structure restored terminator activity. However, multiple changes in the stem sequence that should have either maintained or increased stability reduced terminator activity. These results suggest that the ability of the stem-loop structure to signal transcription termination depends on sequence specificity and secondary structure.

Analysis of the complex transcription termination region of the Escherichia coli rrnB gene

The complex terminator region of the Escherichia coli rrnB gene was analyzed by subcloning the terminators T1 and T2 and the inverted repeats IR1 and IR2 individually, or in various combinations, in a normal or inverted orientation into a terminator probe vector. The in vivo terminating efficiency was assayed by measuring the galactokinase activity encoded by the downstream galK gene. Termination efficiencies of all fragments were compared in two constructs, differing in the presence or absence of readthrough translation over the investigated terminator signal. The following main conclusions were drawn. (a) T1 and T2 are both efficient terminators in isolated forms. (b) IR1 and IR2 have some terminating effect (much lower than the proper terminators), especially in the inverted orientation. Their presence modifies the effect of the proper terminators in a quite unpredictable way, especially if these regions are translated. (c) The terminators are not symmetrical; in the inverted orientation T1 is practically inactive and T2 termination is reduced. (d) Translation radically decreases the efficiency of the terminators. (e) Several sequences in the rrnB gene, upstream of the terminator region (one in the 16S RNA and one in the 5S RNA coding region), are very efficient in vivo terminators in the inverted orientation.

Role of a nonmitochondrial Ca2+ pool in the synergistic stimulation by cyclic AMP and vasopressin of Ca2+ uptake in isolated rat hepatocytes

The subcellular distribution of 45Ca2+ accumulated by isolated rat hepatocytes exposed to dibutyryl cyclic AMP (dbcAMP) followed by vasopressin (Vp) was studied by means of a nondisruptive technique. When treated with dbcAMP followed by vasopressin, hepatocytes obtained from fed rats accumulated an amount of Ca2+ approximately fivefold higher than that attained under control conditions. Ca2+ released from the mitochondrial compartment by the uncoupler carbonyl cyanide p-trifluoromethoxyphenylhydrazone (FCCP) accounted for only a minor portion of the accumulated Ca2+. The largest portion was released by the Ca2+ ionophore A23187 and was attributable to a nonmitochondrial compartment. DbcAMP + Vp-treatment also caused a maximal stimulation of glucose production and a twofold increase in cellular glucose 6-phosphate levels. In hepatocytes obtained from fasted rats, dbcAMP + Vp-stimulated Ca2+ accumulation was lower, although with the same subcellular distribution, and was associated with a minimal glucose production. In the presence of gluconeogenetic substrates (lactate plus pyruvate) hepatocytes from fasted rats were comparable to cells isolated from fed animals. However, Ca2+ accumulation and glucose 6-phosphate production could be dissociated in the absence of dbcAMP, in the presence of lactate/pyruvate alone. Under this condition in fact Vp induced only a minimal accumulation of Ca2+ in hepatocytes isolated from fasted rats, although glucose production was markedly increased. Moreover, treatment of fed rat hepatocytes with 1 mM ATP caused a maximal activation of glycogenolysis, but only a moderate stimulation of cellular Ca2+ accumulation. In this case, sequestration of Ca2+ occurred mainly in the mitochondrial compartment. By contrast, the addition of ATP to dbcAMP-pretreated hepatocytes induced a large accumulation of Ca2+ in a nonmitochondrial pool. Additional experiments using the fluorescent Ca2+ indicator Fura-2 showed that dbcAMP pretreatment can enlarge and prolong the elevation of cytosolic free Ca2+ caused by Vp. A nonmitochondrial Ca2+ pool thus appears mainly responsible for the Ca2+ accumulation stimulated by dbcAMP and Vp in isolated hepatocytes, and cyclic AMP seems able to activate Ca2+ uptake in such a nonmitochondrial pool.

Prediction of rho-independent Escherichia coli transcription terminators. A statistical analysis of their RNA stem-loop structures

Escherichia coli rho-independent transcription terminators are characterized by an RNA structure having a G+C-rich stem-loop followed by a series of uridine residues, but they can be only partially predicted by the stability of this structure or by its primary sequence. A large number of such terminators have been identified or proposed in the literature, and we have constituted a list of them (148 found in 1021 x 10(3) base-pairs of E. coli DNA sequences) in order to analyze statistically the corresponding RNA hairpins. We show that the size of the loops presents a narrow distribution, that their sequences are not random, and that most loops are closed by a C.G base-pair. In particular, 55% of the loops are tetranucleotides and the most abundant loop sequences are UUCG and GAAA. These loops are abundant in prokaryotic and eukaryotic RNAs, and are known to enhance the stability of RNA hairpins. We propose that these tetraloops play an important role in the nucleation of the nascent RNA structures, as does also the presence of a C.G base-pair closing a hairpin loop. This analysis allows us to propose a model of formation of an RNA hairpin during the termination process and to construct an algorithm of prediction of the terminators in a given DNA sequence. For the E. coli sequences, it clearly distinguishes inter- from intracistronic terminator-like structures, and selects 141 of the 148 rho-independent terminators given in the literature, with a very low background. It also predicts with reasonable accuracy the in vitro termination efficiency of known rho-independent terminators, as well as predicting the existence of 35 as yet uncharacterized terminators.

Multiple control mechanisms for pyrimidine-mediated regulation of pyrBI operon expression in Escherichia coli K-12

Expression of the pyrBI operon of Escherichia coli K-12, which encodes the subunits of the pyrimidine biosynthetic enzyme aspartate transcarbamylase, is negatively regulated over a several-hundredfold range by pyrimidine availability. This regulation occurs, at least in large part, through a UTP-sensitive attenuation control mechanism in which transcriptional termination at the pyrBI attenuator, a rho-independent transcriptional terminator located immediately upstream of the pyrB structural gene, is regulated by the relative rates of transcription and translation within the pyrBI leader region. There is suggestive evidence that an additional, attenuator-independent control mechanism also contributes to this regulation. To measure the level of regulation that occurs through the attenuation and attenuator-independent control mechanisms, we constructed a mutant strain in which a 9-base-pair deletion was introduced into the attenuator of the chromosomal pyrBI operon. This deletion, which removes the run of thymidine residues at the end of the attenuator, completely abolishes rho-independent transcriptional termination activity. When the mutant strain was grown under conditions of pyrimidine excess, the level of operon expression was 51-fold greater than that of an isogenic pyrBI+ strain. Under conditions of pyrimidine limitation, operon expression was increased an additional 6.5-fold in the mutant. These results demonstrate that the attenuation control mechanism is primarily responsible for pyrimidine-mediated regulation but that there is a significant contribution by an attenuator-independent control mechanism.

Sense and antisense transcripts of traM, a conjugal transfer gene of the antibiotic resistance plasmid R100

The region of the antibiotic resistance plasmid R100 that encodes the plasmid-specific transfer gene traM has two tandemly aligned promoters separated by 145 nucleotides. The principal transcripts are 705 and 562 nucleotides long. Minor transcripts are 1550 and 1700 nucleotides long. The 705-base transcript appears to encode an 11 kD traM protein. The 562-base transcript does not encode a detectable protein. When subcloned on short fragments, the promoter for the 562-base transcript initiates efficiently but that for the 705 site does not. The 3' ends of the 705 and 562 base transcripts end inside the traJ ORF. Thus they provide additional sense RNA to compete with traJ for finP, the antisense translational regulator of traJ. A model is proposed for the participation of these sense and antisense transcripts in the control of expression of the traJ gene.