Expression of the unc genes in Escherichia coli

Structure, Regulation, and Significance of Cyanobacterial and Chloroplast Adenosine Triphosphate Synthase in the Adaptability of Oxygenic Photosynthetic Organisms

In cyanobacteria and chloroplasts (in algae and plants), ATP synthase plays a pivotal role as a photosynthetic membrane complex responsible for producing ATP from adenosine diphosphate and inorganic phosphate, utilizing a proton motive force gradient induced by photosynthesis. These two ATP synthases exhibit similarities in gene organization, amino acid sequences of subunits, structure, and functional mechanisms, suggesting that cyanobacterial ATP synthase is probably the evolutionary precursor to chloroplast ATP synthase. In this review, we explore the precise synthesis and assembly of ATP synthase subunits to address the uneven stoichiometry within the complex during transcription, translation, and assembly processes. We also compare the regulatory strategies governing ATP synthase activity to meet varying energy demands in cyanobacteria and chloroplasts amid fluctuating natural environments. Furthermore, we delve into the role of ATP synthase in stress tolerance and photosynthetic carbon fixation efficiency in oxygenic photosynthetic organisms (OPsOs), along with the current researches on modifying ATP synthase to enhance carbon fixation efficiency under stress conditions. This review aims to offer theoretical insights and serve as a reference for understanding the functional mechanisms of ATP synthase, sparking innovative ideas for enhancing photosynthetic carbon fixation efficiency by utilizing ATP synthase as an effective module in OPsOs.

Escherichia coli robustly expresses ATP synthase at growth rate‐maximizing concentrations

Fitness‐enhancing adaptations of protein expression and its regulation are an important aspect of bacterial evolution. A key question is whether evolution has led to optimal protein expression that maximizes immediate growth rate (short‐term fitness) in a robust manner (consistently across diverse conditions). Alternatively, they could display suboptimal short‐term fitness, because they cannot do better or because they instead strive for long‐term fitness maximization by, for instance, preparing for future conditions. To address this question, we focus on the ATP‐producing enzyme F₁F₀ H⁺‐ATPase, which is an abundant enzyme and ubiquitously expressed across conditions. Its expression is highly regulated and dependent on growth rate and nutrient conditions. For instance, during growth on sugars, when metabolism is overflowing acetate, glycolysis supplies most ATP, while H⁺‐ATPase is the main source of ATP synthesis during growth on acetate. We tested the optimality of H⁺‐ATPase expression in Escherichia coli across different nutrient conditions. In all tested conditions, wild‐type E. coli expresses its H⁺‐ATPase remarkably close (within a few per cent) to optimal concentrations that maximize immediate growth rate. This work indicates that bacteria can indeed achieve robust optimal protein expression for immediate growth‐rate maximization.

ATP Synthesis by Oxidative Phosphorylation

The F1F0-ATP synthase (EC 3.6.1.34) is a remarkable enzyme that functions as a rotary motor. It is found in the inner membranes of Escherichia coli and is responsible for the synthesis of ATP in response to an electrochemical proton gradient. Under some conditions, the enzyme functions reversibly and uses the energy of ATP hydrolysis to generate the gradient. The ATP synthase is composed of eight different polypeptide subunits in a stoichiometry of α3β3γδεab2c10. Traditionally they were divided into two physically separable units: an F1 that catalyzes ATP hydrolysis (α3β3γδε) and a membrane-bound F0 sector that transports protons (ab2c10). In terms of rotary function, the subunits can be divided into rotor subunits (γεc10) and stator subunits (α3β3δab2). The stator subunits include six nucleotide binding sites, three catalytic and three noncatalytic, formed primarily by the β and α subunits, respectively. The stator also includes a peripheral stalk composed of δ and b subunits, and part of the proton channel in subunit a. Among the rotor subunits, the c subunits form a ring in the membrane, and interact with subunit a to form the proton channel. Subunits γ and ε bind to the c-ring subunits, and also communicate with the catalytic sites through interactions with α and β subunits. The eight subunits are expressed from a single operon, and posttranscriptional processing and translational regulation ensure that the polypeptides are made at the proper stoichiometry. Recent studies, including those of other species, have elucidated many structural and rotary properties of this enzyme.

Hybrid rotors in F1Fo ATP synthases: subunit composition, distribution, and physiological significance

The c ring of the Na+ F1Fo ATP synthase from the anaerobic acetogenic bacterium Acetobacterium woodii is encoded by three different genes: atpE1, atpE2 and atpE3. Subunit c1 is similar to typical V-type c subunits and has four transmembrane helices with one ion binding site. Subunit c2 and c3 are identical at the amino acid level and are typical F-type c subunits with one ion binding site in two transmembrane helices. All three constitute a hybrid FoVo c ring, the first found in nature. To analyze whether other species may have similar hybrid rotors, we searched every genome sequence publicly available as of 23 February 2015 for F1Fo ATPase operons that have more than one gene encoding the c subunit. This revealed no other species that has three different c subunit encoding genes but twelve species that encode one Fo- and one Vo-type c subunit in one operon. Their c subunits have the conserved binding motif for Na+. The organisms are all anaerobic. The advantage of hybrid c rings for the organisms in their environments is discussed.

Assembly of F1F0-ATP synthases

F1F0-ATP synthases are multimeric protein complexes and common prerequisites for their correct assembly are (i) provision of subunits in appropriate relative amounts, (ii) coordination of membrane insertion and (iii) avoidance of assembly intermediates that uncouple the proton gradient or wastefully hydrolyse ATP. Accessory factors facilitate these goals and assembly occurs in a modular fashion. Subcomplexes common to bacteria and mitochondria, but in part still elusive in chloroplasts, include a soluble F1 intermediate, a membrane-intrinsic, oligomeric c-ring, and a membrane-embedded subcomplex composed of stator subunits and subunit a. The final assembly step is thought to involve association of the preformed F1-c10-14 with the ab2 module (or the ab8-stator module in mitochondria)--mediated by binding of subunit δ in bacteria or OSCP in mitochondria, respectively. Despite the common evolutionary origin of F1F0-ATP synthases, the set of auxiliary factors required for their assembly in bacteria, mitochondria and chloroplasts shows clear signs of evolutionary divergence. This article is part of a Special Issue entitled: Chloroplast Biogenesis.

Assembly of the Escherichia coli FoF1 ATP synthase involves distinct subcomplex formation

The ATP synthase (FoF1) of Escherichia coli couples the translocation of protons across the cytoplasmic membrane by Fo to ATP synthesis or hydrolysis in F1. Whereas good knowledge of the nanostructure and the rotary mechanism of the ATP synthase is at hand, the assembly pathway of the 22 polypeptide chains present in a stoichiometry of ab2c10α3β3γδϵ has so far not received sufficient attention. In our studies, mutants that synthesize different sets of FoF1 subunits allowed the characterization of individually formed stable subcomplexes. Furthermore, the development of a time-delayed in vivo assembly system enabled the subsequent synthesis of particular missing subunits to allow the formation of functional ATP synthase complexes. These observations form the basis for a model that describes the assembly pathway of the E. coli ATP synthase from pre-formed subcomplexes, thereby avoiding membrane proton permeability by a concomitant assembly of the open H+-translocating unit within a coupled FoF1 complex.

Production of fully assembled and active Aquifex aeolicus F1FO ATP synthase in Escherichia coli

BACKGROUND

F1FO ATP synthases catalyze the synthesis of ATP from ADP and inorganic phosphate driven by ion motive forces across the membrane. A number of ATP synthases have been characterized to date. The one from the hyperthermophilic bacterium Aquifex aeolicus presents unique features, i.e. a putative heterodimeric stalk. To complement previous work on the native form of this enzyme, we produced it heterologously in Escherichia coli.

METHODS

We designed an artificial operon combining the nine genes of A. aeolicus ATP synthase, which are split into four clusters in the A. aeolicus genome. We expressed the genes and purified the enzyme complex by affinity and size-exclusion chromatography. We characterized the complex by native gel electrophoresis, Western blot, and mass spectrometry. We studied its activity by enzymatic assays and we visualized its structure by single-particle electron microscopy.

RESULTS

We show that the heterologously produced complex has the same enzymatic activity and the same structure as the native ATP synthase complex extracted from A. aeolicus cells. We used our expression system to confirm that A. aeolicus ATP synthase possesses a heterodimeric peripheral stalk unique among non-photosynthetic bacterial F1FO ATP synthases.

CONCLUSIONS

Our system now allows performing previously impossible structural and functional studies on A. aeolicus F1FO ATP synthase.

GENERAL SIGNIFICANCE

More broadly, our work provides a valuable platform to characterize many other membrane protein complexes with complicated stoichiometry, i.e. other respiratory complexes, the nuclear pore complex, or transporter systems.

Subunit δ is the key player for assembly of the H(+)-translocating unit of Escherichia coli F(O)F1 ATP synthase

The ATP synthase (F(O)F1) of Escherichia coli couples the translocation of protons across the cytoplasmic membrane to the synthesis or hydrolysis of ATP. This nanomotor is composed of the rotor c10γε and the stator ab2α3β3δ. To study the assembly of this multimeric enzyme complex consisting of membrane-integral as well as peripheral hydrophilic subunits, we combined nearest neighbor analyses by intermolecular disulfide bond formation or purification of partially assembled F(O)F1 complexes by affinity chromatography with the use of mutants synthesizing different sets of F(O)F1 subunits. Together with a time-delayed in vivo assembly system, the results demonstrate that F(O)F1 is assembled in a modular way via subcomplexes, thereby preventing the formation of a functional H(+)-translocating unit as intermediate product. Surprisingly, during the biogenesis of F(O)F1, F1 subunit δ is the key player in generating stable F(O). Subunit δ serves as clamp between ab2 and c10α3β3γε and guarantees that the open H(+) channel is concomitantly assembled within coupled F(O)F1 to maintain the low membrane proton permeability essential for viability, a general prerequisite for the assembly of multimeric H(+)-translocating enzymes.

Cloning, expression, purification, and characterization of the membrane protein UncI from Escherichia coli

The Escherichia coli unc-operon encodes the genes for the subunits of the F0F1-ATP synthase and an integral membrane protein of unknown function called UncI. UncI influences the cell-growth and activity of F0F1, but its exact function is still unknown. The expression level is too low to extract milligram amounts of UncI from E. coli membranes and the existing purification protocol based on methanol/chloroform is not suitable for structural and functional studies. Here we present protocols to increase the expression level, to purify UncI in a detergent where UncI is monodisperse, and we characterize its oligomeric state.

Intertwined translational regulations set uneven stoichiometry of chloroplast ATP synthase subunits

The (C)F1 sector from H(+)-ATP synthases comprises five subunits: alpha, beta, gamma, delta and epsilon, assembled in a 3:3:1:1:1 stoichiometry. Here, we describe the molecular mechanism ensuring this unique stoichiometry, required for the functional assembly of the chloroplast enzyme. It relies on a translational feedback loop operating in two steps along the assembly pathway of CF1. In Chlamydomonas, production of the nucleus-encoded subunit gamma is required for sustained translation of the chloroplast-encoded subunit beta, which in turn stimulates the expression of the chloroplast-encoded subunit alpha. Translational downregulation of subunits beta or alpha, when not assembled, is born by the 5'UTRs of their own mRNAs, pointing to a regulation of translation initiation. We show that subunit gamma, by assembling with alpha(3)beta(3) hexamers, releases a negative feedback exerted by alpha/beta assembly intermediates on translation of subunit beta. Moreover, translation of subunit alpha is transactivated by subunit beta, an observation unprecedented in the biogenesis of organelle proteins.

Genetics of acid adaptation in oral streptococci

A growing body of information has provided insights into the mechanisms by which the oral streptococci maintain their niches in the human mouth. In at least one case, Streptococcus mutans, the organism apparently uses a panel of proteins to survive in acidic conditions while it promotes the formation of dental caries. Oral streptococci, which are not as inherently resistant to acidification, use protective schemes to ameliorate acidic plaque pH values. Existing information clearly shows that while the streptococci are highly related, very different strategies have evolved for them to take advantage of their particular location in the oral cavity. The picture that emerges is that the acid-adaptive regulatory mechanisms of the oral streptococci differ markedly from those used by Gram-negative bacteria. What future research must determine is the extent and complexity of the acid-adaptive systems in these organisms and how they permit the organisms to maintain themselves in the face of a low-pH environment and the microbial competition present in their respective niches.

Adaptation of oral streptococci to low pH

The strategies employed by oral streptococci to resist the inimical influences of acidification reflect the diverse and dynamic niches of the human mouth. All of the oral streptococci are capable of rapid degradation of sugar to acidic end-products. As a result, the pH value of their immediate environment can plummet to levels where glycolysis and growth cease. At this point, the approaches for survival in acid separate the organisms. Streptococcus mutans, for example, relies on its F-ATPase, to protect itself from acidification by pumping protons out of the cells. S. salivarius responds by degrading urea to ammonia and S. sanguis produces ammonia by arginolysis. The mechanisms by which these organisms regulate their particular escape route are now being explored experimentally. The picture that emerges is that the acid-adaptive regulatory mechanisms of the oral streptococci differ markedly from those employed by Gram-negative bacteria. What remains to be elucidated are the breadth of the acid-response systems in these organisms and how they permit the microbes to sustain themselves in the face of low pH and the bacterial competition present in their respective niches. In this article, we summarize reports concerning the means by which oral streptococci either utilize acidification to subdue their competitors or protect themselves until pH values return to a more favorable level.

Transcriptional regulation of the proton-translocating ATPase (atpIBEFHAGDC) operon of Escherichia coli: control by cell growth rate

The F0F1 proton-translocating ATPase complex of Escherichia coli, encoded by the atpIBEFHAGDC operon, catalyzes the synthesis of ATP from ADP and Pi during aerobic and anaerobic growth when respiratory substrates are present. It can also catalyze the reverse reaction to hydrolyze ATP during nonrespiratory conditions (i.e., during fermentation of simple sugars) in order to maintain a electrochemical proton gradient across the cytoplasmic membrane. To examine how the atp genes are expressed under different conditions of cell culture, atpI-lacZ operon fusions were constructed and analyzed in single copy on the bacterial chromosome or on low-copy-number plasmids. Expression varied over a relatively narrow range (about threefold) regardless of the complexity of the cell growth medium, the availability of different electron acceptors or carbon compounds, or the pH of the culture medium. In contrast to prior proposals, atp operon expression was shown to occur from a single promoter located immediately before atpI rather than from within it. The results of continuous-culture experiments suggest that the cell growth rate rather than the type of carbon compound used for growth is the major variable in controlling atp gene expression. Together, these studies establish that synthesis of the F0F1 ATPase is not greatly varied by modulating atp operon transcription.

Degradation of Escherichia coli uncB mRNA by multiple endonucleolytic cleavages

The mechanism of segmental decay of the uncB sequence near the 5' end of the 7-kb Escherichia coli unc operon mRNA was investigated. Northern (RNA) blots of mRNA expressed from a plasmid carrying the uncBE portion of the operon revealed that the uncB message was rapidly degraded by multiple internal cleavages which resulted in the formation of at least five discrete species having a common 3' end. Turnover studies indicated that processing rapidly converted all species to the smallest. Identification of the 5' ends by primer extension analysis revealed that the cleavages were made either in the uncB coding region or in the intercistronic region between uncB and uncE, the latter being the most 3' cleavage. An rne mutant strain contained much higher levels of the uncBE message, implying that RNase E, the product of the rne gene, is essential for the normal degradation of uncB, and a number of the 5' ends were not detected in the rne mutant. The cleavage sites in chromosomally encoded unc mRNA were also identified by primer extension. These studies reveal that the segmental decay of the uncB region of unc mRNA occurs rapidly through a series of endonucleolytic cleavages. The rapid decay of uncB is expected to play a role in limiting expression of this gene relative to that of the other genes of the operon.

Prokaryotic translation: the interactive pathway leading to initiation

Finding answers to the many open questions concerning the mechanism and control of prokaryotic translation remains one of the central challenges of molecular biology. In fact, recent experimental data even force us to reconsider aspects that were previously thought to be established fact. Here, we attempt a synthesis of new and not-so-new information, which leads to a revised and testable working hypothesis for translational initiation.

Effects of deletions in the uncA-uncG intergenic regions on expression of uncG, the gene for the gamma subunit of the Escherichia coli F1Fo-ATPase

The gamma subunit of the E. coli F1Fo-ATPase is coded for by uncG. This gene is poorly expressed compared to uncA (alpha subunit), which precedes uncG in the unc operon. The genes are separated by a 50-nucleotide intergenic region. We examined the effects of a set of deletions in this region on the relative expression of uncA'-'lacZ and uncG'-'lacZ translational fusion genes located either in the chromosomal unc operon or at the chromosomal lambda att site. The gene for the alpha subunit was expressed 3-6-times better than the gene for the gamma subunit, depending upon chromosomal location. Deletion analysis revealed that the uncA-uncG intergenic region significantly affects expression of uncG, but the Shine-Dalgarno region is not absolutely required for expression of uncG. Different deletions resulted in either increased or decreased expression of uncG.

Assembly of the Escherichia coli F1F0 ATPase, a large multimeric membrane-bound enzyme

The F1F0 proton translocating ATPase of Escherichia coli is a large membrane-bound enzyme complex consisting of more than 20 polypeptides that are encoded by the unc operon. Besides being a system for analysing the enzymology of ATP synthesis and energy coupling, the ATPase is a model system for determining how large oligomeric membrane-bound proteins are synthesized and assembled. The assembly of the ATPase involves differential gene expression and assembly of the subunits within the membrane and with each other. This review discusses the influence of F1 subunits on the assembly and proton permeability of the F0 proton channel, and the possible advantages to assembly of the particular arrangement of genes in the unc operon.

RNase E-dependent cleavages in the 5' and 3' regions of the Escherichia coli unc mRNA

The endonucleolytic processing of the unc mRNA encoding the eight subunits of the Escherichia coli F1F0-ATPase was studied. Northern (RNA) blots of mRNA expressed from a plasmid which contained the 3'-terminal portion of the operon including the uncDC sequences revealed, in addition to the expected 2-kb mRNA, a 0.5-kb RNA species which hybridized to an uncC antisense RNA probe. An uncD antisense RNA probe hybridized to only the 2-kb mRNA, implying that the upstream 1.5-kb fragment is rapidly degraded. The 5' end of the 0.5-kb fragment was determined by primer extension analysis to be 11 bases into the coding region of the uncC gene. In RNase E-deficient strains, the amount of the 0.5-kb product was strongly reduced while the levels of the precursor uncDC transcript remained high. Similar RNase E-dependent processing was found in the chromosomally encoded unc mRNA. As this RNase E-dependent cleavage directly inactivates uncC and appears to leave uncD susceptible to degradation, it seems unlikely to play a role in differential expression of the gene products but may be an important event in unc mRNA degradation. RNase E mutants also showed altered processing of the chromosomally encoded unc mRNA in the uncB region near the 5' end. The expected full-length (7-kb) transcript was recognized when RNA from the RNase E-deficient strain was subjected to Northern blot analysis with uncB- and uncC-specific probes. RNA from strains with functional RNase E lacked the 7-kb transcript but had a 6.2-kb mRNA detectable with the uncC but not the uncB probe. RNase E is therefore implicated in multiple cleavages of the unc mRNA.

Effects of inducing expression of cloned genes for the F0 proton channel of the Escherichia coli F1F0 ATPase

To evaluate whether expression of cloned genes for the F0 proton channel of the Escherichia coli F1F0 ATPase is sufficient to cause membrane proton permeability, plasmids carrying different combinations of the uncB, E, and F genes, encoding the a, c, and b subunits of the F0 sector, cloned behind the inducible lac promoter in pUC9 or pUC18, were constructed. The effects of inducing F0 synthesis in an unc deletion strain were monitored by measuring cell growth rate, quantitating F0 subunits by immunoblotting, and measuring the ability of membranes to maintain a respiration-induced proton gradient and to bind F1 and carry out energy-coupling reactions. The levels of functional reconstitutable F0 in membranes could be increased four- to sixfold with no change in cellular growth rate or membrane proton permeability (assayed by fluorescence quenching). These results were obtained in uninduced cultures, so the F0 genes were presumably being transcribed from some promoter besides lac. Induction of transcription of all three F0 genes produced increased amounts of F0 subunits in membranes as determined by immunoblot and F1-binding assays, but, when reconstituted with F1, the F0 in membranes isolated from induced cultures was significantly less functional than the F0 in membranes isolated from uninduced cultures. Such induction did result in growth inhibition, but there was no correlation between growth inhibition and either increased membrane proton permeability or the presence of functional, reconstitutable F0.

Structures of chaperonins from an intracellular symbiont and their functional expression in Escherichia coli groE mutants

An intracellular symbiont harbored by the aphid bacteriocyte, a specialized fat body cell, synthesizes in vivo substantially only one protein, symbionin, which is a member of the chaperonin-60 family of molecular chaperones. Nucleotide sequence determination of the symbionin region of the endosymbiont genome revealed that it contains the two-cistron operon sym. Just like the Escherichia coli groE operon, the sym operon was dually led by a heat shock and an ordinary promoter sequence. According to the nucleotide sequence, symbionin was 85.5% identical to GroEL of E. coli at the amino acid sequence level. SymS, another protein encoded in the sym operon, which is a member of chaperonin-10, was 79.6% identical to GroES. Complementation experiments with E. coli groE mutants showed that the chaperonin-10 and chaperonin-60 genes from the endosymbiont are expressed in E. coli and that they can function as molecular chaperones together with endogenous GroEL and GroES, respectively.

Translational coupling varying in efficiency between different pairs of genes in the central region of the atp operon of Escherichia coli

A series of atp::lacZ fusions has been constructed for use in a study of translational coupling in the central region of the Escherichia coli atp operon. Five genes, atpE, atpF, atpH, atpA and atpG, were shown to be translationally coupled to various degrees of tightness. A new lac promoter vector, compatible with the atp::lacZ fusion vectors, was used to express individual atp genes in the same hosts as the fusion genes. The H(+)-ATPase subunits thus synthesized exercised no significant trans-regulation on the expression of the atp::lacZ fusions, indicating that the coupling is primarily cis. The mechanism of this coupling was investigated using in vitro mutagenesis. At least in the case of the pair atpHA, coupling seems to involve facilitated binding of fresh ribosomes to the atpA translational initiation regions.

Post-transcriptional control in the polycistronic operon environment: studies of the atp operon of Escherichia coli

Post-transcriptional control mechanisms assume special significance in polycistronic operons. Differential gene expression in the atp operon of Escherichia coli is primarily attributable to translational control and, to a lesser extent, to control of mRNA stability. At the same time, the polycistronic environment influences, to varying degrees, the relative importance of the different types of post-transcriptional control. The present article briefly reviews more recent results obtained through studies of the atp operon. Investigations of the pathway and kinetics of mRNA decay have yielded new information about the role of degradative mechanisms in the overall scheme of control. Moreover, translational coupling has been shown to feature as a major form of interaction between the atp genes. The relevance of these and other data is discussed in the wider context of the post-transcriptional control mechanisms generally available to E. coli.

An upstream uncD sequence modulates translation of Escherichia coli uncC

The effect of upstream uncD sequences on expression of the Escherichia coli uncC gene, encoding the epsilon subunit of F1-ATPase, was studied. uncC expression was reduced severalfold in plasmid constructs bearing, in addition to uncC, a region of uncD located between 85 and 119 bases upstream from the uncC initiation codon. This reduction was independent of in-frame translation of the uncD sequences. An mRNA stem-loop structure in which sequences located within the inhibitory region of uncD base pair with the uncDC intercistronic region is suggested to function in modulating uncC expression.

Ribosomal affinity and translational initiation in Escherichia coli. In vitro investigations using translational initiation regions of differing efficiencies from the atp operon

The atp operon of Escherichia coli comprises nine genes that are differentially expressed. The control of the atp genes' expression rates has been shown to be exercised primarily at the level of translational initiation, but how is this achieved in molecular terms? In order to study the interactions of 30 S ribosomal subunits with specifically the translational initiation regions (TIRs) of atpB, atpE and atpG, restriction fragments bearing these TIRs were excised from the atp operon and cloned into an SP6 promoter transcription vector. mRNA transcripts were made in vitro and used in primer extension inhibition studies and equilibrium mRNA-30 S ribosomal subunit binding measurements. The binding of 30 S ribosomal subunits blocked primer extension 14 to 15 bases downstream from the respective translational start codons. The affinities of binding of 30 S ribosomal subunits showed the relationship atpE greater than atpB greater than atpG. This was also the order of the efficiency of translation promoted by the respective TIRs, both in vivo and on the in vitro synthesized mRNA fragments. Thus, the affinity of 30 S ribosomal subunits is at least to some extent correlated with the rate of translational initiation.

Ribosome-binding sites and RNA-processing sites in the transcript of the Escherichia coli unc operon

The polycistronic mRNA encoding the nine genes of the unc operon of Escherichia coli was studied. We demonstrated the ribosome-binding capabilities of six of the nine unc genes, uncB, uncE, uncF, uncH, uncA, and uncD, by using the technique of primer extension inhibition or "toeprinting." No toeprint was detected for the other genes, uncI, uncG, and uncC. The lack of a toeprint for uncG suggests that this gene is expressed by some form of translational coupling, such that either uncG is read by ribosomes which have translated the preceding gene, uncA, or translation of uncA is required for ribosome binding at the uncG site. RNA sequencing and primer extension in the regions of uncI and uncC, the first and last genes in the operon, respectively, gave less intense signals than those obtained for the other unc genes. This suggested that there are fewer copies of those regions of the transcript and that processing of the unc transcript occurred. Using primer extension and RNA sequencing, we identified sites in the unc transcript at which processing appears to take place, including a site which may remove much of the uncI portion of the transcript. Northern (RNA) blot analysis of unc RNA is consistent with the presence of an RNA-processing site in the uncI region of the transcript and another in the uncH region. These processing events may account for some of the differential levels of expression of the unc genes.

Independent and coupled translational initiation of atp genes in Escherichia coli: experiments using chromosomal and plasmid-borne lacZ fusions

The translational initiation rates directed by the translational initiation regions (TIRs) of the atpB, atpH, atpA and atpG genes of Escherichia coli were investigated using lacZ fusions present on plasmids as well as integrated into the chromosome. This was the first investigation of the translational efficiency of the atpB gene, whose unfused product (subunit a) can be toxic to the cell. The specific mRNA levels, rates of in vivo protein synthesis and beta-galactosidase activities encoded by the atp::lacZ fusions were compared in order to obtain valid estimates of relative translation rates. The results indicate that in the E. coli atp operon, translation directed by the atpB, atpH and atpG TIRs is less efficient than that directed by the atpA TIR, and are thus consistent with earlier measurements of direct atp gene expression. Initiation is, however, to differing extents, controlled by coupling to the translation of upstream neighbours. There is particularly tight coupling between atpH and atpA. Increasing the distance between these two genes whilst maintaining the original atpA TIR structure decreased the degree of coupling. The influence of manipulations of the atpG TIR structure upon translational efficiency was quantitatively more pronounced when the atpG fusions were present as a single copy per chromosome. This is likely to be related to the mRNA binding characteristics of 30S ribosomal subunits and/or to the influence of other (trans-acting) factors. The control of independent and coupled initiation at the atp TIRs is discussed in relation to mRNA structure and possible cis and trans regulatory phenomena.

The role of bases upstream of the Shine-Dalgarno region and in the coding sequence in the control of gene expression in Escherichia coli: translation and stability of mRNAs in vivo

A range of translational initiation regions (TIR) was created by combining synthetic DNA fragments derived from the atpB-atpE intercistronic sequence of Escherichia coli with the cDNA sequence encoding mature human interleukin 2 (IL-2), the E. coli fnr gene, or an fnr::lacZ gene fusion. Both the overall rates of gene expression and the relative concentrations and stabilities of the corresponding mRNA species were estimated in strains bearing the constructs on plasmids. These measurements served as the basis for analyses of the relationship between the structure of the TIR and the true rates of translation that it promotes. The constructs involving the IL-2 cDNA were predicted to allow much less stable secondary structure within the TIR than those involving the N-terminal region of the fnr gene. Thus by combining one set of upstream sequences with two different types of N-terminal coding sequence, it was possible to distinguish between the respective influences of primary and secondary structure upon initiation. The data indicate that in the presence of a given Shine-Dalgarno (SD)/start codon combination, the decisive factor for translational initiation efficiency is the stability of base pairing involving, or in the vicinity of, this region. The sequences contributing to this secondary structure can be many bases upstream of the SD region and/or downstream of the start codon. There was no indication that the specific base sequence upstream of the SD region could, other than to the extent that it contributed to the local secondary structure, significantly influence the efficiency of translational initiation.

Post-transcriptional control in Escherichia coli: translation and degradation of the atp operon mRNA

An attractive subject for investigations of post-transcriptional control is the atp operon, whose nine genes are differentially expressed. The primary mode of control of atp gene expression is exercised at the translational level. It has been clearly demonstrated for almost all of the atp genes that the primary and secondary structures of their respective translational initiation regions direct translational initiation rates that correspond well to the requirements for these subunits in the cell. The relationship between the structure of the translational initiation region, including bases upstream from the Shine-Dalgarno region and downstream from the start codon, and the rates of initiation that it determines, has been investigated in more detail using various polycistronic and monocistronic systems. No evidence could be found for a role of codon usage bias in controlling overall translation rates. The functional half-lives of atpE and of the other six cistrons downstream from it are similar. The chemical stabilities of the first two cistrons of the polycistronic atp mRNA may, however, be lower, and we are investigating the possibility that there may also be control of atp gene expression exercised at the level of mRNA stability. The effects of manipulations of the intercistronic regions of at least the plasmid borne atp operon are consistent with a model of mRNA decay in which rate control is associated with endonucleolytic cleavages within individual cistrons. The experimental data are discussed in relation to the possible ways in which primary and secondary structures of the mRNA might control translational efficiency and stability.

DNA sequence of a gene cluster coding for subunits of the F0 membrane sector of ATP synthase in Rhodospirillum rubrum. Support for modular evolution of the F1 and F0 sectors

A region was cloned from the genome of the purple non-sulphur photobacterium Rhodospirillum rubrum that contains genes coding for the membrane protein subunits of the F0 sector of ATP synthase. The clone was identified by hybridization with a synthetic oligonucleotide designed on the basis of the known protein sequence of the dicyclohexylcarbodi-imide-reactive proteolipid, or subunit c. The complete nucleotide sequence of 4240 bp of this region was determined. It is separate from an operon described previously that encodes the five subunits of the extrinsic membrane sector of the enzyme, F1-ATPase. It contains a cluster of structural genes encoding homologues of all three membrane subunits a, b and c of the Escherichia coli ATP synthase. The order of the genes in Rsp. rubrum is a-c-b'-b where b and b' are homologues. A similar gene arrangement for F0 subunits has been found in two cyanobacteria, Synechococcus 6301 and Synechococcus 6716. This suggests that the ATP synthase complexes of all these photosynthetic bacteria contain nine different polypeptides rather than eight found in the E. coli enzyme; the chloroplast ATP synthase complex is probably similar to the photosynthetic bacterial enzymes in this respect. The Rsp. rubrum b subunit is modified after translation. As shown by N-terminal sequencing of the protein, the first seven amino acid residues are removed before or during assembly of the ATP synthase complex. The subunit-a gene is preceded by a gene coding for a small hydrophobic protein, as has been observed previously in the atp operons in E. coli, bacterium PS3 and cyanobacteria. A number of features suggest that the Rsp. rubrum cluster of F0 genes is an operon. On its 5' side are found sequences resembling the -10 (Pribnow) and -35 boxes of E. coli promoters, and the gene cluster is followed by a sequence potentially able to form a stable stem-loop structure, suggesting that it acts as a rho-independent transcription terminator. These features and the small intergenic non-coding sequences suggest that the genes are cotranscribed, and so the name atp2 is proposed for this second operon coding for ATP synthase subunits in Rsp. rubrum. The finding that genes for the F0 and F1 sectors of the enzyme are in separate clusters supports the view that these represent evolutionary modules.

Determinants of translational initiation efficiency in the atp operon of Escherichia coli

Transcription and translation of the atp genes encoding the subunits b, delta, alpha, gamma and epsilon of the Escherichia coli H+-ATPase were studied. The nature and quantities of the respective transcripts initiated from different promoters were compared with overall expression rates thus yielding accurate information about relative translational efficiency and its coupling to mRNA levels. Part of the highly efficient subunit c gene translational initiation region (TIR) was used as a tool in manipulating the TIRs of the other genes. Rate control of atp cistron translation occurs at the initiation level and is determined locally by each gene's TIR. In this way, individual subunit synthesis rates are set to match the requirements for H+-ATPase assembly. There is no (or very restricted) translational coupling between the cistrons. Translational initiation rates of the normally weakly expressed atp genes could be increased by up to a factor of 27 by manipulating the sequences upstream of the start codons, despite biased codon usages. In the presence of an improved upstream sequence, the N-terminal sequence of the subunit gamma gene exerted a limiting effect. This could be relieved by altering the sequence of the first seven codons. The levels of subunit gamma mRNA were more sensitive to changes in translational efficiency than the concentrations of the other atp mRNAs. The relationships between initiation efficiency and primary and secondary structure in the natural and manipulated atp TIRs are discussed in detail.