The genes for the eight subunits of the membrane bound ATP synthase of Escherichia coli

The segregation of Escherichia coli minichromosomes constructed in vivo by recombineering

Circularized regions of the chromosome containing the origin of replication, oriC, can be maintained as autonomous minichromosomes, oriC plasmids. We show that oriC plasmids containing precise, pre-determined segments of the chromosome can be generated by a simple in vivo recombineering technique. We generated two such plasmids carrying fluorescent markers. These were transferred to a recipient strain with a different fluorescent marker near the chromosomal copy of oriC. Thus the fates of the oriC plasmid and chromosomal origins could be followed independently in living cells by fluorescence microscopy. In contrast to a previous report, we show that there is a strong tendency of oriC plasmid copies to accumulate at the cell center as a single or double focus at the plane of cell division. This is not simply due to exclusion from the nucleoid space but rather appears to be a specific recognition and retention of the plasmid by some central-located cell site.

Genomic features and insights into the biology of Mycoplasma fermentans

We present the complete genomic sequence of Mycoplasma fermentans, an organism suggested to be associated with the pathogenesis of rheumatoid arthritis in humans. The genome is composed of 977 524 bp and has a mean G+C content of 26.95 mol%. There are 835 predicted protein-coding sequences and a mean coding density of 87.6 %. Functions have been assigned to 58.8 % of the predicted protein-coding sequences, while 18.4 % of the proteins are conserved hypothetical proteins and 22.8 % are hypothetical proteins. In addition, there are two complete rRNA operons and 36 tRNA coding sequences. The largest gene families are the ABC transporter family (42 members), and the functionally heterogeneous group of lipoproteins (28 members), which encode the characteristic prokaryotic cysteine ‘lipobox’. Protein secretion occurs through a pathway consisting of SecA, SecD, SecE, SecG, SecY and YidC. Some highly conserved eubacterial proteins, such as GroEL and GroES, are notably absent. The genes encoding DnaK-DnaJ-GrpE and Tig, forming the putative complex of chaperones, are intact, providing the only known control over protein folding. Eighteen nucleases and 17 proteases and peptidases were detected as well as three genes for the thioredoxin-thioreductase system. Overall, this study presents insights into the physiology of M. fermentans, and provides several examples of the genetic basis of systems that might function as virulence factors in this organism.

Comparative genome analysis of "Candidatus Phytoplasma australiense" (subgroup tuf-Australia I; rp-A) and "Ca. Phytoplasma asteris" Strains OY-M and AY-WB

The chromosome sequence of "Candidatus Phytoplasma australiense" (subgroup tuf-Australia I; rp-A), associated with dieback in papaya, Australian grapevine yellows in grapevine, and several other important plant diseases, was determined. The circular chromosome is represented by 879,324 nucleotides, a GC content of 27%, and 839 protein-coding genes. Five hundred two of these protein-coding genes were functionally assigned, while 337 genes were hypothetical proteins with unknown function. Potential mobile units (PMUs) containing clusters of DNA repeats comprised 12.1% of the genome. These PMUs encoded genes involved in DNA replication, repair, and recombination; nucleotide transport and metabolism; translation; and ribosomal structure. Elements with similarities to phage integrases found in these mobile units were difficult to classify, as they were similar to both insertion sequences and bacteriophages. Comparative analysis of "Ca. Phytoplasma australiense" with "Ca. Phytoplasma asteris" strains OY-M and AY-WB showed that the gene order was more conserved between the closely related "Ca. Phytoplasma asteris" strains than to "Ca. Phytoplasma australiense." Differences observed between "Ca. Phytoplasma australiense" and "Ca. Phytoplasma asteris" strains included the chromosome size (18,693 bp larger than OY-M), a larger number of genes with assigned function, and hypothetical proteins with unknown function.

Identification of four genes of the Brucella melitensis ATP synthase operon F0 sector: relationship with the Rhodospirillaceae family

We have determined the nucleotide sequence of a cloned DNA fragment from the human and animal pathogen Brucella melitensis. Four genes were identified from a 4069 bp fragment, corresponding to the B. melitensis a, c, b', and b subunits of the ATP synthase F0 sector operon. A duplicated and divergent copy of the b-subunit gene was observed. This feature has been found only in photosynthetic bacteria and chloroplasts. In addition, the gene cluster was separated from the F1 sector, a characteristic described only for the Rhodospirillaceae family.

Bacillus subtilis F0F1 ATPase: DNA sequence of the atp operon and characterization of atp mutants

We cloned and sequenced an operon of nine genes coding for the subunits of the Bacillus subtilis F0F1 ATP synthase. The arrangement of these genes in the operon is identical to that of the atp operon from Escherichia coli and from three other Bacillus species. The deduced amino acid sequences of the nine subunits are very similar to their counterparts from other organisms. We constructed two B. subtilis strains from which different parts of the atp operon were deleted. These B. subtilis atp mutants were unable to grow with succinate as the sole carbon and energy source. ATP was synthesized in these strains only by substrate-level phosphorylation. The two mutants had a decreased growth yield (43 and 56% of the wild-type level) and a decreased growth rate (61 and 66% of the wild-type level), correlating with a twofold decrease of the intracellular ATP/ADP ratio. In the absence of oxidative phosphorylation, B. subtilis increased ATP synthesis through substrate-level phosphorylation, as shown by the twofold increase of by-product formation (mainly acetate). The increased turnover of glycolysis in the mutant strain presumably led to increased synthesis of NADH, which would account for the observed stimulation of the respiration rate associated with an increase in the expression of genes coding for respiratory enzymes. It therefore appears that B. subtilis and E. coli respond in similar ways to the absence of oxidative phosphorylation.

Carbon and energy metabolism of atp mutants of Escherichia coli

The membrane-bound H(+)-ATPase plays a key role in free-energy transduction of biological systems. We report how the carbon and energy metabolism of Escherichia coli changes in response to deletion of the atp operon that encodes this enzyme. Compared with the isogenic wild-type strain, the growth rate and growth yield were decreased less than expected for a shift from oxidative phosphorylation to glycolysis alone as a source of ATP. Moreover, the respiration rate of a atp deletion strain was increased by 40% compared with the wild-type strain. This result is surprising, since the atp deletion strain is not able to utilize the resulting proton motive force for ATP synthesis. Indeed, the ratio of ATP concentration to ADP concentration was decreased from 19 in the wild type to 7 in the atp mutant, and the membrane potential of the atp deletion strain was increased by 20%, confirming that the respiration rate was not controlled by the magnitude of the opposing membrane potential. The level of type b cytochromes in the mutant cells was 80% higher than the level in the wild-type cells, suggesting that the increased respiration was caused by an increase in the expression of the respiratory genes. The atp deletion strain produced twice as much by-product (acetate) and exhibited increased flow through the tricarboxylic acid cycle and the glycolytic pathway. These three changes all lead to an increase in substrate level phosphorylation; the first two changes also lead to increased production of reducing equivalents. We interpret these data as indicating that E. coli makes use of its ability to respire even if it cannot directly couple this ability to ATP synthesis; by respiring away excess reducing equivalents E. coli enhances substrate level ATP synthesis.

Expression of the unc genes in Escherichia coli

The unc (or atp) operon of Escherichia coli comprises eight genes encoding the known subunits of the proton-translocating ATP synthase (H+-ATPase) plus a ninth gene (uncI) of unknown function. The subunit stoichiometry of the H+-ATPase (alpha 3 beta 3 gamma 1 delta 1 epsilon 1 a1b2c10-15) requires that the respective unc genes be expressed at different rates. This review discusses the experimental methods applied to determining how differential synthesis is achieved, and evaluates the results obtained. It has been found that the primary level of control is translational initiation. The translational efficiencies of the unc genes are determined by primary and secondary mRNA structures within their respective translational initiation regions. The respective rates of translation are matched to the subunit requirements of H+-ATPase assembly. Finally, points of uncertainty remain and experimental strategies which will be important in future work are discussed.

Subunit composition of the H+-ATPase complex from anaerobic bacterium Lactobacillus casei

The H+-ATPase complex has been isolated from the membranes of the anaerobic bacterium Lactobacillus casei by two independent methods. 1. The crossed-immunoelectrophoresis of the 14C-labelled ATPase complex against antibodies to a highly purified soluble ATPase has been used. The subunit composition of the complex has been established by autoradiography. The soluble part of L. casei ATPase, in contrast to coupling factor F1-ATPases of aerobic bacteria, chloroplasts and mitochondria which include two kinds of large subunit (alpha and beta), consists of one kind of large subunit with a molecular mass of 43 kDa. Moreover, a minor polypeptide of 25 kDa has been found in the soluble ATPase. Factor F0 of L. casei ATPase complex consists of a 16-kDa subunit and two subunits with molecular masses less than 14 kDa. 2. A dicyclohexylcarbodiimide-sensitive ATPase complex has been isolated from L. casei membranes by treating them with a mixture of octyl glucoside and sodium cholate. The complex, purified by centrifugation on a sucrose density gradient, contains the main subunits with molecular masses of 43 kDa, 25 kDa and 16 kDa and a dicyclohexylcarbodiimide-binding subunit with a molecular mass less than 14 kDa.

An antibody-binding site in the native enzyme between amino acid residues 205-287 of the gamma-subunit of F1 from Escherichia coli

A monoclonal antibody was isolated specific for the isolated denatured gamma-subunit of F1 from Escherichia coli and binding to native F1. The binding site of this antibody was identified between amino acid residues 205-287 of the polypeptide chain thus being located at the surface of the F1 complex.

Topological studies suggest that the pathway of the protons through F0 is provided by amino acid residues accessible from the lipid phase

The structure of the F0 part of ATP synthases from E. coli and Neurospora crassa was analyzed by hydrophobic surface labeling with [125I]TID. In the E. coli F0 all three subunits were freely accessible to the reagent, suggesting that these subunits are independently integrated in the membrane. Labeled amino acid residues were identified by Edman degradation of the dicyclohexylcarbodiimide binding (DCCD) proteins from E. coli and Neurospora crassa. The very similar patterns obtained with the two homologous proteins suggested the existence of tightly packed alpha-helices. The oligomeric structure of the DCCD binding protein appeared to be very rigid since little, if any, change in the labeling pattern was observed upon addition of oligomycin or DCCD to membranes from Neurospora crassa. When membranes were pretreated with DCCD prior to the reaction with [125I]TID an additionally labeled amino acid appeared at the position of Glu-65 which binds DCCD covalently, indicating the location of this inhibitor on the outside of the oligomer. It is suggested that proton conduction occurs at the surface of the oligomer of the DCCD binding protein. Possibly this oligomer rotates against the subunit alpha or beta and thus enables proton translocation. Conserved residues in subunit alpha, probably located in the lipid bilayer, might participate in the proton translocation mechanism.

Structure and function of the ATPase-ATP synthase complex of mitochondria as compared to chloroplasts and bacteria

An overview of the structure and function of the mitochondrial ATPase-ATP synthase complex is presented. Attempts are made to identify the analogies and differences between mitochondrial, chloroplastic and bacterial complexes. The relatively more precise information available on the structure of the E. coli enzyme is used to try and understand the apparently more complex structure of the mitochondrial enzyme. Recent ideas on the mechanism of ATP hydrolysis and ATP synthesis will be summarized.

Synthesis of maize chloroplast ATP-synthase beta-subunit fusion proteins in Escherichia coli and binding to the inner membrane

The maize chloroplast gene for the beta subunit (atpB) of the chloroplast CF1 component of ATPase from maize, when fused to either the lacZ or ral genes in the vectors pMC1403 or pHUB4, is expressed in Escherichia coli as a fusion protein with beta-galactosidase or with bacteriophage lambda Ral sequences. Some of the fusion proteins are converted to a membrane-bound form, as determined by differential and sucrose-gradient centrifugation. The specificity of membrane binding has been examined using E. coli unc mutants that are defective in binding of the F1 ATPase component to the F0 receptor site on the membrane, and by the use of two different length maize atpB::lacZ gene fusions. We show that the first 365 N-terminal amino acids (aa) of the maize beta subunit are involved in binding to the E. coli inner membrane, and that this binding is probably mediated by the bacterial F0 receptor.

Nucleotide sequence of the Rhodospirillum rubrum atp operon

The nucleotide sequence was determined of a 8775-base-pair region of DNA cloned from the photosynthetic non-sulphur bacterium Rhodospirillum rubrum. It contains a cluster of five genes encoding F1-ATPase subunits. The genes are arranged in the same order as F1 genes in the Escherichia coli unc operon. However, as in the related organism Rhodopseudomonas blastica, neither genes for components of F0, the membrane sector of ATP synthase, nor a homologue of the E. coli uncI gene are associated with this locus, as they are in E. coli.

DNA sequence around the Escherichia coli unc operon. Completion of the sequence of a 17 kilobase segment containing asnA, oriC, unc, glmS and phoS

The nucleotide sequence is described of a region of the Escherichia coli chromosome extending from oriC to phoS that also includes the loci gid, unc and glmS. Taken with known sequences for asnA and phoS this completes the sequence of a segment of about 17 kilobases or 0.4 min of the E. coli genome. Sequences that are probably transcriptional promoters for unc and phoS can be detected and the identity of the unc promoter has been confirmed by experiments in vitro with RNA polymerase. Upstream of the promoter sequence is an extensive region that appears to be non-coding. Conserved sequences are found that may serve to concentrate RNA polymerase in the vicinity of the unc promoter. Hairpin loop structures resembling known rho-independent transcription termination signals are evident following the unc operon and glmS. The glmS gene encoding the amidotransferase, glucosamine synthetase, has been identified by homology with glutamine 5-phosphoribosylpyrophosphate amidotransferase.

Structure of the membrane-embedded F0 part of F1F0 ATP synthase from Escherichia coli as inferred from labeling with 3-(Trifluoromethyl)-3-(m-[125I]iodophenyl)diazirine

3-(Trifluoromethyl)-3-(m-[125I]iodophenyl)diazirine [( 125I]TID) is a photoactivatable carbene precursor designed to label selectively the hydrophobic core of membranes. We have used this reagent to obtain information on the topological organization of the membrane-embedded subunits of F1F0 ATP synthase from Escherichia coli. The study included [125I]TID labeling of F0 subunits in different structural (conformational) states and Edman degradations of the labeled polypeptides in order to assign the covalently bound radioactivity to individual amino acid residues. Released phenylthiohydantoin amino acids were analyzed by thin-layer chromatography, and the radioactive derivatives were visualized by autoradiography. The data suggest that labeling patterns can be correlated in a meaningful manner with reagent accessibility and hence with protein-lipid contact. Subunit b appears to be anchored to the membrane by a short N-terminal segment. As almost all of the amino acids of this part are accessible to the reagent, it is inferred that this segment has little interaction with the other subunits. In contrast, in the two segments of subunit c that were labeled with [125I]TID, only certain amino acids reacted with the label. The pattern of these labeled residues is compatible with that of tightly packed alpha-helices.

Rhodopseudomonas blastica atp operon. Nucleotide sequence and transcription

The nucleotide sequence has been determined of a 12,368 base-pair region of DNA cloned from the non-sulphur photosynthetic bacterium Rhodopseudomonas blastica. It contains a cluster of six genes of which five encode the subunits of F1-ATPase; the sixth codes for an unknown protein. The genes are arranged in the same order as in the Escherichia coli unc operon, except that the unknown gene is placed between those for gamma and beta subunits. Neither the genes for F0 subunits, nor a homologue of the E. coli uncI gene is associated with this locus. The six genes are transcribed from a single promoter and we have designated this region the R. blastica atp operon. The two distal genes, beta and epsilon, may also be transcribed from a second promoter. Initiation and termination points for transcription have been identified by primer extensions and S1 nuclease mapping experiments. Signals involved in initiation of translation (Shine and Dalgarno sequences) and termination of transcription in the photosynthetic bacterium resemble those in E. coli. However, no common features can be identified in these two bacteria between 5' regions adjacent to sites of initiation of transcription. The sequence also contains a gene that encodes a protein homologous to discoidin, a cell surface lectin of Dictyostelium discoideum thought to be involved in cell--cell aggregation. Seven other reading frames have not been identified.

The DCCD-reactive aspartyl-residue of subunit C from the Escherichia coli ATP-synthase is important for the conformation of F0

The effect of various point mutations in subunits a and and c of the E. coli ATP-synthase was characterized. In each of the mutants there was no F0-dependent H+-conduction, but still an ATPase-activity comparable to wildtype activities. In addition, the subunit b could be extracted from the mutant's F0 but not from the F0 of wildtype. The effects are interpreted as a change in the conformation of F0 caused by the different mutations.

The promoters of the atp operon of Escherichia coli K12

The nucleotide sequence has been determined of a 900 bp segment of chromosomal DNA located between 2.6 and 3.5 kb left of the origin of replication, oriC. This segment, which overlaps with the known sequence of the atp operon coding for the eight subunits of the Escherichia coli K12 ATP synthase, contains two coding sequences with the same polarity (counterclockwise) as the atp genes: One of these, designated atpI, which codes for the N-terminal part of a 14 kD polypeptide, is located in front (upstream) of the atpB gene (the first structural gene in the atp operon), the other one codes for the C-terminal part of the gidB gene. The 606 bp segment located between the gidB and the atpI genes contains no coding sequences. By employing the nuclease S1 mapping technique, we have determined a promoter, designated atpIp, for the atp operon located in front of the atpI gene; two additional, weak transcription starts were located within the atpI gene. No transcription start sites were detected up to 1,000 bp upstream of the atpIp promoter, neither were any transcription start sites detected within the cluster of the eight structural atp genes. The atp operon transcription terminates at a site approximately 50 bp downstream from the atpC gene.

Cloning and expression of uncI, the first gene of the unc operon of Escherichia coli

The unc operon of Escherichia coli consists of eight genes coding for the eight subunits of the proton-translocating ATPase. In vitro transcription-translation of DNA cloned from the beginning of the operon onto plasmids reveals that the reading frame uncI, which precedes the other genes of the operon, codes for a protein with a molecular weight of 14,500, called i. In minicells, the i protein is synthesized in amounts comparable to the amounts of the ATPase subunits, suggesting that it may be part of the ATPase complex. The presence of the unc promoter and uncI on a plasmid containing the other eight genes of the unc operon has little effect on the differential expression of the unc genes or the partitioning of the newly synthesized subunits into soluble or sedimentable fractions in the in vitro system. The i protein partitions into the sedimentable fraction.

Escherichia coli minichromosomes containing the pSC101 partitioning locus are stably inherited

The par region of pSC101, required in cis to promote its stable inheritance, was joined, in combination with the tetr determinant of pBR325, to large and small minichromosomes. These hybrid minichromosomes were examined for stability and found to be no more stable than their parent minichromosomes. Indeed, one recombinant plasmid, pEH21, showed reduced stability, which was not attributable to a reduced copy number. Neither pEH21 nor pEH22, a plasmid composed of the same DNA arranged differently, was stabilized by the presence of a Par+ pSC101 derived replicon in the same cell. We conclude that the par region of pSC101 does not stabilize minichromosomes.

Escherichia coli mutants defective in the uncH gene

Plasmids carrying cloned segments of the unc operon of Escherichia coli have been used in genetic complementation analyses to identify three independent mutants defective in the uncH gene, which codes for the delta subunit of the ATP synthetase. Mutations in other unc genes have also been mapped by this technique. ATPase activity was present in extracts of the uncH mutants, but the enzyme was not as tightly bound to the membrane as it was in the parental strain. ATP-dependent membrane energization was absent in membranes isolated from the uncH mutants and could not be restored by adding normal F1 ATPase from the wild-type strain. F1 ATPase prepared from uncH mutants could not restore ATP-dependent membrane energization when added to wild-type membranes depleted of F1. Membranes of the uncH mutants were not rendered proton permeable as a result of washing with low-ionic-strength buffer.

In vitro membrane association of the F0 polypeptides of the Escherichia coli proton translocating ATPase

The F0 polypeptides a, b, and c of the H+-translocating ATPase associated with membranes when synthesized in vitro. This association occurred when the membranes were present either cotranslationally or post-translationally. In addition, the F0 polypeptides associated with liposomes. The membrane association seemed to be an insertion process since there was protection of polypeptides a and c from proteolysis. The in vitro insertion of the F0 polypeptides a, b, and c was independent of the synthesis of each polypeptide and of the F1 polypeptides.

Differential polypeptide synthesis of the proton-translocating ATPase of Escherichia coli

We investigated the regulation of the synthesis of the eight polypeptides of the Escherichia coli proton-translocating ATPase. A plasmid carrying the eight genes of the unc operon was used to direct in vivo and in vitro protein synthesis of the eight polypeptides. Analysis of these data indicates that the ATPase polypeptides are synthesized in unequal amounts both in vitro and in vivo. We identified several regions within the unc operon at which expression of a gene is either increased or decreased from that of the preceding gene. Since genetic information indicates a single polycistronic mRNA for all eight genes of this operon, the observed differential synthesis of the polypeptides is most likely the result of translational regulation. The effect of varying the temperature suggests that the secondary structure in the mRNA may affect the rate of translation initiation in the region between uncE and uncF.

Topological and functional aspects of the proton conductor, F0, of the Escherichia coli ATP-synthase

The isolated H+ conductor, F0, of the Escherichia coli ATP-synthase consists of three subunits, a, b, and c. H+-permeable liposomes can be reconstituted with F0 and lipids; addition of F1-ATPase reconstitutes a functional ATP-synthase. Mutants with altered or missing F0 subunits are defective in H+ conduction. Thus, all three subunits are necessary for the expression of H+ conduction. The subunits a and b contain binding sites for F1. Computer calculations, cross-links, membrane-permeating photo-reactive labels, and proteases were used to develop tentative structural models for the individual F0 subunits.

The nucleotide sequence of the atp genes coding for the F0 subunits a, b, c and the F1 subunit delta of the membrane bound ATP synthase of Escherichia coli

The nucleotide sequence has been determined of a 2,500 base pair segment of the E. coli chromosome located between 3.75 and 6.25 kb counterclockwise of the origin of replication at 83.5 min. The sequence contains the atp genes coding for subunits a-, b-, c-, delta- and part of the alpha-subunit of the membrane bound ATP synthase. The precise start positions of the atpE (c), atpF (b), atpH (delta) and atpA (alpha) genes have been defined by comparison of the potential coding sequences with the known amino acid sequence of the c-subunit and the determined N-terminal amino acid sequences of the respective subunits. The genes are expressed in the counterclockwise direction. Their order (counterclockwise) is: atpB (a), atpE (c), atpF (b), atpH (delta) and atpA(alpha). The coding sequences for subunits b and delta yield polypeptides of 156 and 177 amino acids, respectively, in accordance with the established sizes of these subunits; the one for the c-subunit, the DCCD binding protein, fits perfectly with its known sequence of 79 amino acids. The a-subunit is comprised within a coding sequence yielding a polypeptide of 271 amino acids. It is suggested, however, that the a-subunit (atpB) contains only 201 amino acids, in accordance with its known size, starting from a translation initiation site within the larger coding sequence. The stoichiometry of the F0 sector subunits is discussed and a model is proposed for the functioning of the highly charged b-subunit of the F0 sector as the actual proton conductor.