Regulatory region of the gene for the ompA protein, a major outer membrane protein of Escherichia coli

Understanding Beta-Lactam-Induced Lysis at the Single-Cell Level

Mechanical rupture, or lysis, of the cytoplasmic membrane is a common cell death pathway in bacteria occurring in response to β-lactam antibiotics. A better understanding of the cellular design principles governing the susceptibility and response of individual cells to lysis could indicate methods of potentiating β-lactam antibiotics and clarify relevant aspects of cellular physiology. Here, we take a single-cell approach to bacterial cell lysis to examine three cellular features-turgor pressure, mechanosensitive channels, and cell shape changes-that are expected to modulate lysis. We develop a mechanical model of bacterial cell lysis and experimentally analyze the dynamics of lysis in hundreds of single Escherichia coli cells. We find that turgor pressure is the only factor, of these three cellular features, which robustly modulates lysis. We show that mechanosensitive channels do not modulate lysis due to insufficiently fast solute outflow, and that cell shape changes result in more severe cellular lesions but do not influence the dynamics of lysis. These results inform a single-cell view of bacterial cell lysis and underscore approaches of combatting antibiotic tolerance to β-lactams aimed at targeting cellular turgor.

Mechanics and Dynamics of Bacterial Cell Lysis

Membrane lysis, or rupture, is a cell death pathway in bacteria frequently caused by cell wall-targeting antibiotics. Although previous studies have clarified the biochemical mechanisms of antibiotic action, a physical understanding of the processes leading to lysis remains lacking. Here, we analyze the dynamics of membrane bulging and lysis in Escherichia coli, in which the formation of an initial, partially subtended spherical bulge ("bulging") after cell wall digestion occurs on a characteristic timescale of 1 s and the growth of the bulge ("swelling") occurs on a slower characteristic timescale of 100 s. We show that bulging can be energetically favorable due to the relaxation of the entropic and stretching energies of the inner membrane, cell wall, and outer membrane and that the experimentally observed timescales are consistent with model predictions. We then show that swelling is mediated by the enlargement of wall defects, after which cell lysis is consistent with both the inner and outer membranes exceeding characteristic estimates of the yield areal strains of biological membranes. These results contrast biological membrane physics and the physics of thin, rigid shells. They also have implications for cellular morphogenesis and antibiotic discovery across different species of bacteria.

Allelic Variation in Outer Membrane Protein A and Its Influence on Attachment of Escherichia coli to Corn Stover

Understanding the genetic factors that govern microbe-sediment interactions in aquatic environments is important for water quality management and reduction of waterborne disease outbreaks. Although chemical properties of bacteria have been identified that contribute to initiation of attachment, the outer membrane proteins that contribute to these chemical properties still remain unclear. In this study we explored the attachment of 78 Escherichia coli environmental isolates to corn stover, a representative agricultural residue. Outer membrane proteome analysis led to the observation of amino acid variations, some of which had not been previously described, in outer membrane protein A (OmpA) at 10 distinct locations, including each of the four extracellular loops, three of the eight transmembrane segments, the proline-rich linker and the dimerization domain. Some of the polymorphisms within loops 1, 2, and 3 were found to significantly co-occur. Grouping of sequences according to the outer loop polymorphisms revealed five distinct patterns that each occur in at least 5% of our isolates. The two most common patterns, I and II, are encoded by 33.3 and 20.5% of these isolates and differ at each of the four loops. Statistically significant differences in attachment to corn stover were observed among isolates expressing different versions of OmpA and when different versions of OmpA were expressed in the same genetic background. Most notable was the increased corn stover attachment associated with a loop 3 sequence of SNFDGKN relative to the standard SNVYGKN sequence. These results provide further insight into the allelic variation of OmpA and implicate OmpA in contributing to attachment to corn stover.

The Bam (Omp85) complex is involved in secretion of the autotransporter haemoglobin protease

Autotransporters are large virulence factors secreted by Gram-negative bacteria. They are synthesized with a C-terminal domain that forms a β-barrel pore in the outer membrane implicated in translocation of the upstream ‘passenger’ domain across the outer membrane. However, recent structural data suggest that the diameter of the β-barrel pore is not sufficient to allow the passage of partly folded structures observed for several autotransporters. Here, we have used a stalled translocation intermediate of the autotransporter Hbp to identify components involved in insertion and translocation of the protein across the outer membrane. At this intermediate stage the β-domain was not inserted and folded as an integral β-barrel in the outer membrane whereas part of the passenger was surface exposed. The intermediate was copurified with the periplasmic chaperone SurA and subunits of the Bam (Omp85) complex that catalyse the insertion and assembly of outer-membrane proteins. The data suggest a critical role for this general machinery in the translocation of autotransporters across the outer membrane.

Bacterial expression of the major antigenic regions of porcine rotavirus VP7 induces a neutralizing immune response in mice

The outer capsid protein of rotavirus, VP7, is a major neutralization antigen. A chimeric protein comprising Escherichia coli (E. coli) outer membrane protein A (OmpA) and part of porcine rotavirus VP7 containing all three antigenic regions (217 amino acids) was expressed in Salmonella and E. coli as an outer-membrane associated protein. Mice immunized intraperitoneally or orally, respectively, with live E. coli or Salmonella cells expressing this chimeric protein produced antibodies against native VP7 as determined by enzyme-linked immunosorbent assays and neutralization tests. This indicates that the VP7 fragment from a porcine rotavirus which is antigenically similar to human rotavirus serotype 3, when expressed in bacteria as a chimeric protein, can form a structure resembling its native form at least in some of the major neutralization domains. These results indicate that the use of a live bacterial vector expressing rotavirus VP7 may represent a strategy for the development of vaccines against rotavirus-induced diarrhoea in infants.

Linkage map of Escherichia coli K-12, edition 10: the traditional map

This map is an update of the edition 9 map by Berlyn et al. (M. K. B. Berlyn, K. B. Low, and K. E. Rudd, p. 1715-1902, in F. C. Neidhardt et al., ed., Escherichia coli and Salmonella: cellular and molecular biology, 2nd ed., vol. 2, 1996). It uses coordinates established by the completed sequence, expressed as 100 minutes for the entire circular map, and adds new genes discovered and established since 1996 and eliminates those shown to correspond to other known genes. The latter are included as synonyms. An alphabetical list of genes showing map location, synonyms, the protein or RNA product of the gene, phenotypes of mutants, and reference citations is provided. In addition to genes known to correspond to gene sequences, other genes, often older, that are described by phenotype and older mapping techniques and that have not been correlated with sequences are included.

The ompA 5' untranslated region impedes a major pathway for mRNA degradation in Escherichia coli

The unusual longevity of the Escherichia coli ompA transcript is determined by its 5' untranslated region (UTR), which functions in vivo as an mRNA stabilizer. Here we show that this 5' UTR can prolong the lifetime in E. coli of a variety of heterologous mRNAs to which it is joined, either as a gene fusion or as an operon fusion. Statistical extrapolation suggests that it is quite likely that most E. coli mRNAs could be stabilized in this manner. We conclude that the ompA 5' UTR impedes a major pathway for mRNA degradation in E. coli and that stabilization by fusion to this UTR does not require translational readthrough of the heterologous mRNA segment by ribosomes that initiate translation at the ompA ribosome-binding site. Additional experiments indicate that the E. coli ribonuclease whose action is slowed by the ompA 5' UTR is not RNase III.

Cloning and nucleotide sequence of anaerobically induced porin protein E1 (OprE) of Pseudomonas aeruginosa PAO1

The porin oprE gene of Pseudomonas aeruginosa PAO1 was isolated. Its nucleotide sequence indicated that the structural gene of 1383 nucleotide residues encodes a precursor consisting of 460 amino acid residues with a signal peptide of 29 amino acid residues, which was confirmed by the N-terminal 23-amino-acid sequence and the reaction with anti-OprE polyclonal antiserum. Anaerobiosis induced OprE production at the transcription level. The transcription start site was determined to be 40 nucleotides upstream from the ATG initiation codon. The control region contained an appropriately situated E sigma 54 recognition site and the putative second half of an ANR box. The amino acid sequence of OprE had some clusters of sequence homologous with that of OprD of P. aeruginosa, which might be responsible for the outer membrane permeability of imipenem and basic amino acids.

A 5'-terminal stem-loop structure can stabilize mRNA in Escherichia coli

The 5'-untranslated region of the long-lived Escherichia coli ompA transcript functions as an mRNA stabilizer capable of prolonging the lifetime in E. coli of a number of heterologous messages to which it is fused. To elucidate the structural basis of differential mRNA stability in bacteria, the domains of the ompA 5'-untranslated region that allow it to protect mRNA from degradation have been identified by mutational analysis. The presence of a stem-loop no more than 2-4 nucleotides from the extreme 5' terminus of this RNA segment is crucial to its stabilizing influence, whereas the sequence of the stem-loop is relatively unimportant. The potential to form a hairpin very close to the 5' end is a feature common to a number of stable prokaryotic messages. Moreover, the lifetime of a normally labile message (bla mRNA) can be prolonged in E. coli by adding a simple hairpin structure at its 5' terminus. Accelerated degradation of ompA mRNA in the absence of a 5'-terminal stem-loop appears to start downstream of the 5' end. We propose that E. coli messages beginning with a single-stranded RNA segment of significant length are preferentially targeted by a degradative ribonuclease that interacts with the mRNA 5' terminus before cleaving internally at one or more distal sites.

Differentiation of lactococci by rRNA gene restriction analysis

Strains of the subspecies of Lactococcus lactis could be differentiated by rRNA gene restriction fragment length polymorphisms (RFLP). 16S rRNA-specific oligonucleotide as well as polynucleotide DNA probes were used for the detection of restriction fragments. In addition, a site-specific probe was designed for the intergenic spacer region of 23S and 5S rRNA genes. For all lactococcal strains the putative presence of six rRNA operons was confirmed. A non-radioactive hybridization assay was used based on hybrid detection by chemiluminescence. Specific patterns were found for any of the strains investigated. Subspecies-specific restriction fragments could be identified in addition to the strain-specific patterns.

Pseudomonas aeruginosa outer membrane lipoprotein I gene: molecular cloning, sequence, and expression in Escherichia coli

Lipoprotein I (OprI) is one of the major proteins of the outer membrane of Pseudomonas aeruginosa. Like porin protein F (OprF), it is a vaccine candidate because it antigenically cross-reacts with all serotype strains of the International Antigenic Typing Scheme. Since lipoprotein I was expressed in Escherichia coli under the control of its own promoter, we were able to isolate the gene by screening a lambda EMBL3 phage library with a mouse monoclonal antibody directed against lipoprotein I. The monocistronic OprI mRNA encodes a precursor protein of 83 amino acid residues including a signal peptide of 19 residues. The mature protein has a molecular weight of 6,950, not including bound glycerol and lipid. Although the amino acid sequences of protein I of P. aeruginosa and Braun's lipoprotein of E. coli differ considerably (only 30.1% identical amino acid residues), peptidoglycan in E. coli, are identical. Using lipoprotein I expressed in E. coli, it can now be tested whether this protein alone, without P. aeruginosa lipopolysaccharide contaminations, has a protective effect against P. aeruginosa infections.

Sequence and transcriptional start site of the Pseudomonas aeruginosa outer membrane porin protein F gene

Porin F is one of the major proteins of the outer membrane of Pseudomonas aeruginosa. It forms water-filled pores of variable size. Porin F is a candidate for a vaccine against P. aeruginosa because it antigenically cross-reacts in all serotype strains of the International Antigenic Typing Scheme. We have isolated the gene for porin F from a lambda EMBL3 bacteriophage library by using oligodeoxynucleotide hybridization probes and have determined its nucleotide sequence. Different peptide sequences obtained from isolated porin F confirmed the deduced protein sequence. The mature protein consists of 326 amino acid residues and has a molecular weight of 35,250. The precursor contains an N-terminal signal peptide of 24 amino acid residues. S1 protection and primer extension experiments, together with Northern (RNA) blots, indicate that the mRNA coding for porin F is monocistronic with short untranslated regions of about 58 bases at the 5' end and about 47 bases at the 3' end. The sequences in the -10 and -35 regions upstream of the transcriptional start site are closely related to the Escherichia coli promoter consensus sequences, which explains why the porin F gene is expressed in E. coli under the control of its own promoter. The amino acid sequence of porin F is not homologous to the different E. coli porins OmpF, OmpC, LamB, and PhoE. On the other hand, a highly homologous region of 30 amino acids between the OmpA proteins of different enteric bacteria and porin F of P. aeruginosa was detected. The core region of the homology to E. coli OmpA had 11 of 12 amino acid residues in common.

Detection of transcription-pausing in vivo in the trp operon leader region

To determine whether RNA polymerase pauses during transcription in vivo, we have examined transcripts of the trp operon leader regions of Serratia marcescens and Escherichia coli. Labeled RNAs synthesized in E. coli strains containing plasmids bearing wild-type or mutant trp leader regions of S. marcescens or E. coli were isolated by hybridization and analyzed by polyacrylamide gel electrophoresis. The labeled RNAs synthesized in vivo on the S. marcescens wild-type and deletion mutant plasmids were the same size as the in vitro pause and leader transcripts. Hybridization of the presumed in vivo pause RNAs, and control in vitro pause RNAs, to M13 phage DNA containing a trp leader region deletion followed by treatment with S1 nuclease produced identical protected RNA species, proving that the in vitro and in vivo RNAs were identical. The amount of labeled pause RNAs relative to leader RNAs decreased following a chase with unlabeled uridine. E. coli RNAs identical to the previously characterized in vitro pause and leader transcripts were demonstrated by electrophoretic band position and fingerprint analysis. The finding that transcription pausing occurs in vivo is consistent with the view that transcription pausing and ribosome release of paused transcription complexes are responsible for the coupling of translation with transcription that is crucial to attenuation.

crp genes of Shigella flexneri, Salmonella typhimurium, and Escherichia coli

The complete nucleotide sequences of the Salmonella typhimurium LT2 and Shigella flexneri 2B crp genes were determined and compared with those of the Escherichia coli K-12 crp gene. The Shigella flexneri gene was almost like the E. coli crp gene, with only four silent base pair changes. The S. typhimurium and E. coli crp genes presented a higher degree of divergence in their nucleotide sequence with 77 changes, but the corresponding amino acid sequences presented only one amino acid difference. The nucleotide sequences of the crp genes diverged to the same extent as in the other genes, trp, ompA, metJ, and araC, which are structural or regulatory genes. An analysis of the amino acid divergence, however, revealed that the catabolite gene activator protein, the crp gene product, is the most conserved protein observed so far. Comparison of codon usage in S. typhimurium and E. coli for all genes sequenced in both organisms showed that their patterns were similar. Comparison of the regulatory regions of the S. typhimurium and E. coli crp genes showed that the most conserved sequences were those known to be essential for the expression of E. coli crp.

The nature of ompA mutants of Escherichia coli K12 exhibiting temperature-sensitive bacteriophage resistance

A class of ompA mutants of Escherichia coli, exhibiting temperature-sensitive resistance towards phages using the OmpA protein as receptor, was analysed. The mutants produce detectable levels of the protein at 42 degrees C but not at 30 degrees C (Manning and Reeves 1976). They were found to have a deletion (one isolate) or insertions (three isolates) upstream of the coding part of the ompA gene. Several previously characterized mutants possessing insertions or a deletion in the non-translated 5' area of the gene also exhibited a similar temperature-sensitive phage resistance. This cold-sensitive phenotype is explained in terms of the recent discovery that the stability of ompA mRNA is regulated by the rate of cell growth (Nilsson et al. 1984).

High-level expression in Escherichia coli of biologically active bovine growth hormone

High-level synthesis of bovine growth hormone (bGH) in Escherichia coli was achieved by maximizing gene transcription and optimizing the translational efficiency of bGH mRNA. Nearly all of the recombinant hormone was found in the pellet fraction after bacterial cell lysis. This property allowed the purification of bGH nearly to homogeneity. Protein sequence analysis indicated that greater than 93% of the purified hormone had the amino-terminal methionine residue removed by E. coli, yielding mature bGH. In a hypophysectomized rat assay system, purified bacterial-produced bGH demonstrated growth-promoting activity equivalent to that of pituitary-derived bovine growth hormone.

Compilation and analysis of Escherichia coli promoter DNA sequences

The DNA sequence of 168 promoter regions (-50 to +10) for Escherichia coli RNA polymerase were compiled. The complete listing was divided into two groups depending upon whether or not the promoter had been defined by genetic (promoter mutations) or biochemical (5' end determination) criteria. A consensus promoter sequence based on homologies among 112 well-defined promoters was determined that was in substantial agreement with previous compilations. In addition, we have tabulated 98 promoter mutations. Nearly all of the altered base pairs in the mutants conform to the following general rule: down-mutations decrease homology and up-mutations increase homology to the consensus sequence.

Decay of mRNA in Escherichia coli: investigation of the fate of specific segments of transcripts

An assay was developed to investigate the fate of specific segments of beta-lactamase (bla) and ompA gene transcripts in Escherichia coli. DNA probes cloned in bacteriophage M13 were treated with an endonuclease capable of cleaving single-stranded DNA, the fragments produced were annealed with total cellular RNA, and the resulting RNA . DNA hybrids were subjected to S1 nuclease treatment and gel fractionation. By using this assay, direct evidence was obtained for 3'-to-5' directionality in the decay of the long-lived mRNA encoded by the ompA gene, and no preferential stability was observed for translated versus untranslated mRNA segments. In the case of bla mRNA, initial cleavage of the full-length transcript was rate limiting, and no decay intermediates were detected. No difference in degradation rate was seen for bla transcripts having variant 3' or 5' termini.

Nucleotide sequence of the amylase gene from Bacillus subtilis

The gene coding for amylase (EC.3.2.1.1) has been isolated and sequenced from Bacillus subtilis by cloning in lambda Charon4A and pBR322. The entire coding sequence and large preceding and following regions, comprising the presumed transcriptional and translational regulatory regions, were sequenced. The coding sequence shows a large open reading frame with a translated molecular weight of 72,800 and a presumed signal sequence of approximately thirty-two amino acids. When the intact gene is present in Escherichia coli, it confers the ability to degrade starch, indicating that the gene is expressed in a functional state.

Characterisation of the promoters for the ompA gene which encodes a major outer membrane protein of Escherichia coli

The regulatory region of the ompA gene from Escherichia coli has been characterized by biochemical and genetic approaches. Two overlapping promoters, P1 and P2, organized in that order with respect to the ompA coding sequence, were identified and it was found that ompA possesses an unusually long leader region. Both P1 and P2 were active in an in vitro transcription system although S1 mapping analysis of the ompA mRNA made in vivo showed that P2 was mainly responsible for transcription of the gene. Confirmation of this was obtained by studying down-promoter mutants of ompA cloned in pSC101. These mutants were classified into two groups, deletions and insertions. The deletions, which were caused by the IS102 insertion element found in pSC101 removed the--35 regions of both P1 and P2. However, since P2 was distally situated with respect to the IS element it was less extensively damaged and it is proposed that the residual P2 sequence is responsible for the low level of expression observed. In addition to an IS102 insertion in the promoter region four IS1 insertion mutants were characterized. These had integrated at different positions in the ompA leader region and were all incompletely polar.

Characterization of translational initiation sites in E. coli

We characterize the Shine and Dalgarno sequence of 124 known gene beginnings. This information is used to make "rules" which help distinguish gene beginning from other sites in a library of over 78,000 bases of mRNA. Gene beginnings are found to have information besides the initiation codon and Shine and Dalgarno sequence which can be used to make better "rules".

The nucleotide sequence coding for major outer membrane protein OmpA of Shigella dysenteriae

The nucleotide sequence of the ompA gene from Shigella dysenteriae has been determined and the amino acid sequence of the pro-OmpA protein predicted. Sequence comparison between the ompA genes of S.dysenteriae and Escherichia coli showed that features such as mRNA secondary structure and codon usage, as well as polypeptide function, have been conserved during evolution. The pro-OmpA protein of S.dysenteriae consists of 351 residues, as opposed to the 346 of the E.coli protein and also shows several amino acid changes. These changes have been used to interpret differences in the biological activity of the two proteins.

Regulation of the OmpA outer membrane protein of Escherichia coli

The role of lipopolysaccharide in regulating the expression of the ompA outer membrane protein gene of Escherichia coli K-12 was studied by isolating mutants defective in the biosynthesis of lipopolysaccharide and by examining transcription of lacZ in strains carrying operon fusions in which lacZ is expressed from the ompA promoter. By selecting for simultaneous resistance to phages K3 and U3, we obtained mutants defective in rfaC (biosynthesis of core heptose) and in rfaP (phosphorylation of core heptose), and both of these mutant strains failed to express OmpA protein in the outer membrane. Expression of lacZ from the ompA or by foreign ompA alleles which are not expressed in E. coli K-12. Expression was increased in strains carrying rfaC and rfaP mutations. No precursor or degraded form of OmpA protein accumulated in cells which could not express the protein in the outer membrane. This lack of accumulation of precursor was observed even in the presence of phenethyl alcohol, which caused accumulation of OmpA precursor in wild-type cells. We present a model for the regulation of this gene which is consistent with these observations and which involves modulation of transcription coupled to translation of the protein.

Codon catalog usage is a genome strategy modulated for gene expressivity

The nucleic acid sequence bank now contains 161 mRNAs, 43 new genes are added. One sequence, that of B. mori fibroin, is dropped due to uncertainty on the starting point for translation. Frequencies of all codons are given for each gene added and for each genome type in the total bank. A new series of correspondence analyses on codon use is presented, substantiating the genome hypothesis. Internal regulation of mRNA expression by different third base choices between quartet and duet codons is proposed for bacterial genes.