Cloned structural gene (ompA) for an integral outer membrane protein of Escherichia coli K-12: localization on hybrid plasmid pTU100 and expression of a fragment of the gene

Xanthomonas albilineans OmpA1 appears to be functionally modular and both the OMC and C-like domains are necessary for leaf scald disease of sugarcane

Several EZ-Tn5 insertions in gene locus XALc_0557 (OmpA1) of the sugarcane leaf scald pathogen Xanthomonas albilineans XaFL07-1 were previously found to strongly affect pathogenicity and endophytic stalk colonization. XALc_0557 has a predicted OmpA N-terminal outer membrane channel (OMC) domain and an OmpA C-like domain. Further analysis of mutant M468, with an EZ-Tn5 insertion in the upstream OMC domain coding region, revealed impaired epiphytic and endophytic leaf survival, impaired resistance to sodium dodecyl sulfate (SDS), structural defects in the outer membrane (OM), and hyperproduction of OM vesicles. Cloned full-length XALc_0557 complemented M468 for all phenotypes tested, including pathogenicity, resistance to SDS, and ability to survive both endophytically and epiphytically. Another construct, pCT47.3, which expressed only the C-like domain of XALc_0557, restored resistance to SDS in M468 but failed to complement any other mutant phenotype, indicating that the C-like domain functioned independently of the OMC domain to help maintain OM integrity. pCT47.3 also complemented pathogenicity, resistance to SDS, and stalk colonization in mutant M1152, which carries an EZ-Tn5 insert in the C-like coding region, indicating that both predicted domains are modular and necessary but neither is sufficient for X. albilineans pathogenicity, endophytic survival in, and epiphytic survival on sugarcane.

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.

Colicin U, a novel colicin produced by Shigella boydii

A novel colicin, designated colicin U, was found in two Shigella boydii strains of serovars 1 and 8. Colicin U was active against bacterial strains of the genera Escherichia and Shigella. Plasmid pColU (7.3 kb) of the colicinogenic strain S. boydii M592 (serovar 8) was sequenced, and three colicin genes were identified. The colicin U activity gene, cua, encodes a protein of 619 amino acids (Mr, 66,289); the immunity gene, cui, encodes a protein of 174 amino acids (Mr, 20,688); and the lytic protein gene, cul, encodes a polypeptide of 45 amino acids (Mr, 4,672). Colicin U displays sequence similarities to various colicins. The N-terminal sequence of 130 amino acids has 54% identity to the N-terminal sequence of bacteriocin 28b produced by Serratia marcescens. Furthermore, the N-terminal 36 amino acids have striking sequence identity (83%) to colicin A. Although the C-terminal pore-forming sequence of colicin U shows the highest degree of identity (73%) to the pore-forming C-terminal sequence of colicin B, the immunity protein, which interacts with the same region, displays a higher degree of sequence similarity to the immunity protein of colicin A (45%) than to the immunity protein of colicin B (30.5%). Immunity specificity is probably conferred by a short sequence from residues 571 to residue 599 of colicin U; this sequence is not similar to that of colicin B. We showed that binding of colicin U to sensitive cells is mediated by the OmpA protein, the OmpF porin, and core lipopolysaccharide. Uptake of colicin U was dependent on the TolA, -B, -Q, and -R proteins. pColU is homologous to plasmid pSB41 (4.1 kb) except for the colicin genes on pColU. pSB41 and pColU coexist in S. boydii strains and can be cotransformed into Escherichia coli, and both plasmids are homologous to pColE1.

Isolation of a mRNA instability sequence that is cis-dominant to the ompA stability determinant in Escherichia coli

Transcriptional fusions with ompA and bla have been used to identify a novel mRNA instability element. A 287-nucleotide (nt) sequence containing a repetitive extragenic palindrome (REP) from the chloramphenicol acetyltransferase (cat) gene was inserted into the 3' untranslated region (UTR) of the ompA gene. In one orientation, the insert had no effect on the half-life of the ompA-cat chimeric transcript. In the other orientation, however, the sequence functioned as a destabilizing element and was dominant to the 5'-UTR ompA and REP stability elements. The orientation-dependent effect of the instability sequence suggests that sequence rather than structure alone is important to the function of the instability determinant. In addition, the instability sequence also destabilized an ompA-bla fusion construct when fused to its 3'-UTR region. A sensitive RNA ligation/PCR amplification technique was developed and used to analyze RNA decay intermediates. The results indicated that degradation of the chimeric transcript initiated within the 287-nt inserted sequence.

Synonymous codon selection controls in vivo turnover and amount of mRNA in Escherichia coli bla and ompA genes

A number of silent codon changes were made in two Escherichia coli genes. For the ompA gene, the replacement of seven consecutive frequently used codons with synonymous infrequently used codons reduced the ompA mRNA level and its half-life. For the bla gene, the exchange of 24 codons for the most frequently used synonymous codons extended the bla mRNA half-life. A modification of ribosome traffic could account for these observations.

Membrane topology and assembly of the outer membrane protein OmpA of Escherichia coli K12

The 325-residue outer membrane protein OmpA of Escherichia coli has been proposed to consist of a membrane-embedded moiety (residues 1 to about 170) and a C-terminal periplasmic region. The former is thought to comprise eight transmembrane segments in the form of antiparallel beta-strands, forming an amphiphilic beta-barrel, connected by exposed turns. Several questions concerning this model were addressed. Thus no experimental evidence had been presented for the turns at the inner leaflet of the membrane and it was not known whether or not the periplasmic part of the polypeptide plays a role in the process of membrane incorporation. Oligonucleotides encoding trypsin cleavage sites were inserted at the predicted turn sites of the ompA gene and it was shown that the encoded proteins indeed become accessible to trypsin at the modified sites. Together with previous results, these data also show that the turns on both sides of the membrane do not possess specifically topogenic information. In two cases one of the two expected tryptic fragments was lost and could be detected at low concentration in only one case. Therefore, bilateral proteolytic digestion of outer membranes can cause loss of beta-strands and does not necessarily produce a reliable picture of protein topology. When ompA genes were constructed coding for proteins ending at residue 228 or 274, the membrane assembly of these proteins was shown to be partially defective with about 20% of the proteins not being assembled. No such defect was observed when, following the introduction of a premature stop codon, a truncated protein was produced ending with residue 171.(ABSTRACT TRUNCATED AT 250 WORDS)

Genetic and molecular characterization of the Escherichia coli secD operon and its products

The secD operon of Escherichia coli is required for the efficient export of proteins. We have characterized this operon, and found that, in addition to secD and secF, it contains the upstream gene yajC, but not the genes queA or tgt, in contrast to previous reports. An analysis of yajC mutations constructed in vitro and recombined onto the chromosome indicates that yajC is neither essential nor a sec gene. The secD operon is not induced in response to either secretion defects or temperature changes. TnphoA fusions have been used to analyze the topology of SecD in the inner membrane; the protein contains six transmembrane stretches and a large periplasmic domain. TnphoA fusions to SecD and SecF have also been recombined onto the chromosome and used to determine the level of these proteins within the cell. Our results indicate that there are fewer than 30 SecD and SecF molecules per cell.

Protein secretion in Bacillus species

Bacilli secrete numerous proteins into the environment. Many of the secretory proteins, their export signals, and their processing steps during secretion have been characterized in detail. In contrast, the molecular mechanisms of protein secretion have been relatively poorly characterized. However, several components of the protein secretion machinery have been identified and cloned recently, which is likely to lead to rapid expansion of the knowledge of the protein secretion mechanism in Bacillus species. Comparison of the presently known export components of Bacillus species with those of Escherichia coli suggests that the mechanism of protein translocation across the cytoplasmic membrane is conserved among gram-negative and gram-positive bacteria differences are found in steps preceding and following the translocation process. Many of the secretory proteins of bacilli are produced industrially, but several problems have been encountered in the production of Bacillus heterologous secretory proteins. In the final section we discuss these problems and point out some possibilities to overcome them.

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.

Structure and function of a bacterial mRNA stabilizer: analysis of the 5' untranslated region of ompA mRNA

The 5' untranslated region (UTR) of the Escherichia coli ompA transcript functions in vivo as a growth rate-regulated mRNA stabilizer. The secondary structure of this mRNA segment has been determined by a combination of three methods: phylogenetic analysis, in vitro probing with a structure-specific RNase, and methylation by dimethylsulfate in vivo and in vitro. These studies reveal that despite extensive sequence differences, the 5' UTRs of the ompA transcripts of E. coli, Serratia marcescens, and Enterobacter aerogenes can fold in a remarkably similar fashion. Furthermore, the Serratia and Enterobacter ompA 5' UTRs function as effective mRNA stabilizers in E. coli. Stabilization of mRNA by the Serratia ompA 5' UTR is growth rate dependent. These findings indicate that the features of the ompA 5' UTR responsible for its ability to stabilize mRNA in a growth rate-regulated manner are to be found among the structural similarities shared by these diverse evolutionary variants.

A novel transcriptional response by the cat gene during slow growth of Escherichia coli

A novel response to growth rate was found with expression of the chloramphenicol acetyltransferase (cat) gene in Escherichia coli. The amount of cat mRNA relative to total RNA increased about 11-fold as growth rates decreased 5- to 6-fold, without an increase in translation. The accumulation of cat mRNA was in contrast to decreased cellular concentrations of total RNA, trxA, ompA, or 23S rRNA as the growth rate decreased and was not due to changes in gene dosage or mRNA stability. Stability of the cat mRNA does not appear to be regulated by growth rate. No significant change in either chemical or functional stability was observed within a five- to sixfold range of growth rates when chemostat-grown cells were used. However, cat mRNA stability was affected by growth medium composition. The half-life of cat mRNA decreased about threefold, with an approximate fourfold increase in generation time due to changes in growth medium. Transcriptional studies have indicated that accumulation of cat mRNA at slow growth rates is the result of a specific transcriptional response to changes in cellular generation times. We propose that increases in the cellular concentration of a specific message at slow growth rates may reflect an additional type of survival response in E. coli.

Requirement of the SecB chaperone for export of a non-secretory polypeptide in Escherichia coli

The SecB protein of Escherichia coli is a cytosolic component of the export machinery which can prevent some precursors from prematurely folding into export-incompatible conformations by binding to the newly synthesised polypeptide. The feature(s) of target proteins recognised by SecB, however, are unclear and have been a matter of controversy. Also, it has not been asked if binding of SecB is specific for secretory proteins. We demonstrate here that a non-secretory polypeptide, a fragment of a tail fiber protein of phage T4, fused to the signal peptide of the outer membrane protein OmpA has a very strong SecB requirement for export and that the signal peptide itself cannot, at least not alone, be responsible for this action of SecB. The data reported, together with those of the literature, suggest that SecB recognizes the polypeptide backbone of the target protein.

Insertion of peptides into cell-surface-exposed areas of the Escherichia coli OmpA protein does not interfere with export and membrane assembly

Peptides, 21 amino acids (aa) in length, were inserted into cell-surface-exposed areas of the Escherichia coli outer membrane protein, OmpA, corresponding to aa positions 70 or 154 or at both sites simultaneously. The corresponding hybrid proteins were exported and normally assembled in the outer membrane. The results of protease-accessibility experiments are compatible with the presence of the peptides at the cell surface.

Transcription of the sulA-ompA region of Escherichia coli during the SOS response and the role of an antisense RNA molecule

The transcriptional pattern of the 22 min region of the Escherichia coli chromosome containing the linked sulA and ompA genes, which encode an SOS-inducible inhibitor of cell division and a constitutively expressed, major outer membrane protein, respectively, has been re-examined. During normal growth, the sulA gene was repressed whereas the ompA gene produced a stable 1250 nucleotide transcript. Counter-transcription of sulA occurred from a promoter situated in the sulA-ompA intergenic region and the product of this transcriptional circuit, named isf, is a 353 nucleotide untranslated RNA. Since the isf RNA is complementary to the 3'-end of the sulA transcript, it could modulate sulA function by serving as an anti-messenger. On induction of the SOS-response, massive transcription of sulA took place, resulting in the 'silencing' of the isf gene, production of an abundant approximately 615 nucleotide sulA mRNA and a novel hybrid transcript of approximately 2100 nucleotides encoding both the SulA and OmpA proteins. Production of the latter RNA species, caused by transcription reading through the sulA terminator, the intergenic region and the coding sequences, was accompanied by a decrease in the abundance of the ompA mRNA as a result of promoter occlusion. However, the amount of OmpA protein produced was only slightly reduced.

Translational control of exported proteins that results from OmpC porin overexpression

The regulation of synthesis and export of outer membrane proteins of Escherichia coli was examined by overexpressing ompC in multicopy either from its own promoter or from an inducible promoter in an expression vector. Overexpression of OmpC protein resulted in a nearly complete inhibition of synthesis of the OmpA and LamB outer membrane proteins but had no effect on synthesis of the periplasmic maltose-binding protein. Immunoprecipitation of labeled proteins showed no evidence of accumulation of uncleaved precursor forms of OmpA or maltose-binding protein following induction of OmpC overexpression. The inhibition of OmpA and LamB was tightly coupled to OmpC overexpression and occurred very rapidly, reaching a high level within 2 min after induction. OmpC overexpression did not cause a significant decrease in expression of a LamB-LacZ hybrid protein produced from a lamB-lacZ fusion in which the fusion joint was at the second amino acid of the LamB signal sequence. There was no significant decrease in rate of synthesis of ompA mRNA as measured by filter hybridization of pulse-labeled RNA. These results indicate that the inhibition is at the level of translation. We propose that cells are able to monitor expression of exported proteins by sensing occupancy of some limiting component in the export machinery and use this to regulate translation of these proteins.

Site-specific endonucleolytic cleavages and the regulation of stability of E. coli ompA mRNA

The stability of ompA mRNA is growth-rate dependent. We show that the 5' noncoding region of this mRNA provides a target for site-specific endonucleases. The rate of degradation of ompA mRNA parallels the rate of these endonucleolytic cleavages, implying that endonucleolytic rather than exonucleolytic attack is the initial step in ompA mRNA degradation. Thus the 5' noncoding region appears to be a determinant of mRNA stability, and endonucleolytic cleavages in the 5' noncoding region may well regulate expression of the ompA gene.

The Escherichia coli cell division proteins FtsY, FtsE and FtsX are inner membrane-associated

The cell division genes ftsY, ftsE and ftsX form an operon mapping at 76 min on the Escherichia coli chromosome. The protein products of these genes have been identified previously. We have studied the cellular location of the radiolabelled Fts proteins using maxicells and standard fractionation procedures. Previous protein sequence homologies suggested an inner membrane location for FtsE. We have confirmed this predicted location and have shown that FtsY and FtsX are also inner membrane-associated. These results are in agreement with the hypothesis that FtsE may act at the inner membrane, in a "septalsome" complex, by coupling ATP hydrolysis to the process of bacterial cell division.

lon-sulA regulatory function affects the efficiency of transposition of Tn5 from lambda b221 cI857 Pam Oam to the chromosome

In transposition of Tn5 from lambda b221 cI857 Pam Oam rex::Tn5 to the chromosome, lon mutants of Escherichia coli K12 are less efficient than lon+ parents. Reduced frequency of transposition of Tn5 is recovered to the wild type level by adding DL-pantoyl lactone, an agent which suppresses Lon- phenotypes. A suppressor mutation, sulA (or sfiA), suppresses the deficiency of transposition as well as other known lon-associated phenotypes, whereas a lon sulB (or sfiB) double mutant is phenotypically Lon+ but still transposition-deficient. An additive effect of the sulA genes on teh chromosome and on a high copy number plasmid is found in inhibiting transposition of Tn5. A hypothesis that the SulA product someway regulates transposition of Tn5 negatively is proposed.

The stability of E. coli gene transcripts is dependent on determinants localized to specific mRNA segments

To map the structural features responsible for the 5-fold difference in stability of the E. coli ompA and bla gene transcripts, we have constructed gene fusions that encode chimeric ompA/bla transcripts and a deletion that eliminates a large internal segment of bla mRNA. Shortening of bla transcripts by internal deletion or replacement of the 3' end with the corresponding segment of the ompA transcript had little effect on bla mRNA stability. However, fusion of a 5'-terminal 147 nucleotide segment of the ompA message 5' to full-length or truncated bla transcripts increased the half-life of the bla segments 3- to 5-fold. These and other findings indicate that E. coli transcripts contain discrete structural determinants of stability and instability that can influence the decay rate of linked mRNA segments derived from other genes.

Bacteriophage receptor area of outer membrane protein OmpA of Escherichia coli K-12

A number of T-even-like bacteriophages use the outer membrane protein OmpA of Escherichia coli as a receptor. We had previously analyzed a series of ompA mutants which are resistant to such phages and which still produce the OmpA protein (R. Morona, M. Klose, and U. Henning, J. Bacteriol. 159:570-578, 1984). Mutational alterations were found near or at residues 70, 110 and 154. Based on these and other results a model was proposed showing the amino-terminal half of the 325-residue protein crossing the outer membrane repeatedly and being cell surface exposed near residues 25, 70, 110, and 154. We characterized, by DNA sequence analysis, an additional 14 independently isolated phage-resistant ompA mutants which still synthesize the protein. Six of the mutants had alterations identical to the ones described before. The other eight mutants possessed seven new alterations: Ile-24----Asn, Gly-28----Val, deletion of Glu-68, Gly-70----Cys, Ser-108----Phe, Ser-108----Pro, and Gly-154----Asp (two isolates). Only the latter alteration resulted in a conjugation-deficient phenotype. The substitutions at Ile-24 and Gly-28 confirmed the expectation that this area of the protein also participates in its phage receptor region. It is unlikely that still other such sites of the protein are involved in the binding of phage, and it appears that the phage receptor area of the protein has now been characterized completely.

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).

Lethal mutations in the structural gene of an outer membrane protein (OmpA) of Escherichia coli K12

The gene ompA encodes a major outer membrane protein of Escherichia coli. Localized mutagenesis of the part of the gene corresponding to the 21-residue signal sequence and the first 45 residues of the protein resulted in alterations which caused cell lysis when expressed. DNA sequence analyses revealed that in one mutant type the last CO2H-terminal residue of the signal sequence, alanine, was replaced by valine. The proteolytic removal of the signal peptide was much delayed and most of the unprocessed precursor protein was fractioned with the outer membrane. However, this precursor was completely soluble in sodium lauryl sarcosinate which does not solubilize the OmpA protein or fragments thereof present in the outer membrane. Synthesis of the mutant protein did not inhibit processing of the OmpA or OmpF proteins. In the other mutant type, multiple mutational alterations had occurred leading to four amino acid substitutions in the signal sequence and two affecting the first two residues of the mature protein. A reduced rate of processing could not be clearly demonstrated. Membrane fractionation suggested that small amounts of this precursor were associated with the plasma membrane but synthesis of this mutant protein also did not inhibit processing of the wild-type OmpA or OmpF proteins. Several lines of evidence left no doubt that the mature mutant protein is stably incorporated into the outer membrane. It is suggested that the presence, in the outer membrane, of the mutant precursor protein in the former case, or of the mutant protein in the latter case perturbs the membrane architecture enough to cause cell death.

Role of the SulB (FtsZ) protein in division inhibition during the SOS response in Escherichia coli: FtsZ stabilizes the inhibitor SulA in maxicells

Induction of the SOS response in Escherichia coli by DNA-damaging treatments results in the synthesis of the SulA polypeptide, and this is sufficient to cause the resulting inhibition of cell division. Mutations at either sulA (sfiA) or sulB (sfiB) suppress this division inhibition. The SulB protein is identical to FtsZ, a protein required for normal division in E. coli. In the presence of FtsZ, the half-life of SulA synthesized in maxicells is approximately 12 min. In contrast, in the absence of FtsZ or in the presence of a mutant form of FtsZ (SulB114) that prevents division inhibition in vivo, SulA is extremely unstable with a half-life of only 3 min. Both FtsZ and SulA are isolated with the inner membrane of E. coli maxicells in the presence of MgCl2. We propose that the SulA inhibitor interacts directly with FtsZ in vivo to block the essential division function of this protein.

Escherichia coli K-12 outer membrane protein (OmpA) as a bacteriophage receptor: analysis of mutant genes expressing altered proteins

The outer membrane protein OmpA of Escherichia coli K-12 serves as a receptor for a number of T-even-like phages. We have isolated a series of ompA mutants which are resistant to such phages but which still produce the OmpA protein. None of the mutants was able to either irreversibly or reversibly bind the phage with which they had been selected. Also, the OmpA protein is required for the action of colicins K and L and for the stabilization of mating aggregates in conjugation. Conjugal proficiency was unaltered in all cases. Various degrees of colicin resistance was found; however, the resistance pattern did not correlate with the phage resistance pattern. DNA sequence analyses revealed that, in the mutants, the 325-residue OmpA protein had suffered the following alterations: Gly-65----Asp, Gly-65----Arg, Glu-68----Gly, Glu-68----Lys (two isolates), Gly-70----Asp (four isolates), Gly-70----Val, Ala-Asp-Thr-Lys-107----Ala-Lys (caused by a 6-base-pair deletion), Val-110----Asp, and Gly-154----Ser. These mutants exhibited a complex pattern of resistance-sensitivity to 14 different OmpA-specific phages, suggesting that they recognize different areas of the protein. In addition to the three clusters of mutational alterations around residues 68, 110, and 154, a site around residue 25 has been predicted to be involved in conjugation and in binding of a phage and a bacteriocin (R. Freudl, and S. T. Cole, Eur. J. Biochem, 134:497-502, 1983; G. Braun and S. T. Cole, Mol. Gen. Genet, in press). These four areas are regularly spaced, being about 40 residues apart from each other. A model is suggested in which the OmpA polypeptide repeatedly traverses the outer membrane in cross-beta structure, exposing the four areas to the outside.

Host range mutants of bacteriophage Ox2 can use two different outer membrane proteins of Escherichia coli K-12 as receptors

The Escherichia coli K-12 outer membrane protein OmpA functions as the receptor for bacteriophage Ox2. We isolated a host range mutant of this phage which was able to grow on an Ox2-resistant ompA mutant producing an altered OmpA protein. From this mutant, Ox2h5, a second-step host range mutant was recovered which formed turbid plaques on a strain completely lacking the OmpA protein. From one of these mutants, Ox2h10, a third-step host range mutant, Ox2h12, was isolated which formed clear plaques on a strain missing the OmpA protein. Ox2h10 and Ox2h12 apparently were able to use both outer membrane proteins OmpA and OmpC as receptors. Whereas there two proteins are very different with respect to primary structures and functions, the OmpC protein is very closely related to another outer membrane protein, OmpF, which was not recognized by Ox2h10 or Ox2h12. An examination of the OmpC amino acid sequence, in the regions where it differs from that of OmpF, revealed that one region shares considerable homology with a region of the OmpA protein which most likely is required for phage Ox2 receptor activity.

Cell-division control in Escherichia coli: specific induction of the SOS function SfiA protein is sufficient to block septation

Blocks in DNA replication cause a rapid arrest of cell division in Escherichia coli. We have previously established that the function SfiA (SulA), induced under these conditions as part of the SOS response, is involved in this inhibition of division. To separate the effects of SfiA from those of other SOS functions, we have constructed a plac-sfiA operon fusion, permitting specific induction of SfiA protein by addition of the lac operon inducer isopropyl beta-D-thiogalactopyranoside (IPTG). In lon mutants, in which the unstable SfiA protein has a longer half-life, IPTG caused a rapid arrest of cell division. Under these conditions, there is no concomitant induction of the SOS response. IPTG also caused a rapid arrest of cell division in lon+ strains. These results demonstrate that induction of the SfiA protein is sufficient to cause inhibition of division. Mutations in the sfiB gene can suppress IPTG-induced SfiA-mediated inhibition of division. At higher SfiA concentrations, however, even sfiB mutants cease division; an additional mutation genetically inseparable from sfiB restores normal division. These observations reinforce the hypothesis that the SfiB protein, probably required for cell septation, is the target of action of the SfiA division inhibitor.

DNA sequence analysis of the Serratia marcescens ompA gene: implications for the organisation of an enterobacterial outer membrane protein

The cloned ompA gene from Serratia marcescens was fully expressed in Escherichia coli and its product correctly assembled into the outer membrane. The S. marcescens polypeptide was not functionally equivalent to the E. coli OmpA protein, which serves as a phage receptor and as a component of several colicin uptake systems. DNA sequence analysis of the gene showed that three regions of the protein likely to be exposed on the cell surface not only differed extensively from the corresponding regions of the E. coli polypeptide but also from all other sequenced OmpA proteins. It is suggested that this sequence polymorphism represents a safety mechanism by which the various enterobacterial species can avoid cross-infection by noxious agents such as phages or colicins.

Regulation of cell division in Escherichia coli: SOS induction and cellular location of the sulA protein, a key to lon-associated filamentation and death

Mutations in sulA (sfiA) block the filamentation and death of capR (lon) mutants that occur after treatments that either damage DNA or inhibit DNA replication and thereby induce the SOS response. Previous sulA-lacZ gene fusion studies showed that sulA is transcriptionally regulated by the SOS response system (lexA/recA). SulA protein has been hypothesized to be additionally regulated proteolytically through the capR (lon) protease, i.e., in lon mutants lacking a functional ATP-dependent protease there would be more SulA protein. A hypothesized function for SulA protein is an inhibitor of cell septation. To investigate aspects of this model, we attempted to construct lon, lon sulA, and lon sulB strains containing multicopy plasmids specifying the sulA+ gene. Multicopy sulA+ plasmids could not be established in lon strains because more SulA protein accumulates than in a lon+ strain. When the sulA gene was mutated by a mini Mu transposon the plasmid could be established in the lon strains. In contrast, sulA+ plasmids could be established in lon+, lon sulA, and lon sulB strains. The sulA+ plasmids caused lon sulA and lon sulB cells to exist as filaments without SOS induction and to be sensitive to UV light and nitrofurantoin. Evidence implicated higher basal levels of SulA protein in these lon plasmid sulA+ strains as the cause of filamentation. We confirmed that the SulA protein is an 18-kilodalton polypeptide and demonstrated that it was induced by treatment with nalidixic acid. The SulA protein was rapidly degraded in a lon+ strain, but was comparatively more stable in vivo in a lon sulB mutant. Furthermore, the SulA protein was localized to the membrane by several techniques.

Molecular characterization of the gene coding for major outer membrane protein OmpA from Enterobacter aerogenes

The ompA gene from Enterobacter aerogenes was subcloned into a low-copy-number plasmid vector and the resultant plasmid, pTU7En, used to study its expression in Escherichia coli K12. Although the gene was strongly expressed and large amounts of OmpA protein were present in the outer membrane its product was not functionally identical to the E. coli polypeptide. In particular, the E. aerogenes OmpA protein was unable to confer sensitivity to OmpA-specific phages of E. coli. When the primary structure of the protein was deduced from the nucleotide sequence of its gene it was found that three domains differed extensively from the corresponding regions of the E. coli protein. As two of these are known to be exposed on the cell surface we inferred that these alterations are responsible for differences in the biological activity of the two proteins.

Gene fusions using the ompA gene coding for a major outer-membrane protein of Escherichia coli K12

It has been shown previously that fragments of the Escherichia coli major outer membrane protein OmpA lacking CO2H-terminal parts can be incorporated into this membrane in vivo [Bremer et al. (1982) Eur. J. Biochem. 122, 223-231]. The possibility that these fragments can be used, via gene fusions, as vehicles to transport other proteins to the outer membrane has been investigated. To test whether fragments of a certain size were optimal for this purpose a set of plasmids was prepared encoding 160, 193, 228, 274, and 280 NH2-terminal amino acids of the 325-residue OmpA protein. The 160-residue fragment was not assembled into the outer membrane whereas the others were all incorporated with equal efficiencies. Thus, if any kind of OmpA-associated stop transfer is required during export the corresponding signal might be present between residues 160 and 193 but not CO2H-terminal to 193. The ompA gene was fused to the gene (tet) specifying tetracycline resistance and the gene for the major antigen (vp1) of foot-and-mouth disease virus. In the former case a 584-residue chimeric protein is encoded consisting NH2-terminally of 228 OmpA residues followed by 356 CO2H-terminal residues of the 396-residue 'tetracycline resistance protein'. In the other case the same part of OmpA is followed by 250 CO2H-terminal residues of the 213-residue Vp1 plus 107 residues partly derived from another viral protein and from the vector. Full expression of both hybrids proved to be lethal. Lipophilic sequences bordered by basic residues, present in the non-OmpA parts of both hybrids were considered as candidates for the lethal effect. A plasmid was constructed which codes for 280 OmpA residues followed by a 31-residue tail containing the sequence: -Phe-Val-Ile-Met-Val-Ile-Ala-Val-Ser-Cys-Lys-. Expression of this hybrid gene was lethal but by changing the reading frame for the tail to encode another, 30-residue sequence the deleterious effect was abolished. It is possible that the sequence incriminated acts as a stop signal for transfer through the plasma membrane thereby jamming export sites for other proteins and causing lethality. If so, OmpA appears to cross the plasma membrane completely during export.

A genetic approach to defining the sites of interaction of a membrane protein with different external agents

In addition to a role in maintaining outer membrane structural integrity, the OmpA protein of Escherichia coli serves as a receptor for different phages, is required in the recipient cell for efficient conjugation, and functions in the internalization of receptor-bound colicins. To determine whether the same or different sites of OmpA protein are needed for these different functions, this paper presents the properties of a collection of ompA mutants selected as being defective in phage receptor function, but containing normal amounts of OmpA protein. Of 44 mutants examined, most were affected in more than one OmpA protein function, showing that there is considerable overlap in sites needed for different functions. The pattern of this overlap can be represented in a phenotypic map of OmpA protein functions.

Mutations in multicopy Tn10 tet plasmids that confer resistance to inhibitory effects of inducers of tet gene expression

Escherichia coli K-12 strains that carry the Tn10 tetracycline resistance determinant (tet) on multicopy plasmids are hypersensitive to 5a,6-anhydrotetracycline and heated chlortetracycline, two tetracycline derivatives that are relatively more effective as inducers of tet gene expression than as inhibitors of bacterial growth. Twenty spontaneous mutations that confer resistance to anhydrotetracycline (Atr) and resistance to heated chlortetracycline (Ctr) were isolated and characterized. All of these Atr mutations are located in the Tn10 tet region; the majority (18 of 20) have no effect on tetR repressor function. Atr mutations can increase, reduce, or eliminate the phenotypic expression of plasmid tetracycline resistance (Tcr). IS insertions that result in an Atr Tcs phenotype are clustered in a 150-base-pair promoter-proximal region of the tetA resistance gene. Some Atr mutations reduce expression of the tetA gene by altering either the tetR repressor or the tetA promoter. In addition, it appears that E. coli cannot tolerate constitutive expression of the wild-type tetA gene from a multicopy plasmid containing a tetR deletion. These observations support the proposal that high level expression of the 36-kilodalton tetA gene product inhibits the growth of E. coli. We speculate that this inhibition is related to the interaction of the tetA gene product with the cytoplasmic membrane.

Information within the mature LamB protein necessary for localization to the outer membrane of E coli K12

It has been proposed that the efficient localization of the outer membrane protein LamB requires a functional signal sequence and at least two additional regions contained within the mature protein. We define these regions more precisely by deletion analysis, and we describe methods for cloning deleterious lacZ fusions onto high-copy-number plasmids and generating in-frame deletions. Analysis of the effects of a series of internal lamB deletions on the export of a LamB-LacZ hybrid protein and of the LamB protein itself indicates that necessary informational signal(s) required for localization lie at the amino-terminal end of the protein. In addition, our analysis indicates that there is a region of information close to or within the fusion joint of the largest lamB-lacZ fusion that increases the efficiency of the export process. A unique deletion that removes a protein segment from amino acid 70 to 200 appears to prevent proteolytic removal of the signal sequence. Nevertheless, the mutant protein is exported to the outer membrane.

In vitro construction and characterization of phoA-lacZ gene fusions in Escherichia coli

Using recombinant DNA techniques, we have constructed phoA-lacZ gene fusions. Two of the fusions encode hybrid proteins containing approximately half of alkaline phosphatase at the amino terminus joined to beta-galactosidase. For the one fusion strain analyzed in detail, it was shown that the hybrid protein is found in the membrane fraction of cells. In its membrane location, the beta-galactosidase activity of the hybrid is not sufficient to support cell growth on lactose. Unexpectedly, fusions containing phoA and lacZ joined in the wrong translational reading frame were also obtained. These fusions direct the phosphate-regulated synthesis of beta-galactosidase, apparently via a translation restart mechanism. Thus, when gene fusions are constructed, the presence of properly regulated beta-galactosidase activity does not necessarily indicate that a hybrid protein is being produced.

Characterisation of the promoter for the LexA regulated sulA gene of Escherichia coli

The sulA gene of Escherichia coli, which encodes an inducible inhibitor of cell division, plays a role in the SOS response. Its expression, like that of other SOS genes, is repressed by the LexA protein. This paper reports the identification and characterisation of the promoter for the cloned sulA gene. The promoter bears good resemblance to the consensus promoter sequence and directs the synthesis of two major RNA species both in vitro and in vivo. Comparison of the sequence around the sulA promoter with the operator sequences of other SOS genes revealed the presence of an SOS box, the LexA protein binding site. This overlaps the -10 region of the promoter and covers the transcriptional initiation sites. LexA protein bound to this SOS box, would, therefore, effectively block transcription.

Apparent bacteriophage-binding region of an Escherichia coli K-12 outer membrane protein

The 325-residue OmpA protein is one of the major outer membrane proteins of Escherichia coli. It serves as the receptor for several T-even-like phages and is required for the action of certain colicins and for the stabilization of mating aggregates in conjugation. We have isolated two mutant alleles of the cloned ompA gene which produce a protein that no longer functions as a phage receptor. Bacteria possessing the mutant proteins were unable to bind the phages, either reversibly or irreversibly. However, both proteins still functioned in conjugation, and one of them conferred colicin L sensitivity. DNA sequence analysis showed that the phage-resistant, colicin-sensitive phenotype exhibited by one mutant was due to the amino acid substitution Gly leads to Arg at position 70. The second mutant, which contained a tandem duplication, encodes a larger product with 8 additional amino acid residues, 7 of which are a repeat of the sequence between residues 57 and 63. In contrast to the wild-type OmpA protein, this derivative was partially digested by pronase when intact cells were treated with the enzyme. The protease removed 64 NH2-terminal residues, thereby indicating that this part of the protein is exposed to the outside. It is argued that the phage receptor site is most likely situated around residues 60 to 70 of the OmpA protein and that the alterations characterized have directly affected this site.

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.

Strategies for cultivation of recombinant organisms

An overview on the strategies for cultivation of recombinant organisms is presented in three sections, that is, the stability of plasmids, expression of cloned genes and an example of a genetically engineered microorganism.

Genetic analysis of protein export in Escherichia coli

Genetic studies on the secretion process in gram-negative bacteria have made considerable progress. Within the near future, such studies should lead to a detailed understanding of the important features of signal sequences and how they function. The cloning of the structural gene for an enzyme that cleaves signal sequences from precursors of secreted proteins will allow the genetic characterization of this locus and its function. Finally, the isolation and characterization of mutants that affect components of the cell's secretory apparatus are also under way. These mutants permit the detection of genes and their products that are involved in secretion. A combination of the genetic approaches and in vitro studies should lead to a picture of the details of passage of proteins through a membrane.