- Volume 141, Issue 11, 1995
Volume 141, Issue 11, 1995
- Review Article
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From morphogenes to morphogenesis
More LessSummary: If the concept of organization is of such importance as it appears to be, it is something of a scandal that biologists have not yet begun to take it seriously but should have to confess that we have no adequate conception of it. The first duty of the biologist would seem to be to try and make clear this important concept.
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- Microbiology Comment
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- Biotechnology
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Informed strain improvement for lignin degradation by Phanerochaete chrysosporium
More LessSummary: The effect of breeding from the white rot fungus Phanerochaete chrysosporium ME446 on performance for lignin mineralization was examined. This model for informed strain improvement without mutagenesis is based on abundant restriction fragment length polymorphisms (RFLPs). Under optimized conditions for lignin mineralization, extracellular manganese peroxidase (MnP) but not lignin peroxidase (LiP) could be detected, so measurement of LiP activity is not a valid assay for lignin degradation. Mineralization of 14C-labelled synthetic lignin (14C-DHP) was used to compare the performance of the wild-type strain ME446 with those of sets of progeny strains. Meiotic progeny from strain ME446, heterokaryotic progeny of crosses between such strains, and meiotic progeny of one heterokaryotic strain were examined. In each case, a minority of strains performed more efficiently than the parental strain ME446. The greatest range of lignin-mineralization performance (70-fold) was found within the set of initial progeny of ME446 and the narrowest was within the set of secondary homokaryotic strains. This is consistent with the view that a moderate number of determinants contribute to lignin mineralization performance. However, performance did not correlate with the possession of any single allele of those for 38 previously defined RFLP markers. The results show that lignin mineralization performance can be improved by cycles of crosses and fruiting, without mutagenesis.
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- Environmental Microbiology
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Amplification of 16S ribosomal RNA genes of autotrophic ammonia-oxidizing bacteria demonstrates the ubiquity of nitrosospiras in the environment
Summary: Oligonucleotide sequences selected from the 16S rRNA genes of various species of ammonia-oxidizing bacteria were evaluated as specific PCR amplification primers and probes. The specificities of primer pairs for eubacterial, Nitrosospira and Nitrosomonas rRNA genes were established with sequence databases, and the primer pairs were used to amplify DNA from laboratory cultures and environmental samples. Eubacterial rRNA genes amplified from samples of soil and activated sludge hybridized with an oligonucleotide probe specific for Nitrosospira spp., but not with a Nitrosomonas-specific probe. Lakewater and sediment samples were analysed using a nested PCR technique in which eubacterial rRNA genes were subjected to a secondary amplification with Nitrosomonas or Nitrosospira specific primers. Again, the presence of Nitrosospira DNA, but not Nitrosomonas DNA, was detected and this was confirmed by hybridization of the amplified DNA with an internal oligonucleotide probe. Enrichments of lakewater and sediment samples, incubated for two weeks in the presence of ammonium, produced nitrite and were found to contain DNA from both Nitrosospira and Nitrosomonas as determined by nested PCR amplification and probing of 16S rRNA genes. This demonstrates that Nitrosospira spp. are widespread in the environment. The implications of the detection of Nitrosomonas DNA only after enrichment culture are discussed.
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Rapid screening for bacterial phenotypes capable of biodegrading anionic surfactants: development and validation of a microtitre plate method
More LessSummary: The Biolog microtitre plate assay, which is based on tetrazolium dye reduction as an indicator of sole-carbon-source utilization, has been evaluated as a rapid method to investigate the biodegradation of five classes of anionic surfactant by pure and mixed cultures of bacteria. The assay gave reproducible results over a fourfold range of inoculum optical density, and the surfactant concentration was selected to provide a compromise between the length of the lag period prior to colour production and the maximum colour produced. A kinetic model was developed and used to analyse the appearance of colour in the assay and was found to give rise to three biologically significant parameters describing the processes underlying the assay. No false-positives were obtained with environmental isolates. The small number of false-negatives obtained (< 8% of the total) could be explained by the methodology used to prepare the bacterial inoculum. All isolates which were positive in the Biolog assay were shown to be both primary and ultimate degraders of the test surfactant. These results show that the method provides a useful means of studying the biodegradation of anionic surfactants by both pure and mixed cultures of bacteria and will find use in the rapid analysis of biodegradation kinetics and specificities of larger numbers of individual isolates than hitherto possible. In addition, an important benefit of the methodology is that it can be used for direct analysis of the biodegradation potential of whole bacterial communities without having to make an artificial selection during laboratory growth.
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- Genetics And Molecular Biology
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Ectopic expression of the Streptomyces coelicolor whiE genes for polyketide spore pigment synthesis and their interaction with the act genes for actinorhodin biosynthesis
More LessSummary: The whiE gene cluster of Streptomyces coelicolor is normally expressed shortly before sporulation in the aerial mycelium, leading to production of the grey polyketide spore pigment. By placing the whiE genes under the control of the thiostrepton-inducible tipA promoter, they were artificially expressed on plasmids or in the chromosome during vegetative growth in a strain deleted for the act genes, which control biosynthesis of the polyketide antibiotic actinorhodin. Certain combinations of whiE-ORFI-VII led to production of mycelial pigments; these were exported into the medium when whiE-ORFI was absent, but poorly in its presence. Combined with comparative sequence data, the results allowed deductions to be made, or confirmed, about the normal roles of the eight known genes, whiE-ORFI-VIII, as follows: whiE-ORFIII, IV, V encode the three components (ketosynthase, chain length factor and acyl carrier protein) of the whiE minimal polyketide synthase (PKS) needed for assembly of the carbon chain of the spore pigment precursor; whiE-ORFII, VI, VII are likely to be involved in cyclizations of the nascent carbon chain; whiE-ORFVIII controls a late step in the spore pigment biosynthetic pathway, probably a hydroxylation; and whiE-ORFI may encode a protein needed for correct targeting or retention of spore pigment at an appropriate cellular location. In other experiments, genes encoding components of the act-PKS and whiE-PKS were artificially co-expressed. Each of the three whiE minimal PKS subunit genes could complement lesions in the corresponding act-PKS genes to produce actinorhodin or related mycelial pigments, and each of the three act minimal PKS genes could complement lesions in the whiE minimal PKS genes to cause spore pigmentation. Thus the two sets of PKS subunits, which are encoded by genes that have presumably diverged from a common ancestor, are still capable of biochemical cross-talk, but this is normally prevented because the gene sets are expressed in different tissues of the differentiated Streptomyces colony. Ectopic expression of sets of whiE-PKS genes presumed to be sufficient to assemble a carbon chain caused inhibition of early growth of the strains, perhaps by causing interference with fatty acid biosynthesis; this yielded circumstantial evidence that the whiE-PKS gene products can also interact with those of the fatty acid synthase(s) of the organism.
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Chimeric FimH adhesin of type 1 fimbriae: a bacterial surface display system for heterologous sequences
More LessSummary: The FimH adhesin of type 1 fimbriae has been tested as a display system for heterologous protein segments on the surface of Escherichia coli. This was carried out by introduction of restriction site handles (Bg/ll sites) in two different positions in the fimH gene, followed by in-frame insertion of heterologous DNA segments encoding two reporter sequences. In the selected positions such insertions did not significantly alter the function of the FimH protein with regard to surface location and adhesive ability. The system seemed to be quite flexible, since chimeric versions of the FimH adhesin containing as many as 56 foreign amino acids were transported to the bacterial surface as components of the fimbrial organelles. Furthermore, the foreign protein segments were recognized by insert-specific antibodies when expressed within chimeric proteins on the surface of the bacteria. The results from this feasibility study point to the possibility of using the FimH adhesin as a general surface display system for sizeable protein segments.
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Molecular cloning of a Coxiella burnetii gene encoding a macrophage infectivity potentiator (Mip) analogue
More LessSummary: The gene encoding a protein that reacted with antibodies specific for Legionella pneumophila macrophage infectivity potentiator (LpMip) was cloned from Coxiella burnetii, the obligate intracellular rickettsia that causes Q fever in humans. Nucleotide sequencing analysis revealed an ORF encoding a gene product of 230 amino acids with a molecular mass of 25-5 kDa and a predicted pI of 10-7. The predicted amino acid sequence from the ORF shows similarity with Mip/Mip-like proteins of Legionella (46%) and Chlamydia (30%). Moreover, like LpMip, the amino acid sequence of the C terminus of this protein has over 35% identity to prokaryotic and eukaryotic FK506-binding proteins (FKBPs) that belong to a superfamily of immunophilins and are peptidyl-prolyl cis-trans isomerases (PPlases). When overproduced in Escherichia coli, the C. burnetii protein also exhibited PPlase activity. Taken together, these results demonstrate that C. burnetii encodes a Mip analogue (CbMip). A putative leader peptide at the N terminus of CbMip was detected by computer analysis. Furthermore, TnphoA mutagenesis demonstrated that in E. coli CbMip was secreted. In view of the role of Mip/Mip-like proteins in the pathogenesis of Legionella and Chlamydia, CbMip may be a C. burnetii virulence factor.
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A non-essential glutamyl aminopeptidase is required for optimal growth of Lactococcus lactis MG1363 in milk
More LessSummary: Degenerate PCR primers were designed from the N-terminal amino acid sequence of a glutamyl aminopeptidase (PepA) from Lactococcus lactis. These primers were used to screen a lambda library for clones containing the gene (pepA) encoding PepA. The DNA sequence of a 2-1 kb fragment containing pepA was determined. The sequence revealed the presence of one complete and two incomplete open reading frames (ORFs). The complete ORF encodes a putative protein of 353 amino acids with a predicted N-terminal sequence identical to that determined for purified PepA. The pepA gene was subcloned on an Escherichia coli plasmid vector and production of active PepA was confirmed by means of a zymogram. Mutants of L. lactis in which the pepA gene was inactivated grew to normal cell densities in milk but exhibited a reduced growth rate during the exponential phase. Thus whilst PepA is required for optimal growth it is not essential.
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Isolation and properties of acetate kinase- and phosphotransacetylase-negative mutants of Thermoanaerobacter thermohydrosulfuricus
Summary: Thermoanaerobacter thermohydrosulfuricus (Clostridium thermohydrosulfuricum) ferments carbohydrate substrates to acetate, ethanol and L-lactate. To block acetate production, mutants defective in acetate kinase and/or phosphotransacetylase were isolated after mutagenesis with N-methyl-N'-nitro-N-nitroguanidine by selection for fluoroacetate resistance and subsequent counterselection for growth on pyruvate. Upon growth on glucose, all mutants formed only minor amounts of acetate and markedly less ethanol than the wild-type. The mutants produced L-lactate as the main fermentation product, yielding up to 1-8 mol lactate (mol glucose)−1 as compared to 0-7 mol lactate (mol glucose)−1 obtained with the parent strain. Expression of the genes encoding acetate kinase and phosphotransacetylase was found to be negatively controlled by acetate.
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Arylsulphatase from Alteromonas carrageenovora
More LessSummary: Arylsulphatase activity was identified in cultures of the marine bacterium Alteromonas carrageenovora, using methylumbelliferyl sulphate as substrate. In contrast with most other microbial arylsulphatases, arylsulphatase production in A. carrageenovora was not repressed by sulphate. The structural gene of arylsulphatase (atsA) was cloned and sequenced. An ORF of 984 bp was found, specifying a primary translation product of 328 amino acids with a molecular mass of 35797 Da. Arylsulphatase was partially purified from cell extracts of both A. carrageenovora and recombinant Escherichia coli. Both the recombinant and native enzymes exhibited a pl of 5-5, a Michaelis constant for methylumbelliferyl sulphate of 68 μM, and a molecular mass of approximately 35000 Da in SDS-PAGE analysis. Secondary structure comparisons using hydrophobic cluster analysis suggest functional analogies between the arylsulphatase of A. carrageenovora, that of Mycobacterium leprae and a 33-5 kDa protein from Porphyromonas gingivalis. It is speculated that these proteins are all glycosulphohydrolases, involved with desulphatation of sulphated polysaccharides.
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Membrane topology analysis of the Escherichia coli cytosine permease
More LessSummary: The Escherichia coli codBA operon encodes cytosine permease (CodB) and cytosine deaminase (CodA). CodB mediates uptake of exogenously supplied cytosine, and CodA catalyses the hydrolytic deamination of cytosine to uracil and ammonia. The hydropathic profile of CodB indicates that it is an integral cytoplasmic membrane protein possessing several transmembrane-spanning domains. The membrane topology of CodB was investigated by using gene fusions containing varying lengths of the amino-terminus of CodB fused to either alkaline phosphatase (AP) or β-galactosidase (BG). The AP activities expressed by the CodB-AP fusions are consistent with a topological model in which the amino- and the carboxy-termini of CodB are located in the cytoplasm, and in which CodB possesses 12 membrane-spanning segments. The enzyme activities of most of the CodB-BG fusions support the model. However, the results obtained with some of the CodB-BG fusions illustrate the limitations of using BG as a reporter protein in studies of membrane protein topology.
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The dspA gene product of the cyanobacterium Synechocystis sp. strain PCC 6803 influences sensitivity to chemically different growth inhibitors and has amino acid similarity to histidine protein kinases
More LessSummary: We have cloned and sequenced a gene of the cyanobacterium Synechocystis sp. strain PCC 6803 named dspA (encoding drug sensory protein A; DspA), mutations in which result in cross-resistance to the herbicides difunon and diuron, as well as to the calmodulin antagonists chlorpromazine and trifluoperazine. The dspA gene encodes a polypeptide of 663 amino acids with a predicted molecular mass of 745 kDa. The molecular nature of two mutations in the dspA gene leading to the cross-resistance has been determined. Targeted mutagenesis of the dspA gene was performed using a kanamycin-resistance gene cartridge. Resulting mutant strains were checked for resistance to difunon and chlorpromazine and showed cross-resistance to both agents. The C-terminal portion of the deduced amino acid sequence of DspA shares significant similarity with the conserved region of histidine protein kinases (HPKs). Hydrophobicity analysis of the amino acid sequence of DspA indicated the existence of two hydrophobic regions in the N-terminal portion that are characteristic of the bacterial sensory HPK family. We suggest that protein DspA is a HPK involved in chemical sensing.
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A ribonucleic antiterminator sequence (RAT) and a distant palindrome are both involved in sucrose induction of the Bacillus subtilis sacXY regulatory operon
More LessSummary: The Bacillus subtilis sacXY regulatory operon is involved in sucrose induction of the levansucrase sacB gene by an antitermination mechanism. In the presence of sucrose, the activated SacY antiterminator protein stabilizes the secondary structure of a ribonucleic antiterminator sequence (RAT) located in the leader region of the sacB transcript, and overlapping a rho-independent transcription terminator. Formation of the SacY-RAT complex prevents alternative formation of the terminator, allowing transcription of the downstream sequences. In the absence of sucrose, inhibition of SacY activity by SacX leads to termination of transcription. Expression of sacXY is also sucrose-inducible. This induction was previously shown to be mediated by SacY itself and/or SacT, another antiterminator involved in induction of genes belonging to a distinct sucrose pathway. These antiterminators are not activated at the same concentration of sucrose. We show here that sacXY induction occurs through activation of either SacY or SacT antiterminators, at their respective sucrose activation concentration. This result demonstrates a link between SacY- and SacT-mediated metabolic pathways. In addition, the sacXY leader region carries a RAT-like sequence, which however does not appear to overlap any apparent rho-independent transcription terminator. Site-directed mutagenesis experiments on this RAT-like sequence demonstrated its involvement in sucrose induction. Deletions generated in the sacXY leader region showed that a palindrome, located 100 nt downstream from the RAT-like sequence, also acts as a cis-acting element. Computer analysis of the leader RNA suggested that formation of the secondary structure of the RAT-like sequence and the palindrome could be mutually exclusive.
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Small cytoplasmic RNA (scRNA) gene from Clostridium perfringens can replace the gene for the Bacillus subtilis scRNA in both growth and sporulation
More LessSummary: Small cytoplasmic RNA (scRNA) is a member of an evolutionary conserved signal-recognition-particle-like RNA family. Using a DNA fragment of Bacillus subtilis scRNA gene as a probe, we cloned and characterized a Clostridium perfringens gene encoding the scRNA. Mapping the 5' and 3' ends of scRNA revealed that C. perfringens scRNA consists of 269 nucleotides: the sequence has about 70% primary sequence homology with B. subtilis scRNA. The predicted secondary structure appeared to be similar to that of B. subtilis scRNA, indicating that there are domains I and II in C. perfringens scRNA, in addition to domain IV. Functional analysis showed that C. perfringens scRNA could compensate for vegetative growth and allow the formation of heat-resistant spores in an scRNA-depleted B. subtilis strain, whereas Escherichia coli 45S RNA could not maintain sporulation. Since both E. coli 45S RNA and C. perfringens scRNA have the same binding specificity to B. subtilis Ffh protein, the difference in complementation activity reflects the function of domains I and II.
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Can phage defence maintain colicin plasmids in Escherichia coli
More LessSummary: We examined the role of plasmid-based phage defence in maintaining plasmids, using colicin plasmids in Escherichia coli as a model system. Experimental data indicated that the possession of a colicin plasmid can confer limited protection against bacteriophages. A continuous culture model, using these experimental values, indicated that the observed limited protection alone could selectively maintain colicin plasmids, without requiring a competitive advantage due to colicinogeny. Phage defence might explain the current maintenance of colicin plasmids, given the naturally occurring high levels of resistance to colicins. This model also suggests that many plasmids might be maintained in natural populations, in part, by phage resistance, including ‘cryptic’ plasmids for which no phenotype is known.
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Methanol oxidation mutants in Methylobacterium extorquens AM1: identification of new genetic complementation groups
More LessSummary: Two-hundred-and-eight new Methylobacterium extorquens AM1 methanol oxidation (Mox) mutants were isolated and placed into complementation groups. Complementation analyses identified new Mox groups in the Mxb and Mxc loci and at a new locus, Mxd. Thirty-seven mutants at the Mxb locus were divided into MxbM and MxbD complementation groups on the basis of their complementation pattern. Twenty-nine mutants at the Mxc locus fell into three complementation groups, MxcB, MxcQ and MxcE. The direction of transcription for genes at this locus could be inferred from the subclones. Eighteen of the new mutants were not complemented by previously isolated M. extorquens AM1 clones but were complemented by two new overlapping clones. This locus was called Mxd and the mutants fell into two complementation groups, MxdR and MxdS. Immunoblots from all these mutant classes showed that all of the Mxb and Mxc strains had substantially reduced levels of MxaF (large subunit of methanol dehydrogenase) and cytochrome c L, compared to the wild-type. These mutants, particularly the Mxb mutants, also had elevated levels of cytochroma c-553. These results are consistent with a role for the MxbMD and MxcBQE complementation groups in the regulation of expression of mxaF. The MxdR and MxdS mutants had normal levels of MxaF and both c-type cytochromes.
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The mxaAKL genes of Methylobacter albus BG8
More LessSummary: The facultative methanol utilizer Methylobacterium extorquens AM1 contains at least three genes (mxaA, K and L) that encode functions involved in providing calcium to the holoenzyme of methanol dehydrogenase, the enzyme that oxidizes methanol to formaldehyde in this strain. Methane-utilizing bacteria (methanotrophs) also contain methanol dehydrogenase, and evidence suggests that similar methanol oxidation (Mox) functions may be present in some of these strains. DNA fragments from Methylobacterium extorquens AM1 specific to mxaA, mxaK and mxaL were isolated for use as hybridization probes against genomic digests of a variety of methanotrophic bacteria. Only the mxaL probe showed substantial hybridization, and it was used to identify and isolate an 8·5 kb HindIII fragment from Methylobacter albus BG8 (a Type I methanotroph). Hybridization of restriction digests of this fragment to individual probes for Methylobacterium extorquens AM1 mxaA, K and L indicated that the relative mxa gene order in Methylobacter albus BG8 is A-K-L. A T7 dual promoter/polymerase protein expression system indicated that five polypeptides are expressed from a 4·5 kb region of Methylobacter albus BG8 DNA in Escherichia coli, all transcribed in the same direction, and they apparently correspond to mxaACKDL. The functions of mxaC and mxaD are currently not known, but the order of mxaDL is reversed in Methylobacter albus BG8 compared to Methylobacterium extorquens AM1. When subclones o the Methylobacter albus BG8 fragment containing these genes were used as hybridization probes to genomic digests of methanotrophic bacteria, specific bands were detected that suggested a similar gene order in most cases. These data indicate that the mxaAKL region is relatively highly conserved in methanotrophs, and that in most cases the mxaAKL genes are grouped together in the same order as in the facultative methanol utilizer Methylobacterium extorquens AM1.
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Expression studies on four members of the pMGA multigene family in Mycoplasma gallisepticum 56
More LessSummary: Expression studies on four members of the pMGA multigene family in Mycoplasma gallisepticumA large family of related genes known as pMGA exists in the avian pathogen Mycoplasma gallisepticum but only a single member of this family was previously found to be expressed in one strain of this bacterium. In this work two unrelated strains of M. gallisepticum were also shown by amino-terminal sequencing to express a unique pMGA polypeptide in both cases. To investigate pMGA gene selection in M. gallisepticum, mRNA expression was analysed in M. gallisepticum strain S6 using reverse transcription-PCR (RT-PCR and Northern blot techniques with probes for several members of the pMGA multigene family. It was shown that the pMGA message is 2·2 kb in size and is monocistronic. RT-PCR detected four different pMGA mRNA molecules but the relative yields were significantly affected by magnesium concentration. By quantitative Northern analysis, the relative abundances of the four pMGA mRNAs in M. gallisepticum S6 total RNA was determined: the pMGA1.1 mRNA predominated [1·88 ng (μg total RNA)−1] but at least three other pMGA genes were found to be transcribed but at much lower levels (20 to 40-fold lower). The pMGA1.1 mRNA is expressed at a level five times higher than the tuf gene known to be one of the most abundantly expressed proteins in the prokaryoti cell. The start point of transcription for pMGA1.1 was determined and probable promoter assigned. From these data it appears likely that transcriptional control plays a major role in the selection of pMGA gene expression in the M. gallisepticum cell. S6
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- Pathogenicity And Medical Microbiology
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Molecular analysis of the cso operon of enterotoxigenic Escherichia coli reveals that CsoA is the adhesin of CS1 fimbriae and that the accessory genes are interchangeable with those of the cfa operon
More LessSummary: A deletion mutation in csoA, the gene encoding the structural subunit protein of CS1 fimbriae of enterotoxigenic Escherichia coli of serotype O6:K15:H16 or H -, was constructed in the subcloned CS1 genetic determinant. The mutation resulted in the abolition of CS1 fimbrial adhesiveness. Complementation, in trans, involving the determinant with the csoA deletion mutation and the gene encoding the structural subunit protein, CsoA, expressed from compatible plasmids, restored the expression and adhesive ability of CS1 fimbriae. In addition, trans-complementation was achieved between the cso determinant with the aforementioned deletion mutation and the cfaB gene encoding the structural subunit protein (CfaB) of CFA/I fimbriae, resulting in the expression of CFA/I fimbriae. The observation that heterologous assembly was possible between these two fimbrial systems, together with the knowledge that the adhesin of CFA/I fimbriae is the structural subunit, was exploited to investigate whether CsoA had adhering properties. A deletion mutation in cfaB was created in the CFA/I fimbrial determinant. Complementation of this mutation with csoA in trans resulted in expression of the CsoA antigen on the bacterial cell surface and restoration of bacterial adherence. As no minor subunits act as the adhesin in CFA/I fimbriae, adhesion was mediated by CsoA. Nucleotide sequencing of the DNA region downstream from csoA confirmed the absence of genes encoding minor subunits which might act as the adhesin. Two open reading frames were revealed which encoded proteins sharing considerable homology with proteins encoded by corresponding ORFs in the CFA/I fimbrial operon. These proteins underlie the functional similarities between the CS1 and CFA/I fimbrial systems, allowing heterologous expression of their respective subunits.
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