- Volume 149, Issue 3, 2003

In bacteria, the first reaction of the tryptophan biosynthetic pathway involves the conversion of chorismate and glutamine to anthranilate by the action of anthranilate synthase, which is composed of the α (trpE gene product) and β (trpG gene product) subunits. In this study, the tryptophan biosynthetic gene trpE of the spirochaete Leptospira meyeri was interrupted by a kanamycin-resistance cassette by homologous recombination. The trpE double cross-over mutant was not able to grow on solid or in liquid EMJH medium. In contrast, the trpE mutant showed a wild-type phenotype when tryptophan or anthranilate was added to the media, therefore showing that disruption of the L. meyeri trpE gene resulted in tryptophan auxotrophy. The authors have also characterized a second selectable marker that allows the construction of a spectinomycin-resistant L. meyeri–E. coli shuttle vector and the functional complementation of the L. meyeri trpE mutant.

A gene encoding a putative peptidoglycan hydrolase, named acmB, which is a paralogue of the major autolysin acmA gene, was identified in the Lactococcus lactis genome sequence. The acmB gene is transcribed in L. lactis MG1363 and its expression is modulated during cellular growth. The encoded AcmB protein has a modular structure with three domains: an N-terminal domain, especially rich in Ser, Thr, Pro and Asn residues, resembling a cell-wall-associated domain; a central domain homologous to the Enterococcus hirae muramidase catalytic domain; and a C-terminal domain of unknown function. A recombinant AcmB derivative, devoid of its N-terminal domain, was expressed in Escherichia coli. It exhibited hydrolysing activity on the peptidoglycan of several Gram-positive bacteria, including L. lactis. Though showing sequence similarity with enterococcal muramidase, AcmB has N-acetylglucosaminidase specificity. The acmB gene was inactivated in order to evaluate the role of the enzyme. AcmB does not appear to be involved in cell separation but contributes to cellular autolysis.

Putrescine can be synthesized either directly from ornithine by ornithine decarboxylase (ODC; the speC product) or indirectly from arginine via arginine decarboxylase (ADC; the speA product). The authors identified the speA and speC genes in Pseudomonas aeruginosa PAO1. The activities of the two decarboxylases were similar and each enzyme alone appeared to direct sufficient formation of the polyamine for normal growth. A mutant defective in both speA and speC was a putrescine auxotroph. In this strain, agmatine deiminase (the aguA product) and N-carbamoylputrescine amidohydrolase (the aguB product), which were initially identified as the catabolic enzymes of agmatine, biosynthetically convert agmatine to putrescine in the ADC pathway: a double mutant of aguAB and speC was a putrescine auxotroph. AguA was purified as a homodimer of 43 kDa subunits and AguB as a homohexamer of 33 kDa subunits. AguA specifically deiminated agmatine with K m and K cat values of 0·6 mM and 4·2 s−1, respectively. AguB was specific to N-carbamoylputrescine and the K m and K cat values of the enzyme for the substrate were 0·5 mM and 3·3 s−1, respectively. Whereas AguA has no structural relationship to any known C–N hydrolases, AguB is a protein of the nitrilase family that performs thiol-assisted catalysis. Inhibition by SH reagents and the conserved cysteine residue in AguA and its homologues suggested that this enzyme is also involved in thiol-mediated catalysis.

Production of the signalling molecule (autoinducer-2) synthesized by LuxS has been proposed to be pivotal to a universal mechanism of inter-species bacterial cell–cell communication (quorum sensing); however recently the function of LuxS has been noted to be integral to central metabolism since it contributes to the activated methyl cycle. This paper shows that when Helicobacter pylori LuxS is overproduced in Escherichia coli, it forms cross-linkable multimers. These multimers persist at comparable levels after 24 h of growth if glucose is omitted from the growth medium; however, the levels of extracellular autoinducer-2 decline (Glucose Retention of AI-2 Levels: GRAIL). Glycerol, maltose, galactose, ribose and l-arabinose could substitute for glucose, but lactose, d-arabinose, acetate, citrate and pyruvate could not. Mutations in (i) metabolic pathways (glycolytic enzymes eno, pgk, pgm; galactose epimerase; the Pta–AckA pathway), (ii) sugar transport (pts components, rbs operon, mgl, trg), and (iii) regulators involved in conventional catabolic repression (crp, cya), cAMP-independent catabolite repression (creC, fruR, rpoS,) the stringent response (relA, spoT) and the global carbon storage regulator (csrA) did not prevent GRAIL. Although the basis of GRAIL remains uncertain, it is clear that the mechanism is distinct from conventional catabolite repression. Moreover, GRAIL is not due to inactivation of the enzymic activity of LuxS, since in E. coli, LuxS contained within stationary-phase cells grown in the absence of glucose maintains its activity in vitro.

In order to further understand the different physiological states of the tubercle bacillus, a frame of reference was sought by first correlating the macromolecular compositions of Escherichia coli with specific growth rates and also with the rates of protein synthesis. Data for DNA : protein : RNA were converted to the average amounts of DNA [ m DNA(av)], protein [ m p(av)] and RNA [ m RNA(av)] per cell. The specific growth rate μ was found to be directly proportional to m RNA(av)/ m p(av). The specific protein synthesis rate per average cell [ω p(av)] was shown to be directly proportional to the third power of the ratio m RNA(av)/ m p(av) which reflects the ribosome concentration. The equations derived were shown apply to both E. coli (μ=1·73 h−1) and Mycobacterium bovis BCG (μ=0·029 h−1).

In Bacillus subtilis, expression of the rocG gene, encoding glutamate dehydrogenase, and the rocABC operon, involved in arginine catabolism, requires SigL (σ54)-containing RNA polymerase as well as RocR, a positive regulator of the NtrC/NifA family. The RocR protein was purified and shown to bind specifically to the intergenic region located between rocG and the rocABC operon. DNaseI footprinting experiments were used to define the RocR-binding site as an 8 bp inverted repeat, separated by one base pair, forming an imperfect palindrome which is present twice within the rocG–rocABC intergenic region, acting as both a downstream activating sequence (DAS) and an upstream activating sequence (UAS). Point mutations in either of these two sequences significantly lowered expression of both rocG and rocABC. This bidirectional enhancer element retained partial activity even when moved 9 kb downstream of the rocA promoter. Electron microscopy experiments indicated that an intrinsically curved region is located between the UAS/DAS region and the promoter of the rocABC operon. This curvature could facilitate interaction of RocR with σ54-RNA polymerase at the rocABC promoter.

Glycolysis is one of the central routes of carbon catabolism in Bacillus subtilis. Several glycolytic enzymes, including the key enzyme glyceraldehyde-3-phosphate dehydrogenase, are encoded in the hexacistronic gapA operon. Expression of this operon is induced by a variety of sugars and amino acids. Under non-inducing conditions, expression is repressed by the CggR repressor protein, the product of the promoter-proximal gene of the operon. Here, it is shown that the amount of glyceraldehyde-3-phosphate dehydrogenase encoded by the second gene of the operon exceeds that of the CggR repressor by about 100-fold. This differential synthesis was attributed to an mRNA processing event that takes place at the 3′ end of the cggR open reading frame and to differential segmental stabilities of the resulting cleavage products. The mRNA specifying the truncated cggR gene is quickly degraded, whereas the downstream processing products encompassing gapA are quite stable. This increased stability is conferred by the presence of a stem–loop structure at the 5′ end of the processed mRNAs. Mutations were introduced in the region of the cleavage site. A mutation affecting the stability of the stem–loop structure immediately downstream of the processing site had two effects. First, the steady-state transcript pattern was drastically shifted towards the primary transcripts; second, the stability of the processed mRNA containing the destabilized stem–loop structure was strongly decreased. This results in a reduction of the amount of glyceraldehyde-3-phosphate dehydrogenase in the cell. It is concluded that mRNA processing is involved in differential syntheses of the proteins encoded by the gapA operon.

Previous work has resulted in the isolation of several mutant glucose permeases (IIGlc or PtsG) of the Escherichia coli phosphotransferase system (PTS) with altered N-terminal amphipathic leader sequences. The mutations were reported to (1) broaden permease substrate specificity, (2) promote facilitated diffusion of some sugars and (3) increase ptsG gene transcription. Detailed biochemical analyses were conducted, showing that one such mutant (V12F-IIGlc) (1) contains dramatically increased amounts of IIGlc, (2) displays correspondingly increased in vitro phosphorylation and in vivo transport activities, (3) shows increased utilization of several metabolizable sugars and (4) shows decreased susceptibility to detergent activation. These results are interpreted as suggesting that the V12F substitution in the N-terminal amphipathic leader sequence of IIGlc alters the facility with which the permease is integrated into the membrane. Consequent changes in conformation alter its catalytic properties and increase its affinity for the pleiotropic transcriptional repressor, Mlc. These changes together are proposed to promote transcription of the ptsG gene and account for the observed phenotypic changes.

The regions flanking the Mycobacterium dnaA gene have extensive sequence conservation, and comprise various DnaA boxes. Comparative analysis of the dnaA promoter and oriC region from several mycobacterial species revealed that the localization, spacing and orientation of the DnaA boxes are conserved. Detailed transcriptional analysis in M. smegmatis and M. bovis BCG shows that the dnaN gene of both species and the dnaA gene of M. bovis BCG are transcribed from two promoters, whereas the dnaA gene of M. smegmatis is transcribed from a single promoter. RT-PCR with total RNA showed that dnaA and dnaN were expressed in both species at all growth stages. Analysis of the promoter activity using dnaA–gfp fusion plasmids and DnaA expression plasmids indicates that the dnaA gene is autoregulated, although the degree of transcriptional autorepression was moderate. Transcription was also detected in the vicinity of oriC of M. bovis BCG, but not of M. smegmatis. These results suggest that a more complex transcriptional mechanism may be involved in the slow-growing mycobacteria, which regulates the expression of dnaA and initiation of chromosomal DNA replication.

A series of Staphylococcus aureus–Escherichia coli shuttle vectors were constructed which contained the replication and maintenance functions of the S. aureus theta-mode multiresistance plasmid pSK1. The utility of the newly constructed vectors was demonstrated by the successful cloning and expression of several genes that had previously proven difficult to express in S. aureus. Additional vectors which permit the generation of transcriptional and translational fusions to an S. aureus blaZ reporter gene were also produced and subsequently employed to determine the relative strengths in S. aureus of a number of promoters. By utilizing the theta-mode replication functions of pSK1, the shuttle vectors described largely avoided the segregational and structural stability problems frequently encountered with Gram-positive rolling-circle-based vectors. In addition, these plasmids represent vectors which are suitable for the analysis of genes in S. aureus at low copy number.

The 16S–23S rRNA internal transcribed spacer (ITS) region of several Streptococcus thermophilus strains and some related dairy streptococci, S. macedonicus, S. salivarius and S. bovis, was analysed by sequence analysis. All the Streptococcus species were easily discriminated on the basis of sequence variations principally located upstream and downstream of the region encompassing the double-stranded processing sites and the tRNAAla gene. Comparison between tRNAAla gene sequences highlighted a high level of sequence conservation among the Streptococcus species investigated despite their belonging to separated phylogenetic clusters, i.e. the S. salivarius and S. bovis rRNA groups. A low but significant degree of variability was detected among the S. thermophilus strains, allowing the identification of four different ITS sequences. Similarity analysis of the ITS sequences showed that the Streptococcus species were clustered in two main branches, one containing S. macedonicus and S. bovis strains, and one containing S. thermophilus and S. salivarius strains. With the aim of developing a rapid tool for the identification of the dairy streptococci species a multiplex ITS-SSCP analysis of two discrete regions within the ITS locus was carried out.

Bartonella henselae is a fastidious, Gram-negative bacterial pathogen of cats and humans. Previous workers have shown that serial passage in vitro leads to attenuation of virulence-associated attributes such as expression of pili, invasion of human epithelial cell lines and the stimulation of endothelial cell proliferation. In contrast to the published data, it was found that pilin expression is frequently preserved in organisms which have undergone phase variation in vitro. Transition from a slow-growing, dry agar-pitting (DAP) to a faster-growing, smooth non-agar-pitting (SNP) form appears to occur predictably and may reflect competition between two populations growing at different rates. Better survival of the slower-growing (DAP) form may explain its relatively easy retrieval from piliated SNP populations allowed to age on solid media. Pilin expression is associated with auto-agglutination in liquid suspension or broth cultures, and appears to be necessary but not sufficient for expression of the agar-pitting phenotype and for the formation of biofilms. Outer-membrane protein variation is seen in association with phase variation, but lipopolysaccharide expression is preserved in piliated as well as extensively passaged non-piliated isolates. The EagI/HhaI infrequent restriction site-PCR fingerprint, which has been previously used to discriminate between serotypes Marseille and Houston, is shown to alter with phase variation in vitro, and there is evidence that genetic change accompanies these events. The extent of genetic and phenotypic variability of phase-variant B. henselae has previously been underestimated. It may lead to new insights into the pathogenicity of this organism, and must be considered when interpreting data arising from such studies.

Legionella pneumophila is a facultative intracellular pathogen that accounts for the majority of cases of Legionnaires' disease in the USA and Europe, but other Legionella spp. have been shown to cause disease. In contrast, Legionella longbeachae is the leading cause of Legionnaires' disease in Australia. The hallmark of Legionnaires' disease caused by L. pneumophila is the intracellular replication within phagocytes in the alveolar spaces, and the Dot/Icm type IV secretion system is essential for intracellular replication. Although it has been presumed that intracellular replication within phagocytes is the hallmark of other virulent legionellae, the virulence traits of Legionella spp. apart from L. pneumophila are not well defined. In this study, 27 strains of Legionella spp. belonging to 16 species that have been isolated from humans or from the environment were examined for five virulence traits exhibited by L. pneumophila: cytopathogenicity, intracellular replication within macrophages, induction of apoptosis/DNA fragmentation, pore-formation-mediated cytolysis of the host cell, and the presence of the dot/icm loci. The strains were divided into two broad groups (low and high cytopathogenic groups) based on cytopathogenicity assays using U937 human-derived macrophages. The other four virulence traits were evaluated in the low and high cytopathogenic groups of Legionella species. Most L. pneumophila serogroup 1 strains were highly cytopathogenic after 72 h, manifested high levels of intracellular growth, induced apoptosis/DNA fragmentation, and exhibited pore-forming activity. The majority of the other species were the low cytopathogenic group that did not induce apoptosis, neither did they exhibit pore-forming activity. All the species of legionellae tested have all the dot/icm loci, when examined by DNA hybridization. No correlation was found between cytopathogenicity and the other four pathogenic traits.

Twenty-one genes encoding surface proteins belonging to the LPXTG family have been identified by in silico analysis of six Staphylococcus aureus genome sequences. Eleven genes encode previously described proteins, while 10 have not yet been characterized. Of these, eight contain the cell-wall sorting signal LPXTG responsible for covalently anchoring proteins to the cell-wall peptidoglycan. The remaining two, SasF and SasD, harbour a single residue variation in the fourth position of the LPXTG motif (LPXAG). Western blotting of lysostaphin-solubilized S. aureus cell-wall proteins demonstrated the release of SasF in the cell-wall fraction, indicating that proteins carrying LPXAG are sorted normally. Analysis of primary sequences of the Staphylococcus aureus surface (Sas) proteins indicated that several share a similar structural organization and a common signal sequence with previously characterized LPXTG proteins of S. aureus and other Gram-positive cocci. Protein SasG has 128 residue B repeats that are almost identical at the DNA level. PCR analysis indicated that recombinants with repeat length variations are present in the bacterial population whereas they are not detectable in the B-repeat-encoding region of sdrD. The sasG and sasH genes are significantly associated with invasive disease isolates compared to nasal carriage isolates. Several IgG samples purified from patients recovering from S. aureus infections had higher titres against Sas proteins than control IgG, suggesting that expression occurred during infection in some patients.

Even though enterococci are a common cause of human infection they can readily be isolated from a range of food sources, including various meat and dairy products. An enterococcal strain, DPC5280, which exhibits a broad spectrum of inhibition against many Gram-positive bacteria was recently isolated from an Irish raw milk sample. Characterization of the inhibition revealed that the strain exhibits haemolytic activity characteristic of the two-component lantibiotic cytolysin and also produces a heat-labile antimicrobial protein of 34 kDa. The latter protein displayed cell wall hydrolytic activity, as evidenced by zymogram gels containing autoclaved lactococcal cells. N-terminal sequencing of the purified protein yielded the sequence ASNEWS which is 100 % identical to enterolysin A (accession no. AF249740), a protein which shares 28 and 29 % identity to the Gly-Gly endopeptidases, lysostaphin and zoocin A, respectively. Indeed, amplification of entL from DPC5280 and sequencing revealed that the protein is 100 % identical to enterolysin A. The DPC5280 strain also contained the determinants associated with multiple virulence factors, including gelatinase, aggregation substance and multiple antibiotic resistance. The linkage of this cell-wall-degrading enzyme to other virulence factors in enterococci may contribute to the competitiveness of pathogenic enterococci when found in complex microbial environments such as food and the gastrointestinal tract.