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Putative endolysin genes of bacteriophages CMP1 and CN77, which infect Clavibacter michiganensis subsp, michiganensis and C. michiganensis subsp, nebraskensis, respectively, were cloned and expressed in Escherichia coil. The His-tagged endolysin of CMP1 consists of 306 amino acids and has a calculated molecular mass of 34.8 kDa, while the His-tagged endolysin of CN77 has 290 amino acids with a molecular mass of 31.9 kDa. The proteins were purified and their bacteriolytic activity was demonstrated. The bacteriolytic activity of both enzymes showed a host range which was limited to the respective C. michiganensis subspecies and did not affect other bacteria, even those closely related to Clavibacter. Due to the high specificity of the CMP1 and CN77 endolysins they may be useful tools for biocontrol of plantpathogenic C. michiganensis without affecting other bacteria in the soil. DOI 10.1099/mic.0.037291-0

Pulsed-field gel electrophoresis analysis of chromosomal single and double restriction profiles of 17 strains belonging to three genera of 'Leuconostocaceae' was done, resulting in physical and genetic maps for three Fructobacillus, six Leuconostoc and four Weissella strains. Ascl, I-Ceul, Notl and Sfil restriction enzymes were used together with Southern hybridization of selected probes to provide an assessment of genomic organization in different species. Estimated genome sizes varied from 1408 kb to 1547 kb in Fructobacillus, from 1644 kb to 2133 kb in Leuconostoc and from 1371 kb to 2197 kb in Weissella. Other genomic characteristics of interest were analysed, such as oriC and terC localization and rrn operon organization. The latter seems markedly different in Weissella, in both number and disposition in the chromosome. Comparisons of intra- and intergeneric features are discussed in the light of chromosome rearrangements and genomic evolution. DOI 10.1099/mic.0.028308-0

The phosphoenolpyruvate: carbohydrate phosphotransferase system (PTS) catalyses carbohydrate transport by coupling it to phosphorylation. Previously, we reported a Corynebacterium glutamicum R [beta]-glucoside PTS encoded by bglF. Here we report that C. glutamicum R contains an additional [beta]-glucoside PTS gene, bglF2, organized in a cluster with a putative phospho-[beta]-glucosidase gene, bglA2, and a putative antiterminator, bglG2. While single gene disruption strains of either bglFor bglF2 were able to utilize salicin or arbutin as sole carbon sources, a double disruption strain exhibited defects in utilization of both carbon sources. Expression of both bglF and bglF2 was induced in the presence of either salicin or arbutin, although disruption of bglG2 affected only bglF2 expression. Moreover, in the presence of either salicin or arbutin, glucose completely repressed the expression of bglF but only slightly repressed that of bglF2. We conclude that BglF and BglF2 have a redundant role in [beta]-glucoside transport even though the catabolite repression control of their encoding genes is different. We also show that expression of both bglF and bglF2 requires the general PTS. DOI 10.1099/mic.0.029496-0

Tetrocarcin A (TCA), produced by Micromonospora chalcea NRRL 11289, is a spirotetronate antibiotic with potent antitumor activity and versatile modes of action. In this study, the biosynthetic gene cluster of TCA was cloned and localized to a 108-kb contiguous DNA region. In silico sequence analysis revealed 36 putative genes that constitute this cluster (including 11 for unusual sugar biosynthesis, 13 for aglycone formation, and 4 for glycosylations) and allowed us to propose the biosynthetic pathway of TCA. The formation of D-tetronitrose, L-amicetose, and L-digitoxose may begin with D-glucose-1-phosphate, share early enzymatic steps, and branch into different pathways by competitive actions of specific enzymes. Tetronolide biosynthesis involves the incorporation of a 3-C unit with a polyketide intermediate to form the characteristic spirotetronate moiety and trans-decalin system. Further substitution of tetronolide with five deoxysugars (one being a deoxynitrosugar) was likely due to the activities of four glycosyltransferases. In vitro characterization of the first enzymatic step by utilization of 1,3-biphosphoglycerate as the substrate and in vivo cross-complementation of the bifunctional fused gene tcaD3 (with the functions of chlD3 and chlD4) to [DELTA]chlD3 and [DELTA]chlD4 in chlorothricin biosynthesis supported the highly conserved tetronate biosynthetic strategy in the spirotetronate family. Deletion of a large DNA fragment encoding polyketide synthases resulted in a non-TCA-producing strain, providing a clear background for the identification of novel analogs. These findings provide insights into spirotetronate biosynthesis and demonstrate that combinatorial-biosynthesis methods can be applied to the TCA biosynthetic machinery to generate structural diversity.

We present evidence that the agr cell-to-cell communication system is present across firmicutes, including the human pathogen Clostridium perfringens. Although we find that the agr system is evolutionarily conserved and that the general functions which it regulates are similar in different species, the individual regulated genes are not the same. This suggests that the regulatory network controlled by agr is dynamic and evolves rapidly.

Listeriolysin O (LLO), a member of the cholesterol-dependent cytolysin (CDC) family, is a major virulence factor of Listeria monocytogenes and contributes to bacterial escape from intracellular killing of macrophages. LLO is activated under weakly acidic conditions; however, the molecular mechanism of this pH-dependent expression of cytolytic activity of LLO is poorly understood. In this study, CDCs including LLO, ivanolysin O (ILO), seeligeriolysin O (LSO), pneumolysin (PLY), streptolysin O (SLO) and perfringolysin O (PFO) were prepared as recombinant proteins and examined for their functional changes after treatment under various pH conditions. Haemolytic and membrane cholesterol-binding activities were not affected in PLY, SLO and PFO at any pH examined. By contrast, all the Listeria-derived cytolysins, LLO, ILO and LSO, were active only at an acidic pH and rapidly inactivated under neutral or alkaline conditions. Once inactivated, LLO could not be reactivated even by a downward pH shift. The hydrophobicity of LLO treated at neutral or alkaline pH was increased. These data suggested that the pH-dependent loss of cytolytic activity appeared to be due to irreversible structural changes of domain 4 that resulted in the loss of target membrane cholesterol binding.

PcrA is a conserved DNA helicase present in all gram-positive bacteria. Bacteria lacking PcrA show high levels of recombination. Lethality induced by PcrA depletion can be overcome by suppressor mutations in the recombination genes recFOR. RecFOR proteins load RecA onto single-stranded DNA during recombination. Here we test whether an essential function of PcrA is to interfere with RecA-mediated DNA recombination in vitro. We demonstrate that PcrA can inhibit the RecA-mediated DNA strand exchange reaction in vitro. Furthermore, PcrA displaced RecA from RecA nucleoprotein filaments. Interestingly, helicase mutants of PcrA also displaced RecA from DNA and inhibited RecA-mediated DNA strand exchange. Employing a novel single-pair fluorescence resonance energy transfer-based assay, we demonstrate a lengthening of doublestranded DNA upon polymerization of RecA and show that PcrA and its helicase mutants can reverse this process. Our results show that the displacement of RecA from DNA by PcrA is not dependent on its translocase activity. Further, our results show that the helicase activity of PcrA, although not essential, might play a facilitatory role in the RecA displacement reaction.

The alternative sigma factor [[sigma].sup.B] has an important role in the acquisition of stress resistance in many gram-positive bacteria, including the food-borne pathogen Bacillus cereus. Here, we describe the identification of the set of [[sigma].sup.B]-regulated genes in B. cereus by DNA microarray analysis of the transcriptome upon a mild heat shock. Twenty-four genes could be identified as being [[sigma].sup.B] dependent as witnessed by (i) significantly lower expression levels of these genes in mutants with a deletion of sigB and rsbY (which encode the alternative sigma factor [[sigma].sup.B] and a crucial positive regulator of [[sigma].sup.B] activity, respectively) than in the parental strain B. cereus ATCC 14579 and (ii) increased expression of these genes upon a heat shock. Newly identified [[sigma].sup.B]-dependent genes in B. cereus include a histidine kinase and two genes that have predicted functions in spore germination. This study shows that the [[sigma].sup.B] regulon of B. cereus is considerably smaller than that of other gram-positive bacteria. This appears to be in line with phylogenetic analyses where [[sigma].sup.B] of the B. cereus group was placed close to the ancestral form of [[sigma].sup.B] in gram-positive bacteria. The data described in this study and previous studies in which the complete [[sigma].sup.B] regulon of the gram-positive bacteria Bacillus subtilis, Listeria monocytogenes, and Staphylococcus aureus were determined enabled a comparison of the sets of [[sigma].sup.B]-regulated genes in the different gram-positive bacteria. This showed that only three genes (rsbV, rsbW, and sigB) are conserved in their [[sigma].sup.B] dependency in all four bacteria, suggesting that the [[sigma].sup.B] regulon of the different gram-positive bacteria has evolved to perform niche-specific functions.

Plasmid pIP501 has a very broad host range for conjugative transfer among a wide variety of gram-positive bacteria and gram-negative Escherichia coli. Functionality of the pIP501 transfer (tra) genes in E. coli was proven by pIP501 retrotransfer to Enterococcus faecalis (B. Kurenbach, C. Bohn, J. Prabhu, M. Abudukerim, U. Szewzyk, and E. Grohmann, Plasmid 50:86-93, 2003). The 15 pIP501 tra genes are organized in a single operon (B. Kurenbach, J. Kopec, M. Magdefrau, K. Andreas, W. Keller, C. Bohn, M. Y. Abajy, and E. Grohmann, Microbiology 152:637-645, 2006). The pIP501 tra operon is negatively autoregulated at the transcriptional level by the conjugative DNA relaxase TraA. Three of the 15 pIP501-encoded Tra proteins show significant sequence similarity to the Agrobacterium type IV secretion system proteins VirB1, VirB4, and VirD4. Here we report a comprehensive protein-protein interaction map of all of the pIP501-encoded Tra proteins determined by the yeast two-hybrid assay. Most of the interactions were verified in vitro by isolation of the protein complexes with pull-down assays. In conjunction with known or postulated functions of the pIP501-encoded Tra proteins and computer-assisted prediction of their cellular location, we propose a model for the first type IV-secretion-like system encoded by a conjugative plasmid from gram-positive bacteria.

Phthalate isomers and their esters are important pollutants whose biodegradation is not well understood. Rhodococcus sp. strain RHA1 is notable for its ability to degrade a wide range of aromatic compounds. RHA1 was previously shown to degrade phthalate (PTH) and to have genes putatively encoding terephthalate (TPA) degradation. Transcriptomic analysis of 8,213 genes indicated that 150 were up-regulated during growth on PTH and that 521 were up-regulated during growth on TPA. Distinct ring cleavage dioxygenase systems were differentially expressed during growth on PTH and TPA. Genes encoding the protocatechuate (PCA) pathway were induced on both substrates, while genes encoding the catechol branch of the PCA pathway were additionally induced only on TPA. Accordingly, protocatechuate-3,4-dioxygenase activity was induced in cells grown on both substrates, while catechol-1,2-dioxygenase activity was induced only in cells grown on TPA. Knockout analysis indicated that pcaL, encoding 3-oxoadipate enol-lactone hydrolase and 4-carboxymuconolactone decarboxylase, was required for growth on both substrates but that pcaB, encoding [BETA]-carboxy-cis,cis-muconate lactonizing enzyme, was required for growth on PTH only. These results indicate that PTH is degraded solely via the PCA pathway, whereas TPA is degraded via a bifurcated pathway that additionally includes the catechol branch of the PCA pathway.

The Rgg family of transcription regulators is widely distributed among gram-positive bacteria, yet how these proteins control transcription is poorly understood. Using Streptococcus pyogenes RopB as a model, we demonstrated that residues invariant among Rgg-like regulators are critical for function and obtained evidence for a mechanism involving protein complex formation.

The regulator VicR of the two-component regulatory system VicRK is essential in several Gram-positive bacteria. However, the authors were able to generate an unconditional vicR insertional mutant of group A Streptococcus. This mutant grew well in rich media but not in non-immune human blood and serum, had attenuated virulence, and was unstable in mice. Complementation of the mutant with vicR expressed in trans restored its phenotype to wild-type. A vicK deletion mutant had a phenotype similar to that of the vicR mutant. Phagocytosis and killing of the vicR mutant were normal, suggesting that VicRK does not regulate processes involved in evasion of host defence. Microarray analysis showed that vicR inactivation down-regulated the transcription of 13 genes, including putative cell wall hydrolase gene pcsB and spy 1058-1060, which encode a putative phosphotransferase system enzyme II for carbohydrate transport, and upregulated the expression of five genes, including spy0183 and spy0184, which encode an osmoprotectant transporter OpuA. Consistent with microarray analysis, the vicR mutant took up more of the osmoprotectants betaine and proline and was sensitive to osmotic stress, indicating that vicR inactivation induced osmotic stress and increased susceptibility to osmotic pressure. Additionally, a spy1060 deletion mutant also displayed attenuated virulence. These results suggest that VicRK regulates processes involved in cell wall metabolism, nutrient uptake, and osmotic protection.

Essential isoprenoid compounds are synthesized using the 2-C-methyl-D-erythritol 4-phosphate (MEP) pathway in many gram-negative bacteria, some gram-positive bacteria, some apicomplexan parasites, and plant chloroplasts. The alternative mevalonate pathway is found in archaea and eukaryotes, including cytosolic biosynthesis in plants. The existence of orthogonal essential pathways in eukaryotes and bacteria makes the MEP pathway an attractive target for the development of antimicrobial agents. A system is described for identifying mutations in the MEP pathway of Salmonella enterica serovar Typhimurium. Using this system, point mutations induced by diethyl sulfate were found in the all genes of the essential MEP pathway and also in genes involved in uptake of methylerythritol. Curiously, none of the MEP pathway genes could be identified in the same parent strain by transposon mutagenesis, despite extensive searches. The results complement the biochemical and bioinformatic approaches to the elucidation of the genes involved in the MEP pathway and also identify key residues for activity in the enzymes of the pathway.

Bacterial surface proteins are important molecules in the infectivity and survival of pathogens. Surface proteins on gram-positive bacteria have been shown to attach via a transpeptidase, termed sortase, that cleaves an LPXTG sequence found close to the C termini of nearly all surface proteins on these bacteria. We previously identified a unique enzyme (LPXTGase) from Streptococcus pyogenes that also cleaves the LPXTG motif with a catalytic activity higher than that of sortase, suggesting that it plays an important role in the attachment process. We have now purified and characterized an LPXTGase from Staphylococcus aureus and found that it has both similar and unique features compared to the S. pyogenes enzyme. The S. aureus enzyme is glycosylated and contains unusual amino acids, like its streptococcal counterpart. Like the streptococcal enzyme, staphylococcal LPXTGase has an overrepresentation of amino acids found in the peptidoglycan, i.e., glutamine/ glutamic acid, glycine, alanine, and iysine, and furthermore, we find that these amino acids are present in the enzyme at precisely the same ratio at which they are found in the peptidoglycan for the respective organism. This suggests that enzymes responsible for wall assembly may also play a role in the construction of LPXTGase.

CodY, a pleiotropic transcriptional regulator conserved in low G+C species of Gram-positive bacteria, was previously described to be the central regulator of proteolysis in Lactococcus lactis. In this study, over 100 potential CodY targets were identified by DNA-microarray analysis. Complementary transcriptional analysis experiments were carried out to validate the newly defined CodY regulon. Moreover, the direct role of CodY in the regulation of several target genes was demonstrated by gel retardation experiments. Interestingly, 45% of CodY-dependent genes encode enzymes involved in amino acid biosynthesis pathways, while most of the other genes are involved in functions related to nitrogen supply. CodY of L. lactis represents the first example of a regulator in Gram-positive bacteria that globally controls amino acid biosynthesis. This global control leads to growth inhibition in several amino-acid-limited media containing an excess of isoleucine. A conserved 15 nt palindromic sequence (AATTTTCNGAAAATT), the so-called CodY-box, located in the vicinity of the--35 box of target promoter regions was identified. Relevance of the CodY-box as an operator for CodY was demonstrated by base substitutions in gel retardation experiments. This motif is also frequently found in the promoter region of genes potentially regulated by CodY in other Gram-positive bacteria.

Terrabacter sp. strain DBF63 is capable of degrading fluorene (FN) to tricarboxylic acid cycle intermediates via phthalate and protocatechuate. Genes were identified for the protocatechuate branch of the [beta]-ketoadipate pathway (pcaR, pcaHGBDCFIJ) by sequence analysis of a 70 kb DNA region of the FN-catabolic linear plasmid pDBF1. RT-PCR analysis of RNA from DBF63 cells grown with FN, dibenzofuran, and protocatechuate indicated that the pcaHGBDCFIJ operon was expressed during both FN and protocatechuate degradation in strain DBF63. The gene encoding [beta]-ketoadipate enol-lactone hydrolase (pcaD) was not fused to the next gene, which encodes [gamma]-carboxymuconolactone decarboxylase (pcaC), in strain DBF63, even though the presence of the pcaL gene (the fusion of pcaD and pcaC) within a pca gene cluster has been thought to be a Gram-positive trait. Quantitative RT-PCR analysis revealed that pcaD mRNA levels increased sharply in response to protocatechuate, and a biotransformation experiment with cis,cis-muconate using Escherichia coil carrying both catBC and pcaD indicated that PcaD exhibited [beta]-ketoadipate enol-lactone hydrolase activity. The location of the pca gene cluster on the linear plasmid, and the insertion sequences around the pca gene cluster suggest that the ecologically important [beta]-ketoadipate pathway genes, usually located chromosomally, may be spread widely among bacterial species via horizontal transfer or transposition events.

Renibacterium salmoninarum is a gram-positive bacterium that causes bacterial kidney disease in salmonid fish. The epitome mapping studies suggest directions for improvement of MAb-based immunoassays for detection of Renibacterium salmoninarum-infected fish.

A single gene cluster encoding components of a putative ATP-binding cassette (ABC) transporter for basic amino acids was identified in the incomplete genome sequence of the thermophilic Gram-positive bacterium Geobacillus stearothermophilus by BLAST searches. The cluster comprises three genes, and these were amplified from chromosomal DNA of G. stearothermophilus, ligated into plasmid vectors and expressed in Escherichia coli The purified solute-binding protein (designated Art J) was demonstrated to bind L-arginine with high affinity ([K.sub.d] = 0.39 [+ or -] 0.06 [micro]M). Competition experiments revealed only partial inhibition by excess L-lysine (38%) and L-ornithine (46%), while no inhibition was observed with L-histidine or other amino acids tested. The membrane-associated transport complex, composed of a permease (designated ArtM) and an ATPase component (designated ArtP), was solubilized from E. coli membranes by decanoylsucrose and purified by metal-affinity chromatography. The ArtMP complex, when incorporated into liposomes formed from a crude extract of G. stearothermophilus lipids, displayed ATPase activity in the presence of ArtJ only. Addition of L-arginine further stimulated the activity twofold. ATP hydrolysis was optimal at 60 [degrees]C and sensitive to the specific inhibitor vanadate. Analysis of kinetic parameters revealed a maximal velocity of ATP hydrolysis of 0.71 [micro]mol [P.sub.i] [min.sup.-1] [(mg protein).sup.-1] and a [K.sub.m(ATP)] of 1 -59 mM. Together, these results identify the ArtJMP complex as a hig[H.sup.-]affinity arginine ABC transporter.

p-Nitrophenol (4-NP) is recognized as an environmental contaminant; it is used primarily for manufacturing medicines and pesticides. To date, several 4-NP-degrading bacteria have been isolated; however, the genetic information remains very limited. In this study, a novel 4-NP degradation gene cluster from a gram-positive bacterium, Rhodococcus opacus SAO101, was identified and characterized. The deduced amino acid sequences of npcB, npcA, and npcC showed identity with phenol 2-hydroxylase component B (reductase, PheA2) of Geobacillus thermoglucosidasius A7 (32%), with 2,4,6-trichlorophenol monooxygenase (TcpA) of Ralstonia eutropha JMP134 (44%), and with hydroxyquinol 1,2-dioxygenase (ORF2) of Arthrobacter sp. strain BA-5-17 (76%), respectively. The npcB, npcA, and npcC genes were cloned into pET-17b to construct the respective expression vectors pETnpcB, pETnpcA, and pETnpcC. Conversion of 4-NP was observed when a mixture of crude cell extracts of Escherichia coli containing pETnpcB and pETnpcA was used in the experiment. The mixture converted 4-NP to hydroxyquinol and also converted 4-nitrocatechol (4-NCA) to hydroxyquinol. Furthermore, the crude cell extract of E. coli containing pETnpcC converted hydroxyquinol to maleylacetate. These results suggested that npcB and npcA encode the two-component 4-NP/4-NCA monooxygenase and that npcC encodes hydroxyquinol 1,2-dioxygenase. The npcA and npcC mutant strains, SDA1 and SDC1, completely lost the ability to grow on 4-NP as the sole carbon source. These results clearly indicated that the cloned npc genes play an essential role in 4-NP mineralization in R. opacus SAO101.

Byline: F. Hernandez Oliveros (1), Y. Zou (1), G. Lopez (2), M. Romero (2), L. Martinez (1), S. Gonzalez-Reyes (1), A. Garcia (2), P. Pena (2), J. A. Tovar (1) Keywords: Bacterial translocation; Rats; Methods; Gram-positive; DNA Abstract: Aim Bacterial translocation (BT) can be demonstrated by blood and lymph node cultures and also by polymerase chain reaction (PCR) detection of DNA of enteric bacteria. Aiming at investigating BT after gastrointestinal operations we assessed it on two endpoints after ischemia--reperfusion (IR) or sham operation (SO). Methods 2 groups of 200-g Brown Norway male rats were treated as follows: SO animals (n=12) had laparotomy alone and IR animals (n=12) had successively 15 min clamping of the portal vein and the mesenteric artery. Half the animals in each group were killed on postoperative (p.o.) day 2 the other half on p.o. day 7. Under sterile conditions regional lymph nodes and vena cava and portal vein blood samples were recovered and cultured for aerobes and anaerobes. Escherichia coli [beta]-galactosidase DNA was assessed in blood samples by PCR. The findings in the two groups were compared by means of [chi].sup.2 tests. Results Post-hepatic (peripheral blood) BT was detected by cultures of gram-negative bacteria in 16% and 0% of SO and IR animals, respectively, on p.o. day 2 and in 16% and 50% on p.o. day 7. These differences were not significant (ns). E. coli DNA was found in one SO rat. Pre-hepatic BT (portal blood and/or lymph nodes) of gram-negative bacteria was found in 16% and 33%, respectively, on day 2 and in 16% and 16% on day 7 (ns). However, if gram-positive cultures were taken into account, the figures were 66% and 66% on day 2 and 66% and 83% on day 7 (ns). No anaerobes could be cultured. Conclusions (1) BT is frequent in surgically manipulated animals. (2) To limit the assessment of BT to Enterobacteriaceae is probably misleading, since consistent amounts of gram-positive bacteria are found in the pre-hepatic territory. (3) PCR tests limited to E. coli DNA alone are likely incomplete. (4) Short periods of vascular clamping do not increase BT on the two endpoints selected in comparison with SO animals. Author Affiliation: (1) Department of Pediatric Surgery, Hospital Universitario La Paz, Paseo de la Castellana, no 261, 28046, Madrid, Spain (2) Department of Clinical Microbiology, Hospital Universitario La Paz, Madrid, Spain Article History: Registration Date: 28/11/2003 Online Date: 10/02/2004

To the Editor: Varibaculum cambriense is an anaerobic, gram-positive, diphtheroid bacterium that was described by Hall et al. in 2003 (1). Biochemical testing, electrophoretic analysis of whole-cell proteins, and phylogenetic [...]

The feedback-resistant mutants of acetohydroxy acid synthase (AHAS) by site-directed mutagenesis of the gene iviN, encoding the regulatory subunit of Corynebacterium glutamicum AHAS is constructed. The mutated ilvN allele was cloned in the newly constructed plasmid pECKA together with other genes of the ilvBNC operon, and the most favorable mutation was introduced into the Corynebacterium glutamicum chromosome.

The ermB gene is reported in one of the Bacteroides strains that can be transferred by conjugation and is located on a conjugative transposon (CTn) that is unrelated to any of the other Bacteroides CTns. Finding supports the hypothesis that CTnBST could have entered Bacteroides from some other genus, possibly from grain-positive bacteria and also that many transmissible antibiotic resistance genes in Bacteroides are carried on CTns.