Chromosome map of Xanthomonas campestris pv. campestris 17 with locations of genes involved in xanthan gum synthesis and yellow pigmentation

Isolation and characterization of a Vibrio owensii phage phi50-12

Vibrio owensii is a widely distributed marine vibrio species that causes acute hepatopancreatic necrosis in the larvae of Panulirus ornatus and Penaeus vannamei, and is also associated with Montipora white syndrome in corals. We characterized V. owensii GRA50-12 as a potent pathogen using phenotypic, biochemical, and zebrafish models. A virulent phage, vB_VowP_phi50-12 (phi50-12), belonging to the N4-like Podoviridae, was isolated from the same habitat as that of V. owensii GRA50-12 and characterized. This phage possesses a unique sequence with no similar hits in the public databases and has a short latent time (30 min), a large burst size (106 PFU/infected cell), and a wide range of pH and temperature stabilities. Moreover, phi50-12 also demonstrated a strong lysis ability against V. owensii GRA50-12. SDS-PAGE revealed at least nine structural proteins, four of which were confirmed using LC–MS/MS analysis. The size of the phi50-12 genome was 68,059 bp, with 38.5% G + C content. A total of 101 ORFs were annotated, with 17 ORFs having closely related counterparts in the N4-like vibrio phage. Genomic sequencing confirmed the absence of antibiotic resistance genes or virulence factors. Comparative studies have shown that phi50-12 has a unique genomic arrangement, except for the well-conserved core regions of the N4-like phages. Phylogenetic analysis demonstrated that it belonged to a group of smaller genomes of N4-like vibrio phages. The therapeutic effect in the zebrafish model suggests that phi50-12 could be a potential candidate for application in the treatment of V. owensii infection or as a biocontrol agent. However, further research must be carried out to confirm the efficacy of phage50-12.

Molecular Characterization of Ahp2, a Lytic Bacteriophage of Aeromonas hydrophila

Aeromonas hydrophila is an opportunistic pathogen that infects fish, amphibians, mammals, and humans. This study isolated a myophage, vB_AhyM_Ahp2 (Ahp2), that lytically infects A. hydrophila. We observed that 96% of the Ahp2 particles adsorbed to A. hydrophila within 18 min. Ahp2 also showed a latent period of 15 min with a burst size of 142 PFU/cell. This phage has a linear double-stranded DNA genome of 47,331 bp with a GC content of 57%. At least 20 Ahp2 proteins were detected by SDS-polyacrylamide gel electrophoresis; among them, a 40-kDa protein was predicted as the major capsid protein. Sequence analysis showed that Ahp2 has a genome organization closely related to a group of Aeromonas phages (13AhydR10RR, 14AhydR10RR, 85AhydR10RR, phage 3, 32 Asp37, 59.1), which infect Aeromonas hydrophila and Aeromonas salmonicida. The tail module encompassing ORF27-29 in the Ahp2 genome was present in all Aeromonas phages analyzed in this study and likely determines the host range of the virus. This study found that Ahp2 completely lyses A. hydrophila AH300206 in 3.5 h at a MOI of 0.0001 and does not lysogenize its host. Altogether, these findings show that Ahp2 is a lytic Aeromonas phage and could be a candidate for therapeutic phage cocktails.

Genomic Characterization of the Novel Aeromonas hydrophila Phage Ahp1 Suggests the Derivation of a New Subgroup from phiKMV-Like Family

Aeromonas hydrophila is an opportunistic pathogenic bacterium causing diseases in human and fish. The emergence of multidrug-resistant A. hydrophila isolates has been increasing in recent years. In this study, we have isolated a novel virulent podophage of A. hydrophila, designated as Ahp1, from waste water. Ahp1 has a rapid adsorption (96% adsorbed in 2 min), a latent period of 15 min, and a burst size of 112 PFU per infected cell. At least eighteen Ahp1 virion proteins were visualized in SDS-polyacrylamide gel electrophoresis, with a 36-kDa protein being the predicted major capsid protein. Genome analysis of Ahp1 revealed a linear doubled-stranded DNA genome of 42,167 bp with a G + C content of 58.8%. The genome encodes 46 putative open reading frames, 5 putative phage promoters, and 3 transcriptional terminators. Based on high degrees of similarity in overall genome organization and among most of the corresponding ORFs, as well as phylogenetic relatedness among their DNAP, RNAP and major capsid proteins, we propose a new subgroup, designated Ahp1-like subgroup. This subgroup contains Ahp1 and members previously belonging to phiKMV-like subgroup, phiAS7, phi80-18, GAP227, phiR8-01, and ISAO8. Since Ahp1 has a narrow host range, for effective phage therapy, different phages are needed for preparation of cocktails that are capable of killing the heterogeneous A. hydrophila strains.

Characterization of genes encoding proteins containing HD-related output domain in Xanthomonas campestris pv. campestris

The Gram-negative plant pathogen Xanthomonas campestris pv. campestris (Xcc) is the causative agent of black rot in crucifers. The production of Xcc virulence factors is regulated by Clp and RpfF. HD-related output domain (HDOD) is a protein domain of unknown biochemical function. The genome of Xcc encodes three proteins (GsmR, HdpA, and HdpB) with an HDOD. The GsmR has been reported to play a role in the general stress response and cell motility and its expression is positively regulated by Clp. Here, the function and transcription of hdpA and hdpB were characterized. Mutation of hdpA resulted in enhanced bacterial attachment. In addition, the expression of hdpA was positively regulated by RpfF but not by Clp, subject to catabolite repression and affected by several stress conditions. However, mutational analysis and reporter assay showed that hdpB had no effect on the production of a range of virulence factors and its expression was independent of Clp and RpfF. The results shown here not only extend the previous work on RpfF regulation to show that it influences the expression of hdpA in Xcc, but also expand knowledge of the function of the HDOD containing proteins in bacteria.

Functional characterization and transcriptional analysis of galE gene encoding a UDP-galactose 4-epimerase in Xanthomonas campestris pv. campestris

The Gram-negative plant pathogen Xanthomonas campestris pv. campestris (Xcc) is the causative agent of black rot in crucifers, a disease that causes tremendous agricultural loss. In this study, the Xcc galE gene was characterized. Sequence and mutational analysis demonstrated that the Xcc galE encodes a UDP-galactose 4-epimerase (EC 5.1.3.2), which catalyzes the interconversion of UDP-galactose and UDP-glucose. Alanine substitution of the putative catalytic residues (Ser124, Tyr147, and Lys151) of GalE caused loss of epimerase activity. Further study showed that the Xcc galE mutant had reduced biofilm formation ability. Furthermore, reporter assays revealed that galE transcription exhibits a distinct expression profile under different culture conditions, is subject to catabolite repression, and is positively regulated by Clp and RpfF. In addition, the galE transcription initiation site was mapped. This is the first time that UDP-galactose 4-epimerase has been characterized in the crucifer pathogen Xcc.

GsmR, a response regulator with an HD-related output domain in Xanthomonas campestris, is positively controlled by Clp and is involved in the expression of genes responsible for flagellum synthesis

In prokaryotes, two-component signal transduction systems, consisting of a histidine kinase and a response regulator, play a critical role in regulating a range of cellular functions. A recent study suggests that XCC3315, a response regulator with a CheY-like receiver domain attached to an uncharacterized HD-related output domain (HDOD domain), plays a role in the general stress response of the Gram-negative bacterium Xanthomonas campestris pv. campestris (Xcc), the causal agent of black rot in cruciferous plants. Here, we demonstrated genetically that XCC3315, designated as gsmR (general stress and motility regulator), is involved in the expression of genes responsible for flagellum synthesis, including rpoN2, flhF, flhB, and fliC. Site-directed mutagenesis revealed that Glu9 and Arg100 in the receiver domain and Gly205, Asp263, His287, Trp298 and His311 in the HDOD are critical amino acids for GsmR function in cell motility regulation. The gsmR transcription initiation site was mapped. Promoter analysis and gel retardation assay revealed that the expression of gsmR is positively controlled by the global transcriptional regulator Clp in a direct manner, and is subject to catabolite repression. Our findings not only extend the previous work on Clp regulation to show that it influences the expression of gsmR in Xcc, but are also the first to characterize the expression of this response regulator gene in this phytopathogen. Furthermore, GsmR is the first HDOD-containing protein of bacteria in which key amino acids have been experimentally identified and characterized.

Genome sequence of Xanthomonas campestris JX, an industrially productive strain for Xanthan gum

Xanthomonas campestris JX, a soil bacterium, is an industrially productive strain for xanthan gum. Here we present a 5.0-Mb assembly of its genome sequence. We have annotated 12 coding sequences (CDSs) responsible for xanthan gum biosynthesis, 346 CDSs encoding carbohydrate metabolism, and 69 CDSs related to virulence, defense, and plant disease.

Isolation and characterization of φkm18p, a novel lytic phage with therapeutic potential against extensively drug resistant Acinetobacter baumannii

AIMS

To isolate phages against extensively drug resistant Acinetobacter baumannii (XDRAB) and characterize the highest lytic capability phage as a model to evaluate the potential on phage therapy.

METHODS AND RESULTS

Eight phages were isolated from hospital sewage and showed narrow host spectrum. Phage φkm18p was able to effectively lyse the most XDRAB. It has a dsDNA genome of 45 kb in size and hexagonal head of about 59 nm in diameter and no tail. Bacterial population decreased quickly from 10(8) CFU ml(-1) to 10(3) CFU ml(-1) in 30 min by φkm18p. The 185 kDa lysis protein encoded by φkm18p genome was detected when the extracted protein did not boil before SDS-PAGE; it showed that the lysis protein is a complex rather than a monomer. Phage φkm18p improved human lung epithelial cells survival rates when they were incubated with A. baumannii. Combination of phages (φkm18p, φTZ1 and φ314) as a cocktail could lyse all genotype-varying XDRAB isolates.

CONCLUSION

Infections with XDRAB are extremely difficult to treat and development of a phage cocktails therapy could be a therapeutic alternative in the future. Phage φkm18p is a good candidate for inclusion in phage cocktails.

Genome, integration, and transduction of a novel temperate phage of Helicobacter pylori

Helicobacter pylori is a common human pathogen that has been identified to be carcinogenic. This study isolated the temperate bacteriophage 1961P from the lysate of a clinical strain of H. pylori isolated in Taiwan. The bacteriophage has an icosahedral head and a short tail, typical of the Podoviridae family. Its double-stranded DNA genome is 26,836 bp long and has 33 open reading frames. Only 9 of the predicted proteins have homologs of known functions, while the remaining 24 are only similar to unknown proteins encoded by Helicobacter prophages and remnants. Analysis of sequences proximal to the phage-host junctions suggests that 1961P may integrate into the host chromosome via a mechanism similar to that of bacteriophage lambda. In addition, 1961P is capable of generalized transduction. To the best of our knowledge, this is the first report of the isolation, characterization, genome analysis, integration, and transduction of a Helicobacter pylori phage.

Transcriptional analysis and functional characterization of XCC1294 gene encoding a GGDEF domain protein in Xanthomonas campestris pv. campestris

The nucleotide cyclic di-GMP is a second messenger in bacteria that regulates a range of cellular functions including the virulence of pathogens. GGDEF is a protein domain involved in the synthesis of cyclic di-GMP. The genome of the crucifer pathogen Xanthomonas campestris pv. campestris (Xcc) encodes 21 proteins with a GGDEF domain. Clp, a homolog of the model transcription factor Crp of Escherichia coli, is a global regulator in Xcc. The aim of this study is to identify genes encoding GGDEF domain proteins whose expression is regulated by Clp. Results of reporter assay and RT-PCR analysis suggested that Clp regulates the expression of a set of genes encoding proteins harboring GGDEF domain. The transcription initiation site of XCC1294, one of the Clp regulated gene encoding a GGDEF domain protein, was mapped. Promoter analysis and gel retardation assay indicated that the transcription of XCC1294 is positively and directly regulated by Clp. Furthermore, transcription of XCC1294 was subject to catabolite repression and affected by several stress conditions. We also showed that mutation of XCC1294 results in enhanced surface attachment. In addition, transcription of three putative adhesin genes (xadA, fhaC, and yapH) was increased in the XCC1294 mutant. Taken together, the data presented here indicate that Clp positively regulates expression of XCC1294, and that XCC1294 serves a regulator of bacterial attachment and regulates different adhesin genes expression.

Functional characterization of copA gene encoding multicopper oxidase in Xanthomonas campestris pv. campestris

The gram-negative plant pathogenic Xanthomonas campestris pv. campestris (Xcc) is the causative agent of black rot in crucifers, a disease causing tremendous loss in agriculture. Copper-containing bactericides have been widely used to control this disease for many years, possibly leading to the development of copper resistance in Xcc. Homologues of copper resistance genes copLAB are present in the Xcc genome, but none has been characterized. In this study, mutations in copL, copA, and copB decreased Xcc copper tolerance. Among them, the copA mutant displayed the most significant reduction. The copA mutant also resulted in a reduction in virulence on the host cabbage. Sequence and mutational analysis demonstrated that copA encodes a multicopper oxidase and that CopA is able to catalyze the oxidation of 2,6-dimethoxyphenol. Alanine substitutions in each of the putative copper binding residues (H538, H583, C584, and H585) of CopA caused a loss of function including copper tolerance and oxidase activity. Furthermore, reporter assays showed that copA transcription is inducible in the presence of copper, subject to catabolite repression, and repressed under conditions of high osmolarity, nitrogen starvation, or oxygen limitation. This is the first time that multicopper oxidase has been characterized in the crucifer pathogen Xcc.

Lytic myophage Abp53 encodes several proteins similar to those encoded by host Acinetobacter baumannii and phage phiKO2

Acinetobacter baumannii is an important Gram-negative opportunistic pathogen causing nosocomial infections. The emergence of multiple-drug-resistant A. baumannii isolates has increased in recent years. Directed toward phage therapy, a lytic phage of A. baumannii, designated Abp53, was isolated from a sputum sample in this study. Abp53 has an isometric head and a contractile tail with tail fibers (belonging to Myoviridae), a latent period of about 10 min, and a burst size of approximately 150 PFU per infected cell. Abp53 could completely lyse 27% of the A. baumannii isolates tested, which were all multiple drug resistant, but not other bacteria. Mg(2+) enhanced the adsorption and productivity of, and host lysis by, Abp53. Twenty Abp53 virion proteins were visualized in SDS-polyacrylamide gel electrophoresis, with a 47-kDa protein being the predicted major capsid protein. Abp53 has a double-stranded DNA genome of 95 kb. Sequence analyses of a 10-kb region revealed 8 open reading frames. Five of the encoded proteins, including 3 tail components and 2 hypothetical proteins, were similar to proteins encoded by A. baumannii strain ACICU. ORF1176 (one of the tail components, 1,176 amino acids [aa]), which is also similar to tail protein gp21 of Klebsiella phage phiKO2, contained repeated domains similar to those within the ACICU_02717 protein of A. baumannii ACICU and gp21. These findings suggest a common ancestry and horizontal gene transfer during evolution. As phages can expand the host range by domain duplication in tail fiber proteins, repeated domains in ORF1176 might have a similar significance in Abp53.

XCC2731, a GGDEF domain protein in Xanthomonas campestris, is involved in bacterial attachment and is positively regulated by Clp

In Xanthomonas campestris pv. campestris (Xcc), which is the causative agent of black rot in crucifers, the virulence factor level is substantially decreased in the mutant deficient in RpfG, a phosphodiesterase that degrades the second messenger cyclic di-GMP. The rpfG mutant also grew in an aggregated state. It is indicated that expression of Pseudomonas GGDEF domain protein WspR (a diguanylate cyclase that synthesizes cyclic di-GMP) in wild-type Xcc can produce a phenocopy of the rpfG mutant. In this study, we showed that over-expression of GGDEF domain protein XCC2731 in wild-type Xcc caused (i) aggregation of cells, (ii) reduction in motility, and (iii) decrease in production of virulence factor extracellular enzymes and exopolysaccharides. Site-directed mutagenesis of the conserved G, G, and E residues of the GGDEF domain in XCC2731 abolished its function. The XCC2731 mutant has attenuated virulence. Furthermore, XCC2731 mutant was affected in surface attachment. Using the 5' RACE method, the XCC2731 transcription initiation site was mapped at nucleotide G, 15nt upstream of the XCC2731 start codon. Transcriptional fusion assay and gel retardation analysis indicated that Clp (cAMP receptor protein-like protein) positively regulates XCC2731 transcription in a direct manner. Reporter analysis also revealed that XCC2731 transcription is subject to catabolite repression, and reduced under conditions of oxygen limitation and high osmolarity. Our findings not only extend previous work on Clp regulation to show that it influences the expression of XCC2731 in Xcc, but also are the first to characterize the GGDEF domain protein gene expression in this phytopathogen.

Transcriptional analysis of pmeA gene encoding a pectin methylesterase in Xanthomonas campestris pv. campestris

Exopolysaccharides and several extracellular enzymes of Xanthomonas campestris pv. campestris (Xcc), the causative agent of black rot in crucifers, are virulence determinants. It is known that Clp (cAMP receptor protein-like protein) and RpfF (an enoyl-CoA hydratase homologue required for the synthesis of the diffusible signal factor, DSF) regulate production of these factors. In this study, plate assay revealed that Xcc possesses pectin methylesterase activity and that its expression is controlled by Clp and RpfF. Mutational analysis has demonstrated that pmeA encodes a pectin methylesterase. Using the 5' RACE method, the pmeA transcription initiation site was mapped. Transcriptional fusion assays showed that pmeA transcription is positively regulated by Clp and RpfF, subject to catabolite repression which is independent of Clp or RpfF, and repressed under conditions of high osmolarity or oxygen limitation. This study not only extends previous work on Clp and RpfF regulation by showing that they both influence the expression of pmeA in Xcc, but also, for the first time, characterizes pectin methylesterase gene expression in Xanthomonas.

Isolation and characterization of phi AB2: a novel bacteriophage of Acinetobacter baumannii

Multidrug-resistant strains of Acinetobacter baumannii (MDRAB) are increasingly being reported worldwide. Bacteriophage therapy is a potential alternative treatment for MDR bacterial infections. Although A. baumannii infection has been experimentally treated with phages, no MDRAB-specific phage has been characterized. In this study, 10 phages with differing host ranges and lysis efficacy for MDRAB were isolated; one of these, phi AB2, was further studied. Electron microscopy revealed phi AB2 to have an isometric head (60 nm), a short tail (diameter, 9 nm; length, 11 nm) and a double-stranded DNA genome--which was resistant to digestion with several restriction endonucleases--estimated to be 40 kb by pulsed-field gel electrophoresis. Partial genome sequencing of a 2.1 kb region gave sequences resembling the tubular proteins A and B of Pseudomonas aeruginosa phage LKA1. These data suggest that phi AB2 resembles phi KMV-like phages and is a new member of the Podoviridae family. It exhibited rapid adsorption (>99% adsorbed in 8 min), a short latent period (<10 min) and a large burst size (ca. 200); moreover, it was capable of infecting a wide spectrum of A. baumannii strains, causing virtually complete lysis, indicating that phi AB2 may be a good candidate as a therapeutic/disinfectant agent to control nosocomial infections caused by MDRAB.

Transcriptional regulation and molecular characterization of the manA gene encoding the biofilm dispersing enzyme mannan endo-1,4-beta-mannosidase in Xanthomonas campestris

Exopolysaccharide and several extracellular enzymes of Xanthomonas campestris pv. campestris (Xcc), the causative agent of black rot in crucifers, are important virulence determinants. It is known that Clp (cAMP receptor protein-like protein) and RpfF (an enoyl-CoA hydratase homologue required for the synthesis of diffusible signal factor, DSF) regulate the production of these determinants. Addition of DSF or Xcc extracellular protein containing partially purified mannanase (EC 3.2.1.78, encoded by manA) can disperse the cell aggregates formed by rpfF mutant. In this study, nucleotide G 64 nt upstream of the manA translation start codon was determined as the transcription initiation site by the 5' RACE technique. Transcriptional fusion assays showed that manA transcription is positively regulated by Clp and RpfF and induced by locust bean gum. The manA coding region was cloned and expressed in E. coli as recombinant ManA (rManA). The rManA was purified by affinity chromatography, and its biochemical properties were characterized. The rManA had a pH optimum at 7.0 (0.1 M Hepes) and a temperature optimum at about 37 degrees C. Sequence and mutational analyses demonstrated that Xcc manA encodes the major mannanase, a member of family 5 of glycosyl hydrolases. This study not only extends previous work on Clp and RpfF regulation by showing that they both influence the expression of manA in Xcc, but it also for the first time characterizes Xanthomonas mannanase at the protein level.

Clp and RpfF up-regulate transcription of pelA1 gene encoding the major pectate lyase in Xanthomonas campestris pv. campestris

Exopolysaccharide and several extracellular enzymes of Xanthomonas campestris pv. campestris (Xcc), the causative agent of black rot in crucifers, are virulence determinants. In this study, two Xcc annotated extracellular pectate lyase genes, pelA1 and pelA2, belonging to family 1 of the polysaccharide lyase, were characterized. Sequence and mutational analyses have demonstrated that pelA1 encodes the major pectate lyase, whereas pelA2 is not transcribed. Using the 5' RACE method, the pelA1 transcription initiation site was mapped at nucleotide G, 103 nt upstream of the pelA1 start codon. Promoter analysis demonstrated that polygalacturonic acid and CaCl(2) induce the expression of pelA1. Transcriptional fusion assays also indicated that Clp (cAMP receptor protein-like protein) and RpfF (an enoyl-CoA hydratase homologue that is required for the synthesis of cis-11-methyl-2-dodecenoic acid, a low molecular weight diffusible signal factor, DSF) positively regulate pelA1 transcription. Gel retardation assays showed that Clp exerts a positive control over expression of pelA1 by direct binding to the upstream Clp-binding site. In conclusion, the present research demonstrated that pelA1 codes for the major pectate lyase in Xcc strain Xc17 and that its expression is up-regulated by Clp and RpfF. This is the first study to characterize pectate lyase gene expression in Xcc.

Genome-scale mutagenesis and phenotypic characterization of two-component signal transduction systems in Xanthomonas campestris pv. campestris ATCC 33913

The gram-negative bacterium Xanthomonas campestris pv. campestris is the causal agent of black rot disease of cruciferous plants. Its genome encodes a large repertoire of two-component signal transduction systems (TCSTSs), which consist of histidine kinases and response regulators (RR) to monitor and respond to environmental stimuli. To investigate the biological functions of these TCSTS genes, we aimed to inactivate all 54 RR genes in X. campestris pv. campestris ATCC 33913, and successfully generated 51 viable mutants using the insertion inactivation method. Plant inoculation identified two novel response regulator genes (XCC1958 and XCC3107) that are involved in virulence of this strain. Genetic complementation demonstrated that XCC3107, designated as vgrR (virulence and growth regulator), also affects bacterial growth and activity of extracellular proteases. In addition, we assessed the survival of these mutants under various stresses, including osmotic stress, high sodium concentration, heat shock, and sodium dodecyl sulfate exposure, and identified a number of genes that may be involved in the general stress response of X. campestris pv. campestris. Mutagenesis and phenotypic characterization of RR genes in this study will facilitate future studies on signaling networks in this important phytopathogenic bacterium.

Identification of a hypothetical protein of plant pathogenic Xanthomonas campestris as a novel beta-galactosidase

Xc17L, a lactose-utilizing mutant of Xanthomonas campestris pv. campestris previously isolated by mutagenesis with nitrous acid, displays a level of beta-galactosidase 3.5-fold higher than that in the parental Xc17. In this study, the gene encoding the enzyme displaying a higher specific activity in Xc17L was inactivated by mini-Tn5 transposition. Sequencing revealed that the product (579 aa, 63.5 kDa) of this gene, designated galD, was previously annotated to encode a hypothetical protein on the genome. Mutation of the gene by marker exchange, complementation test and Western blot analysis together confirmed that galD is indeed the gene involved in beta-galactosidase elevation in Xc17L. With only the N-terminal region possessing similarity to the known beta-galactosidases and partially conserved consensus motif, GalD is recognized as a member of the glycosyl hydrolase family 35. Insertion with GmOmega, which causes polar effects, into the upstream genes followed by Western blotting showed that galD is cotranscribed with the upstream genes and expressed constitutively. Mutation in galD causes no significant changes including pathogenicity in the bacterium.

Characterization of extended-host-range pseudo-T-even bacteriophage Kpp95 isolated on Klebsiella pneumoniae

Kpp95, isolated on Klebsiella pneumoniae, is a bacteriophage with the morphology of T4-type phages and is capable of rapid lysis of host cells. Its double-stranded genomic DNA (ca. 175 kb, estimated by pulsed-field gel electrophoresis) can be cut only by restriction endonucleases with a cleavage site flanked either by A and T or by T, as tested, suggesting that it contains the modified derivative(s) of G and/or C. Over 26 protein bands were visualized upon sodium dodecyl sulfate-polyacrylamide gel electrophoresis of the virion proteins. N-terminal sequencing indicated that the most abundant band (46 kDa) is the major coat protein (gp23) which has been cleaved from a signal peptide likely with a length similar to that of T4. Phylogenetic analyses based on the sequences of the central region (263 amino acid residues) of gp23 and the full length of gp18 and gp19 placed Kpp95 among the pseudo-T-even subgroup, most closely related to the coliphage JS98. In addition to being able to lyse many extended-spectrum beta-lactamase strains of K. pneumoniae, Kpp95 can lyse Klebsiella oxytoca, Enterobacter agglomerans, and Serratia marcescens cells. Thus, Kpp95 deserves further studies for development as a component of a therapeutic cocktail, owing to its high efficiencies of host lysis plus extended host range.

Clp upregulates transcription of engA gene encoding a virulence factor in Xanthomonas campestris by direct binding to the upstream tandem Clp sites

In Xanthomonas campestris, the causative agent of black rot in crucifers, the endoglucanase level is greatly decreased in the mutant deficient in Clp, a homologue of cyclic AMP receptor protein (CRP). It is established that Clp has the same DNA binding specificity as CRP at positions 5, 6, and 7 (GTG motif) of the DNA half site. In this study, the engA transcription initiation site was determined by the 5' RACE method, and two consensus Clp-binding sites, site I and site II centered at -69.5 and -42.5, respectively, were located. Transcriptional fusion assays indicated that Clp greatly activates engA transcription. Site-directed mutagenesis indicated that position 5 of GTG motif in site II is essential for both DNA-protein complex formation in electrophoretic mobility shift assays and engA transcription in vivo. In addition, mutation at position 5 of site I drastically reduces the promoter activity, indicating that binding of Clp to site I exerts a synergistic effect on the transcription activation by site II. engA appears to be the first X. campestris gene known to be activated by Clp via a direct binding to the promoter.

Preparation, crystallization and preliminary X-ray analysis of XC2382, an ApaG protein of unknown structure from Xanthomonas campestris

Xanthomonas campestris pv. campestris is the causative agent of black rot, one of the major worldwide diseases of cruciferous crops. Its genome encodes approximately 4500 proteins, roughly one third of which have unknown function. XC2382 is one such protein, with a MW of 14.2 kDa. Based on a bioinformatics study, it was annotated as an ApaG gene product that serves multiple functions. The ApaG protein has been overexpressed in Escherichia coli, purified and crystallized using the hanging-drop vapour-diffusion method. The crystals diffracted to a resolution of at least 2.30 A. They are tetragonal and belong to space group P4(1/3), with unit-cell parameters a = b = 57.6, c = 122.9 A. There are two, three or four molecules in the asymmetric unit.

Isolation and characterization of novel giant Stenotrophomonas maltophilia phage phiSMA5

Stenotrophomonas maltophilia is one of the most prevalent opportunistic bacteria causing nosocomial infections. It has become problematic because most of the isolates are resistant to multiple antibiotics, and therefore, development of phage therapy has attracted strong attention. In this study, eight S. maltophilia phages were isolated from clinical samples including patient specimens, catheter-related devices, and wastewater. These phages can be divided into four distinct groups based on host range and digestibility of the phage DNAs with different restriction endonucleases. One of them, designated phiSMA5, was further characterized. Electron microscopy showed it resembled Myoviridae, with an isometric head (90 nm in diameter), a tail (90 nm long), a baseplate (25 nm wide), and short tail fibers. The phiSMA5 double-stranded DNA, refractory to digestion by most restriction enzymes, was tested and estimated to be 250 kb by pulsed-field gel electrophoresis. This genome size is second to that of the largest phage, phiKZ of Pseudomonas aeruginosa. In sodium dodecyl sulfate-polyacrylamide gel electrophoresis, 25 virion proteins were visualized. N-terminal sequencing of four of them suggested that each of them might have had its N terminus cleaved off. Among the 87 S. maltophilia strains collected in this study, only 61 were susceptible to phiSMA5, indicating that more phages are needed toward a phage therapy strategy. Since literature search yielded no information about S. maltophilia phages, phiSMA5 appears to be the first reported.

Molecular epidemiology of Bordetella pertussis isolated in Taiwan, 1992-1997

In Taiwan, the number of pertussis cases including various types of infection has been increasing in recent years, especially in 1997. Since 71% of the reported cases concentrated in the densely populated Taipei metropolitan area, concerns have been raised that a highly contagious strain of Bordetella pertussis might have appeared in Taipei. In this study, 114 strains of B. pertussis including those isolated in 1992-1996 (n = 53) and 1997 (n = 61) were subjected to pulsed-field gel electrophoresis (PFGE) of the Xba I digests from their chromosomes. Based on the band patterns, they were divided into 21 subtypes, P1 to P21. The strains isolated in 1997 consist of 17 subtypes including 9 new subtypes which did not appear in the previous years, indicating that the outbreaks in 1997 were not caused by a sole specific virulent strain. Dendrogram analysis indicated that the 21 subtypes can be grouped into five clusters, with the first four subtypes possessing 60 to 95% relatedness to one another, whereas relatedness between cluster 5 (containing P21 only) and the other clusters is less than 50%. Notably, all the subtypes except P12 and P21 appeared at least once in Taipei and the majority of the strains (54%) belong to two clusters, 3 and 4. These results suggest that highly dense population may facilitate spread and accelerate genetic divergence of this pathogen. This is the first report on pertussis molecular epidemiology in Taiwan.

Transcription of Xanthomonas campestris prt1 gene encoding protease 1 increases during stationary phase and requires global transcription factor Clp

Xanthomonas campestris pv. campestris produces three proteases, Prt1, Prt2, and Prt3, the first two of which are involved in pathogenicity. In this study, nucleotide A 84 nt upstream of the prt1 start codon, which is 8 nt downstream of the -10 sequence, was determined as the transcription start site by the 5(') RACE (rapid amplification of cDNA ends) method. Using Pprt1-lacZ transcriptional fusion constructs for assays, several interesting characteristics of prt1 promoter were revealed. The expression is inducible by LB medium or casein proteins and involves the global transcription factor Clp (cyclic AMP receptor protein-like protein). The region containing bp -392 to -80 relative to the prt1 translation initiation codon is required for maximal expression, in which bp -392 to -207 responds to the Clp-mediated regulation and the induction. In presence of inducers and the clp wild-type background, the levels of expression continue to increase following cell growth until 30 h after the cultures entering stationary phase. Since prt1 promoter shows no response to stressful conditions and neither growth nor cell viability is affected by prt1 mutation, Prt1 appears to be a secondary metabolite of X. campestris pv. campestris.

oriC region and replication termination site, dif, of the Xanthomonas campestris pv. campestris 17 chromosome

A 13-kb DNA fragment containing oriC and the flanking genes thdF, orf900, yidC, rnpA, rpmH, oriC, dnaA, dnaN, recF, and gyrB was cloned from the gram-negative plant pathogen Xanthomonas campestris pv. campestris 17. These genes are conserved in order with other eubacterial oriC genes and code for proteins that share high degrees of identity with their homologues, except for orf900, which has a homologue only in Xylella fastidiosa. The dnaA/dnaN intergenic region (273 bp) identified to be the minimal oriC region responsible for autonomous replication has 10 pure AT clusters of four to seven bases and only three consensus DnaA boxes. These findings are in disagreement with the notion that typical oriCs contain four or more DnaA boxes located upstream of the dnaA gene. The X. campestris pv. campestris 17 attB site required for site-specific integration of cloned fragments from filamentous phage phiLf replicative form DNA was identified to be a dif site on the basis of similarities in nucleotide sequence and function with the Escherichia coli dif site required for chromosome dimer resolution and whose deletion causes filamentation of the cells. The oriC and dif sites were located at 12:00 and 6:00, respectively, on the circular X. campestris pv. campestris 17 chromosome map, similar to the locations found for E. coli sites. Computer searches revealed the presence of both the dif site and XerC/XerD recombinase homologues in 16 of the 42 fully sequenced eubacterial genomes, but eight of the dif sites are located far away from the 6:00 point instead of being placed opposite the cognate oriC. The differences in the relative position suggest that mechanisms different from that of E. coli may participate in the control of chromosome replication.

Mutation in the Xanthomonas campestris xanA gene required for synthesis of xanthan and lipopolysaccharide drastically reduces the efficiency of bacteriophage (phi)L7 adsorption

(Phi)L7 is a lytic phage infecting the gram-negative Xanthomonas campestis pv. campestris, a plant pathogen. To study phage-host interaction, a (phi)L7-resistant mutant was isolated from strain Xc17 by mini-Tn5 transposition and designated CH7LR. CH7LR could not plate (phi)L7 in double-layered assay and formed turbid clearing zones when the cell lawn was dropped with a high titer of (phi)L7. Sequence analysis showed that the mutated gene is xanA coding for phosphoglucomutase/phosphomannomutase, required for the synthesis of lipopolysaccharide and exopolysaccharide (xanthan). The involvement of xanA was confirmed by isolating another mutant with interrupted xanA and complementing with the cloned wild-type gene. Nonmucoid mutants are still sensitive to (phi)L7, indicating that xanthan is not involved in (phi)L7 adsorption. Since the mutants still exhibited low efficiencies of phage adsorption, we predict, by analogy with the cases in other bacteriophages of gram-negative bacteria, that other outer membrane components such as a protein are required for the formation of a complex receptor.

UDP-glucose dehydrogenase gene of Xanthomonas campestris is required for virulence

Xanthomonas campestris pv. campestris (Xc) is the casual agent of black rot in crucifers. The Xc gene (udgH) coding for UDP-glucose dehydrogenase, an enzyme catalyzing the conversion of UDP-glucose to UDP-glucuronic acid, was previously shown to be required for the biosynthesis of xanthan gum, a substance necessary for the bacterium to cause disease. In this study, the transcription start site of the udgH was determined and the promoter activity monitored by the xylE reporter system indicated that expression of the udgH increases following cell growth and that the udgH gene may possess a second promoter that is responsive to stationary-phase change retaining high levels of expression. Results of Southern hybridization suggest that the udgH gene may be ubiquitous in Xanthomonas, coincident with the notion that members of this genus are capable of xanthan gum biosynthesis. Mutation of the udgH gene in Xc and X. campestris pv. vesicatoria, the casual agent of leaf spot in pepper and tomato, was found to cause a loss of virulence.

Construction and characterization of a Xanthomonas oryzae pv. oryzae bacterial artificial chromosome library

Xanthomonas oryzae pv. oryzae is an important plant pathogen which causes bacterial blight of rice. To facilitate genome studies of this bacterium, we have constructed a bacterial artificial chromosome (BAC) library of strain MAFF 311018. It consisted of 750 clones representing 16 genome equivalents, and had an insert size ranging from 20 to 220 kb with an average size of 107 kb. This library is the first to be constructed from a X. oryzae pv. oryzae strain. The usefulness of this library was demonstrated through polymerase chain reaction screening of 11 genes and the 16S--23S rDNA spacer region in a 192-clone subset, representing five genome equivalents. The results obtained showed an average of 5.9 BAC clones per screening. This result is in good agreement with the estimated size of the test library, indicating that the constructed BAC library can be used to facilitate genome analysis of X. oryzae pv. oryzae.

Characterization of the IncW cryptic plasmid pXV2 from Xanthomonas campestris pv. vesicatoria

The gram-negative plant pathogen Xanthomonas campestris pv. vesicatoria strain Xv2 harbors an indigenous, cryptic plasmid pXV2 of 14.6 kb. This plasmid can only be maintained in Xanthomonas and is incapable of self-transmission. However, incompatibility testing classified it in IncW, a group containing the smallest number of naturally occurring, broad-host-range, conjugative plasmids. A pXV2 derivative containing only a 5.5-kb PstI fragment is stably maintained. Deletion of a 3.0-kb region from the PstI fragment causes a loss of plasmid stability. Nucleotide sequencing of the 2. 1-kb region essential for autonomous replication revealed a repA gene and a downstream noncoding region containing four iterons, two 17- and two 19-nt direct repeats, and an AT-rich region lying between the two sets of iterons. The sequence of the deduced RepA and the iterons shows homology to the RepA (39% identity) and the iterons, respectively, of the IncW plasmid pSa. Maxicell expression of the repA gene produced a protein of 35 kDa, a size similar to that deduced from the nucleotide sequence. Trans-complementation test confirmed that the repA gene and the iterons are indeed the essential elements for pXV2 replication.