Sequence analysis of the small cryptic Xanthomonas campestris pv. vesicatoria plasmid pXV64 encoding a Rep protein similar to gene II protein of phage 12-2

The complete nucleotide sequence (1,851 bp) was determined for the Xanthomonas campestris pv. vesicatoria plasmid pXV64. Sequence analysis revealed an intergenic region (IG) of 355 bp and two oppositely running open reading frames, ORF1 and ORF2, encoding polypeptides of 39 and 16 kDa, respectively. While the function of ORF2 is not known, ORF1 is suggested to be the gene encoding Rep protein based on (i) similarity in amino acid sequence to that of the gene II protein (gIIP) of filamentous phage 12-2, (ii) presence of a sequence in the ori-containing region which is similar to the sequence around the Rep nicking site in some rolling circle-replicating replicons, and (iii) ability to support replication in trans of the region containing pXV64 ori (392 bp) which is located within the region including IG and a short stretch in the N-terminus of ORF2.

Three-dimensional object representation and invariant recognition using continuous distance transform neural networks

3D object recognition under partial object viewing is a difficult pattern recognition task. In this paper, we introduce a neural-network solution that is robust to partial viewing of objects and noise corruption. This method directly utilizes the acquired 3D data and requires no feature extraction. The object is first parametrically represented by a continuous distance transform neural network (CDTNN) trained by the surface points of the exemplar object. The CDTNN maps any 3D coordinate into a value that corresponds to the distance between the point and the nearest surface point of the object. Therefore, a mismatch between the exemplar object and an unknown object can be easily computed. When encountered with deformed objects, this mismatch information can be backpropagated through the CDTNN to iteratively determine the deformation in terms of affine transform. Application to 3D heart contour delineation and invariant recognition of 3D rigid-body objects is presented.

IS element ISXC6 of Xanthomonas campestris pv. campestris

An insertion sequence element, ISXC6, was isolated from Xanthomonas campestris pv. campestris 17 (Xc17). Sequence analysis showed that it is 1,500 bp long and has 20-bp perfect inverted repeat ends. Upon transposition, a direct repeat TAATTC was generated, flanking this IS. No significant homology was observed between this sequence and other sequences in database. Results of Southern hybridization showed that multiple copies of ISXC6 were present in 7 strains of Xanthomonas examined.

The ori of filamentous phage phi Lf is located within the gene encoding the replication initiation protein

phi Lf is a filamentous phage of Xanthomonas campestris pv. campestris. In this study, the origin for phi Lf replication was located in a 121-bp TaqI fragment within gII, the gene encoding the replication initiation protein. This fragment, ligating with a GmR catridge, was able to be maintained as a plasmid (pT2) in strain Xc17 with the gII being provided in trans. ssDNA of pT2 was detected in the cells, indicating that pT2 may replicate by a rolling circle replication mechanism. Upon superinfection of Xc17 containing pT2 with phi Lf, transducing particles containing ssDNA of pT2 were released, suggesting the presence of packaging signal in the 121-bp TaqI fragment. This fragment contains a sequence homologous to the nicking sites for superfamily I Rep proteins of the rolling circle-replicating replicons, in concert with the presence of conserved amino acid sequence motifs of the superfamily I Rep proteins in the phi Lf gIIP.

Construction of a broad-host-range promoter-probing vector and cloning of promoter fragments of Xanthomonas campestris

A broad-host-range promoter-probing vector, pMY3 (8.0 kb), was constructed for cloning of DNA fragments containing promoter sequences of Xanthomonas campestris pv. campestris. This vector (pMY3) consists of the RK2 replicon, promoterless luxAB genes, the thr attenuator to block the transcription of RNA into the luxAB region, and multiple cloning sites for cloning of the fragment carrying promoter sequences. The feasibility of using pMY3 as a promoter-probing vector in both E. coli and Xc17 was demonstrated by using the lac promoter of E. coli, and the amy promoter of X. campestris in Xc17. Among the 63 promoter-containing fragments cloned from Xc17, only 9 were able to express in E. coli. It appears that X. campestris can recognize most E. coli type promoters, but, E. coli can recognize only a small portion of the X. campestris type promoters.

Detection of congenital cytomegalovirus infection in Chinese newborn infants using polymerase chain reaction

Polymerase chain reaction (PCR) amplification was used to detect cytomegalovirus (CMV) in 1000 urine specimens from Chinese newborns for defining the incidence of congenital CMV infection in the Chinese population. The major immediate-early and the late antigen genes of CMV were amplified and detected by gel electrophoresis. There were 18 congenitally infected infants found when tests were performed with one or both primer pairs. Comparing with tissue culture, PCR of both primer sets provided a sensitivity of 94%, a specificity of 100% and a predictive value of positive result of 100%.

The gene encoding UDP-glucose pyrophosphorylase is required for the synthesis of xanthan gum in Xanthomonas campestris

Xanthomonas campestris pv. campestris produces a large quantity of exopolysaccharide, xanthan gum, rendering the colonies mucoid. G76E was a non-mucoid mutant isolated from Xc17 by Tn5 mutagenesis. A 3.0-kb KpnI-EcoRI fragment from the Xc17 chromosome was able to restore mucoid phenotype to G76E. Sequence analysis of the region responsible for the restoration revealed an open reading frame, ORF324, able to encode a polypeptide of 35,232 Da which shows striking similarity to the UDP-glucose pyrophosphorylases from bacteria. The activity of UDP-glucose pyrophosphorylase reduced drastically in G76E was found to be regained in the presence of the cloned 3.0-kb KpnI-EcoRI fragment. In vitro expression of the gene in the S30 transcription/translation system produced a protein of ca. 35 kDa.

Nucleotide sequence of the gene presumably encoding the adsorption protein of filamentous phage phi Lf

A 1170-nucleotide fragment of phi Lf DNA was sequenced. This fragment contains an open reading frame, ORF367, encoding a protein of 367 amino acids (aa) (36710 Da). ORF367 is located downstream from the gene encoding the major coat protein (gVIIIp) and a Rho-independent termination signal. Sequence analysis revealed that the gene product has a Gly-rich domain (70 aa) at the center and a hydrophobic region (26 aa) at the C terminus. These structural features suggest that ORF367 may encode the adsorption protein of phi Lf.

Isolation and characterization of the recA gene of Xanthomonas campestris pv. campestris

A 1.8-kb NsiI-StuI fragment containing the recA gene of Xanthomonas campestris pv. campestris was cloned by a PCR-based approach and complementation of Escherichia coli HB 101. Sequence analysis of this fragment revealed an ORF (orf343) of 1,032 bp able to encode a protein of 343 amino acids with a calculated MW of 37,021 Da, a size similar to the values detected by in vitro system and Western blotting. It showed 69.6% identity to the E. coli RecA in amino acid sequence. Amino acid residues of the E coli RecA associated with functional activities are conserved in this Xc17 RecA. The recA mutant, L1, constructed by gene replacement, was sensitive to ultraviolet irradiation and methyl methanesulfonate, and deficient in homologous recombination.

A region of the filamentous phage phi Lf genome that can support autonomous replication and miniphage production

A 2028-bp fragment from the RF DNA of phi Lf, a filamentous phage of Xanthomonas campestris pv. campestris, was maintained autonomously as a minireplicon. Upon superinfection of the cells harboring the minireplicon with phi Lf, transducing miniphage particles were released. The minireplicon contained an open reading frame (ORF346) able to encode a polypeptide of MW39144, which possessed consensus motifs found in the Rep proteins from various sources. These findings suggested ORF346 to be the gene encoding replication initiation protein, gene II (gII) of phi Lf. Upstream to ORF346 were sequences with potential to form hairpin structures and a sequence similar to the integration host factor (IHF) binding site, structures similar to the intergenic region (IR) of the Ff phages. A 15 bp AT-rich core for phi Lf integration was found 37 bp downstream to the IHF binding site.

Nucleotide sequence and expression of UDP-glucose dehydrogenase gene required for the synthesis of xanthan gum in Xanthomonas campestris

Xanthomonas campestris pv. campestris, producing large amounts of exopolysaccharide xanthan gum, has a mucoid phenotype. Strain SD7 was a non-mucoid mutant deficient in UDP-glucose dehydrogenase. A DNA fragment able to complement the mutation of SD7 was cloned from the parental wild-type strain Xc11. Sequence analysis of the region required for the complementation revealed an open reading frame which could encode a polypeptide of 445 amino acids with a calculated molecular weight of 48,432, a size similar to that of the product produced by maxicell. The amino acid sequence had significant homology to that of the GDP-mannose dehydrogenase from Pseudomonas aeruginosa.

MRI diagnosis of spinal cord infarction: report of a case

A 62-year-old diabetic women developed acute quadriparesis. Her first symptom was clumsiness of the right limbs, which was followed shortly after by quadriparesis with severe left-sided symptoms. Sensory examination showed pinprick and thermal sensation deficits below the left T6 and right T8 dermatomes. An intramedullary infarction in the cervical cord at C5 to C6 levels was demonstrated by serial magnetic resonance imaging (MRI) studies with Gadolinium-DTPA (Gd-DTPA) enhancement. Based on the findings from this patient and 20 patients with spinal cord infarction reported in the literature, it was concluded that spinal cord infarct lesions are characterized by negative Gd-DTPA enhancement at the acute and chronic stages and positive enhancement at the subacute stage, 1 to 4 weeks after the onset of infarction.

Characterization of two novel filamentous phages of Xanthomonas

Two filamentous phages of Xanthomonas campestris pv. vesicatoria and Xanthomonas oryzae pv. oryzae were isolated and designated phi Xv and phi Xo, respectively. They were similar to other filamentous phages of Xanthomonas in (i) shape, (ii) restrictive host specificity, (iii) high stability, (iv) an ssDNA genome, (v) a dsDNA as the replicative form (RF), (vi) propagation without lysis of host cells and (vii) ability to integrate into the host chromosome. These phages showed sequence homology to filamentous phage phi Lf of X. c. pv. campestris. phi Xv was inactivated by antisera against phi Xv, phi Xo and phi Lf, whereas phi Xo and phi Lf were inactivated only by their respective antisera and the anti-phi Xv serum. Both the single-stranded phage DNAs and the RF DNAs of phi Xv, phi Xo and phi Lf were able to transfect X. c. pv. vesicatoria, X. o. pv. oryzae and X. c. pv. campestris. Physical maps of phi Xv and phi Xo were constructed for the RF DNAs. Genome sizes were estimated, based on mapping data, to be 6.8 kb for phi Xv and 7.6 kb for phi Xo, larger than that of the phi Lf genome (6.0 kb). The difference in genome sizes appeared to result from insertions of large DNA fragments. These fragments and the regions mediating integration were localized in the physical maps.

Nucleotide sequence determination, characterization and purification of the single-stranded DNA-binding protein and major coat protein of filamentous phage phi Lf of Xanthomonas campestris pv. campestris

phi Lf is a filamentous bacteriophage of Xanthomonas campestris pv. campestris, which can integrate its genome into the host chromosome. The nucleotide sequence of an EcoRV-SphI fragment (1018 bp) from the phi Lf replicative form DNA was determined. Four contiguous open reading frames (ORFs), orf98-orf43-orf38-orf42, were revealed. ORFs 98 and 42 were identified as the genes encoding a single-stranded DNA-binding protein (Sbp) and a major coat protein, respectively. Sbp was purified and found to bind with a high affinity to ssDNA prepared from phi Lf phage particles. The major coat protein showed sequence features similar to those of the typical major coat proteins of other filamentous phages. However, it appears to be synthesized as a mature product, similar to the situation with Pf3 but different from that with other filamentous phage major coat proteins which are synthesized as pre-coats and are subject to post-translational processing. The M(r)s, estimated by SDS-PAGE, of both the Sbp (10.9K) and the major coat protein (4.1K) coincide with the values deduced from the nucleotide sequences. ORFs 43 and 38 are proposed to be the genes encoding two minor coat proteins. The order of these four genes is similar to that found in the Escherichia coli filamentous phages.

Molecular cloning, characterization and nucleotide sequence of the gene for secreted alpha-amylase from Xanthomonas campestris pv. campestris

alpha-Amylase (1,4-alpha-D-glucan glucanohydrolase, EC 3.2.1.1) of apparent molecular mass 45 kDa was secreted by Xanthomonas campestris pv. campestris grown in medium containing starch or maltose. We isolated its structural gene from a recombinant lambda library and located it on a 2.7 kb DNA fragment. Nucleotide sequencing of the fragment revealed a potential ORF encoding a protein of 475 amino acid residues, including a potential signal sequence of 35 amino acids. The signal processing site was confirmed by N-terminal amino acid sequence analysis of the exported alpha-amylase. The deduced amino acid sequence of the mature protein is very similar to that of the alpha-amylase of Aeromonas hydrophila. It also contains all four amino acid sequences highly conserved in the alpha-amylases from a wide range of organisms. Expression of the amy gene in Escherichia coli was poor from its own promoter, but was enhanced by the upstream promoter on the vector. The alpha-amylase synthesized in E. coli was located in the periplasm.

Electrotransformation of Xanthomonas campestris by RF DNA of filamentous phage phi Lf

Conditions were optimized for electrotransformation of Xanthomonas campestris pv. campestris by the replicative form (RF) DNA of filamentous phase phi Lf. Early logarithmic cells were washed exhaustively with deionized water and subjected to a pulse at a field strength of 12.5 kV/cm with a 25 microF capacitor and a 400 omega resistor. An efficiency of 5.1 x 10(7) pfu per microgram RF DNA was obtained. Under the same conditions, the broad host range plasmid pLAFR1 (21.6 kb) transformed X. campestris strains at efficiencies around 10(5) pfu per microgram DNA prepared from XcP20H. The advantages of the protocol used in the present study are that the cells can be washed with water instead of complex buffer, and the DNA used can be prepared by the alkaline method of Birnboim & Doly without purification by ultracentrifugation.

Increase of xanthan production by cloning xps genes into wild-type Xanthomonas campestris

Previously, genomic banks of Xanthomonas campestris were constructed in Escherichia coli, using mobilizable broad-host-range cosmids as the vectors. Following conjugal transfer, genes involved in the biosynthesis of xanthan polysaccharide (XPS) were cloned by the ability to restore the mucoid phenotype to the non-mucoid mutants. In this study, all clones were transferred into the wild-type strain Xc17 to evaluate the effects of the cloned genes on XPS production. Most clones showed no significant effect; however, two plasmids, pP2401 and pP2201, caused 10 and 15% yield increases, respectively, compared with that of controls. While it was not clear how pP2201 caused the yield increase, the effect of pP2401 seemed to result from elevated phosphomannose isomerase activity. Since XPS synthesis in X. campestris is a very efficient process, only relatively small increases are to be expected; an enhancement of productivity by 10-15% is important to the commercial production of xanthan.

Characterization of filamentous bacteriophage phi Lf from Xanthomonas campestris pv. campestris

A filamentous phage, phi Lf, which specifically infects Xanthomonas campestris pv. campestris was isolated. The phage particle measured 1,000 (+/- 200) x 8 nm. It formed turbid plaques of about 1 mm in diameter. During multiplication, the progeny virions extruded into the medium without retarding host cell growth. Stocks were stable for 6 months at 4 degrees C and survived treatment at 80 degrees C for 10 min. Treatment with chloroform, ethanol or acetone completely destroyed infectivity; ethyl ether and methanol inactivated 98 to 99% of the phage. SDS-polyacrylamide gel electrophoresis showed a major coat protein band of approximate Mr 4000 whereas an immunoprecipitation test detected the existence of two coat protein species. The phage genome was shown to be a single-stranded DNA molecule. A physical map was constructed and the DNA size was calculated to be 5.9 kb. Cells treated with Tris-HCl containing CaCl2 and polyethylene glycol 6000 were transfected by replicative form DNA at a frequency of 3.4 x 10(3) p.f.u./micrograms.

Construction of lactose-utilizing Xanthomonas campestris and production of xanthan gum from whey

Xanthomonas campestris pv. campestris possesses a low level of beta-galactosidase and therefore is not able to grow and produce significant amounts of xanthan gum in a medium containing lactose as the sole carbon source. In this study, a beta-galactosidase expression plasmid was constructed by ligating an X. campestris phage phi LO promoter with pKM005, a ColE1 replicon containing Escherichia coli lacZY genes and the lpp ribosome-binding site. It was then inserted into an IncP1 broad-host-range plasmid, pLT, and subsequently transferred by conjugation to X. campestris 17, where it was stably maintained. The lacZ gene under the control of the phage promoter was expressed at a high level, enabling the cells to grow in a medium containing lactose. Production of xanthan gum in lactose or diluted whey by the engineered strain was evaluated, and it was found to produce as much xanthan gum in these substrates as the cells did in a medium containing glucose.

Broad host range cosmid pLAFR1 and non-mucoid mutant XCP20 provide a suitable vector-host system for cloning genes in Xanthomonas campestris pv. campestris

For many gram-negative bacteria, whose transformation systems have yet developed, following a two stage manipulation for gene cloning is a common choice. Following this strategy, DNAs are cloned in Escherichia coli, using a mobilizable vector, and the recombinant plasmids conjugally transferred into the original host. In this study, transfer of the broad-host range plasmid pLAFR1 (a 21.6 kb cosmid, TcR, derived from RK2 replicon) from E. coli to Xanthomonas campestris pv. campestris, by the help of plasmid pRK2013, was carried out to optimize the working conditions for gene cloning experiments in this phytopathogenic bacterium. Among several mating procedures tested, the highest frequencies of transfer were found by dropping the mixtures of the donor, helper and recipient cells (at ratios 1:1:10) to a nitrocellulose filter on an agar plate, with all the cells used from the cultures between OD550 0.3 to 0.5. When the non-mucoid mutant P20 was used as the recipient instead of its parental mucoid strain XC11A, 14-fold more transconjugants were obtained. In addition, the plasmid was found to be quite stable in the X. campestris cells. Further experiments showed that pLTA1, which is pLAFR1 with a cloned DNA fragment (4.4 kb) encoding alpha-amylase activity from XC11A, was not only maintained stably but also found to contribute a 8.3-fold over-production of enzyme activity to the transconjugant cells. From these studies, it has been demonstrated that cosmid pLAFR1 and the non-mucoid mutant P20 together provide a suitable vector/host system for cloning genes in X. campestris.

Transformation of Erwinia chrysanthemi by Escherichia coli plasmids DNA

We have demonstrated in this study that CaCl2-MnCl2 treatment is effective in the preparation of competent cells of Erwinia chrysanthemi for transformation. Plasmids pMB9 and pBR322, which are of Escherichia coli origins, were transformed into E. chrysanthemi at frequencies of 1.5 X 10(-7) and 4.5 X 10(-7) per recipient, respectively. The frequencies were 60- to 80-fold lower than those in the well established rec- E. coli; however, the procedure is practically useful in transformation experiments. The plasmids were maintained rather stable in the cells if antibiotics were included in the media. When transformed by pECl and pEC6, which were chimeric plasmids consisting of pBR322 and an E. chrysanthemi chromosomal DNA fragment of 2.4 and 3.5 Mdal, respectively, the transformation frequencies of E. chrysanthemi were at the same range of that by pBR322. Neither colony morphology nor the polypectate degradation ability was changed after transformation by the plasmids. In conclusion, we have established a system of molecular cloning in E. chrysanthemi SR120A exploiting pBR322 as a vector.

Release of alkaline phosphatase from cells of Xanthomonas oryzae by manipulation of surface permeability

Xanthomonas oryzae was shown to contain a constitutive alkaline phosphatase (EC 3.1.3.1.). The enzyme was detectable in intact cells and releasable by osmotic shock or spheroplast formation indicating its periplasmic location in the cell. Sonication released about 85% of the total enzyme, and the releasable amount was increased to 97% when lysozyme was added to the sonicated cells prior to centrifugation. These changes suggest an association of the enzyme with peptidoglycan; the enzyme is not released unless the polymer is digested to small units. Adapted usual method of spheroplast formation released 85%, while modified osmotic shock procedure released about 75% of the enzyme. These procedures released decreased amounts of the enzyme following cell growth reflecting that some changes were taking place toward a tighter association between the enzyme and the cell envelope during aging of the culture. During osmotic shock, the major portion of the released enzyme distributed in supernatant of the first stage (S1) hypertonic solution. The enzyme was inhibited by EDTA, whereas the inhibition was partially removed by dialysis and completely reversed by addition of MgCl2. Data obtained also indicated that X. oryzae seems to have relatively high content of periplasmic protein.