Isolation of a Protein Bound to Canker-forming Factor from Citrus Plant

Interaction analysis using affinity analysis (Affinity Sensors, Cambridge, UK) indicated the presence of proteins bound to Apl1, a virulence factor of Xanthomonas campestris pv. citri required for the formation of canker symptom on citrus, in the fraction 25–50% ammonium sulfate of citrus crude extracts. Three proteins of 25, 50 and 110-kD were eluted from an Apl1-affinity column. Western analysis revealed that Apl1 binds specifically to the 25-kD and 110-kD but not to the 50-kD protein. When crude extracts of soybean and of tobacco were applied to the Apl1-affinity column, only faint bands were detected. This result suggests that Apl1 targets exist specifically in citrus plants. The amino acid sequence of the N-terminal of the 25-kD protein was determined, and homology search analysis revealed that this sequence was almost identical to those commonly present in S-adenosyl-l-methionine : trans-caffeoyl-coenzyme A 3-O-methyltransferase (CCoAMT) from several plants. This enzyme is specific to the substrate trans -caffeoyl-CoA and catalyzes the synthesis of trans-feruloyl-CoA for lignin formation. Received 4 November 1999/ Accepted in revised form 26 November 1999     

Genomic Structure of a Geminivirus in the Genus Begomovirus from Yellow Vein-affected Eupatorium makinor

A virus from yellow vein-affected Eupatorium makinoi was tentatively designated as Eupatorium-infecting geminivirus (EuGV) on the basis of whitefly transmissibility, electron microscopic observation of geminate particles in sap and symptomatology. EuGV-speciflc DNA fragments were obtained by polymerase chain reaction (PCR). Based on the restriction analysis of the PCR products, EuGV was suggested to have a monopartite genome. We determined the putative, complete nucleotide sequence of the EuGV genome which is comprised of 2766 nucleotides. The EuGV sequence had two virus sense open reading frames (ORF)(V1, V2), four complementary sense ORFs (C1–C4) and a non-coding region termed the intergenic region. This genome structure is quite similar to other monopartite begomoviruses already reported. The nucleotide and amino acid sequences were compared with other begomoviruses. The results supported the conclusion that EuGV is distinct and divergent from other begomoviruses, whereas potential sequence motifs reported in other geminiviruses are well conserved. Received 17 March 1999/ Accepted in revised form 12 November 1999     

Similarity between Copper Resistance Genes from Pseudomonas syringae pv. actinidiae and P. syringae pv. tomato

Twenty-eight strains of Pseudomonas syringae pv. actinidiae isolated in 1984, 1987 and 1988 from kiwifruit orchards in Japan were tested for their resistance to copper sulfate. All strains isolated in 1984 were copper sensitive with a minimum inhibitory concentration (MIC) of cupric sulfate of 0.75 mM. However, some strains isolated in 1987 and 1988 were resistant, with the MIC ranging from 2.25 to 3.0 mM. All copper-resistant strains contained at least one of two plasmids, pPaCul (about 70.5 kb) or pPaCu2 (about 280 kb), or both. In a copper-resistant strain Pa429, the location of the copper-resistance gene(s) was examined by insertional inactivation with Tn5. The MIC of copper sulfate in the copper-sensitive mutant obtained by Tn5 tagging decreased from 2.75 to 0.75 mM. The 14.5 kb BamHI fragment, designated pPaCuB14, containing the same locus mutagenized with Tn5 was cloned from pPaCu1. However, pPaCuB14 did not confer copper resistance in the transformant of copper-sensitive strain Pa21R, suggesting that this clone did not contain a full set of copper-resistance gene(s). Then a cosmid library of pPaCu1 was constructed and six cosmid clones hybridized with pPaCuB14 were selected. One of the six cosmids, designated pPaCuC1, conferred a near wild-type level of copper resistance in the transformant of the copper-sensitive strain. pPaCuC1 had a homologous region that hybridized with all of the PCR-amplifled fragments of copA, copB, copR, and copS genes of P. syringae pv. tomato. DNA sequence analysis of the homologous region revealed the existence of four open reading frames (ORF A, B, R and S) oriented in the same direction. The predicted amino acid sequences of ORF A, B, R and S had 80, 70, 97 and 95% identity with CopA, B, R and S of P. syringae pv. tomato, respectively. Received 5 July 2001/ Accepted in revised form 27 September 2001     

<Emphasis Type="Italic">Pseudomonas syringae </Emphasis>Strains Are Classified into Five Groups by Comparing DMA Homology at the <Emphasis Type="Italic">hrp </Emphasis>Neighboring Regions

Previously, we classified Pseudomonas syringae strains into at least three groups (I, II and U) by comparing DNA homology at the hrp cluster and its neighboring regions (Inoue and Takikawa 1999). However, heterogeneous strains remained in the undetermined group (group U). We further classify group U, using pvs. syringae and coronafaciens as references. Comparison of restriction sites for regions of each pathovar revealed distinct differences. By using probes from the two pathovars, comparisons of DNA homology at the regions separated two additional distinct groups (III and IV) from group U. Therefore, P. syringae strains are classified into at least five groups. Received 4 November 1999/ Accepted in revised form 27 January 2000     

Serological and Molecular Characterization of a High Temperature-recovered Virus Belonging to Tospovirus Serogroup IV

A serologically and cytologically distinct gloxinia tospovirus (HT-1) previously isolated from a gloxinia plant infected with Impatiens necrotic spot virus (INSV) when propagated in a high-temperature environment was characterized. Rabbit antisera produced for INSV and Tomato spotted wilt virus (TSWV) nucleocapsids (N) failed to react with HT-1 proteins in western blot analysis. The HT-1 antibodies reacted strongly with homologous antigen but failed to react with INSV and TSWV. However, the HT-1 antiserum reacted in ELISA with Watermelon silver mottle virus (WSMV) from Taiwan and in western blot analysis with the WSMV N protein. A reciprocal test showed that the antiserum prepared against the N protein of WSMV also reacted with the HT-1 N protein in both ELISA and western blot analysis. DNA probes derived from the N gene of HT-1 or WSMV hybridized to RNAs prepared from plants infected with either virus. Stronger signals were obtained with homologous than with heterologous reactions. Neither probe detected INSV or TSWV. The M and S RNAs of HT-1 were sequenced. The M RNA contains two open reading frames (ORF) ; one in the sense orientation encoding a nonstructural (NSm) protein of 308-amino-acids (aa) and the other in the ambisense orientation, a 1122-aa precursor of Gl and G2 glycoproteins. The S RNA also contains two ORFs ; one in the sense orientation encoding a nonstructural (NSs) protein of 439 aa and the other in the ambisense orientation, an N protein of 277 aa. HT-1 is distantly related to INSV and TSWV as shown by low nucleotide (40–52%) and amino acid (28–48%) similarities in the four ORF sequences. The HT-1 virus shares high nucleotide (76–81%) and amino acid (85–92%) similarities with WSMV and peanut bud necrosis virus (PBNV). Based on the serological properties and sequence data, we propose that HT-1 is a distinct species of serogroup IV in the genus Tospovirus. This is the first time that a tospovirus similar to those found in the Far East and in Southeast Asia has been identified in the US. Received 16 October 1999/ Accepted in revised form 20 December 1999     

Hypovirulent strain of the violet root rot fungus <Emphasis Type="Italic">Helicobasidium mompa</Emphasis>

The hyphal tip was isolated from 13 weakly or moderately virulent strains of Helicobasidium mompa to remove double-stranded (ds) RNAs and demonstrate their role as the hypovirulence factor. All of 829 hyphal tip subcultures retained dsRNAs. However, strain v670 containing two large fragments (10kb) and one small fragment (ca. 2.3kb) of dsRNA lost the largest fragment in 3 of 63 subcultures analyzed. One of the three subcultures (v670hti) was used to inoculate carrots to regain virulence compared to the parental strain v670. When isolate v670hti was paired with v670, the largest fragment was reintroduced to v670hti, and its virulence was diminished. Northern blot analysis with two probes hybridizing dsRNA fragments in most H. mompa strains revealed that the largest fragment involved in hypovirulence was different from two other fragments that are common in Japan. These results indicate that the largest dsRNA fragment in strain v670 is associated with hypovirulence in H. mompa.     

Specific detection of<Emphasis Type="Italic">Pythium aphanidermatum</Emphasis> from hydroponic nutrient solution by booster PCR with DNA primers developed from mitochondrial DNA

Pythium aphanidermatum causes damping-off and root rot of vegetable crops in hydroponic systems. A DNA probe was isolated and modified from a library ofHindIII-digested mitochondrial DNA ofP. aphanidermatum that strongly hybridized to DNA ofP. aphanidermatum and weakly hybridized to DNA ofPythium deliense. Cross-hybridizing sequences were absent from DNA of plants and other related fungi. The probe detected as little as 5 ng ofP. aphanidermatum DNA and 250 ng ofP. deliense DNA in slot-blot assays.P. aphanidermatum was detected by a hybridization assay of total DNA extracted directly from infected roots. A pair of oligonucleotide primers P1 and RP2, which allowed amplification of a specific 0.65 kb DNA fragment ofP. aphanidermatum using polymerase chain reaction (PCR), was designed from a specific DNA probe. Specific amplification of this fragment fromP. aphanidermatum was highly sensitive, detecting template DNA as low as 0.1 pg total DNA by booster PCR. Specific booster PCR amplification using P1 and RP2 was successful in detectingP. aphanidermatum in naturally infected nutrient solution and roots of vegetables in a field hydroponic system. http://www.phytoparasitica.org posting Sept. 22, 2002.     

Red Stripe of Rice Is Caused by a Bacterium <Emphasis Type="Italic">Microbacterium</Emphasis> sp.

In an etiological study to identify the causal agent of red stripe of rice, white bacterial colonies were consistently isolated from all diseased leaf samples collected in Indonesia. All the bacterial isolates were pathogenic to rice and caused symptoms similar to red stripe. The bacterial infection in rice leaves was confirmed histologically. Bacterial masses were observed in the lumina of xylem vessels in the lesion area, especially in those of connecting strands. Analysis of the 16S rDNA of the causal bacterium gave best matches to the 16S rDNA sequence of Microbacterium spp. of Microbacteriaceae which includes Clavibacter. Received 9 September 1999/ Accepted in revised form 16 November 1999     

Cloning of DNA fragments specific to the pathotype and race of <Emphasis Type="Italic">Verticillium dahliae</Emphasis>

Japanese isolates of Verticillium dahliae, a causal agent of wilt disease in many plants, are classifiable into pathotypes based on their pathogenicity. Because these pathotypes are morphologically indistinguishable, establishing a rapid identification method is very important for the control of this pathogen in Japan. For cloning DNA fragments that are useful for identification and specific detection of V. dahliae pathotypes, we performed random amplified polymorphic DNA (RAPD) analyses using various isolates. One polymerase chain reaction (PCR) product, E10-U48, was specific to isolates pathogenic to sweet pepper. The other product, B68-TV, was specific to race 1 of isolates pathogenic to tomato. The specificity of these sequences was confirmed by genomic Southern hybridization. Further analyses revealed that the region peripheral to B68-TV obtained from the genomic DNA library includes the sequence specific to all isolates pathogenic to tomato (races 1 and 2). Moreover, sequence tagged site (STS) primers designed from B68-TV and its peripheral region showed race-specific and pathotype-specific amplification in a PCR assay. The probes and primers obtained in this study are likely to be useful tools for the identification and specific detection of pathotypes and races of V. dahliae. The nucleotide sequence data reported are available in the DDBJ/EMBL/GenBank databases under accession number AB095266.     

Pathogenicity, Mating Ability and DNA Restriction Fragment Length Polymorphisms of Pyricularia Populations Isolated from Gramineae, Bambusideae and Zingiberaceae Plants

Eighty-five Pyricularia isolates were collected from 29 host species of Gramineae, Bambusideae and Zingiberaceae plants sampled in Brazil, Uganda, Ivory Coast, India, Nepal, China, Indonesia and Japan. These isolates were compared on the basis of pathogenicity, mating ability and restriction fragment length polymorphisms with single-copy DNA probes. Based on the pathogenicity to eight differential gramineous plants, these isolates were classified into seven pathotypes: finger millet type, foxtail millet type, common millet type, rice type, crabgrass type, Italian ryegrass/ weeping lovegrass type, and non-cereal/grass type. Genetic variation among these isolates was assessed by RFLP analysis with two restriction enzymes and nine single-copy DNA probes isolated from a finger millet strain. An UPGMA dendrogram based on the RFLPs revealed that the 85 isolates could be classified into seven major groups. Isolates from cereal crops (finger millet, foxtail millet, common millet, wheat and rice) and a grass, Brachiaria plantaginea, were clustered into a single group. They were further divided into six subgroups corresponding to the pathotypes. Among cereal crop isolates only an isolate from pearl millet was located into a different group. The remaining isolates were clustered into five groups designated as the crabgrass group, the buffelgrass and jungle rice group, the rice cutgrass, knotroot bristlegrass and Setaria tomentosa group, the bamboo and bamboo grass group and the Zingiber mioga group. The isolates from cereal crops were generally capable of mating with finger millet strains and constituted a closed mating compatibility group. These results suggested that the isolates from cereal crops form a single group with a common ancestor although they are pathogenic to taxonomically diverse plants. A combined analysis of the pathogenicity and genetic similarity suggested that the transmission of M. grisea isolates occurs in natural agroecosystems between finger millet and Eleusine africana, goosegrass or Bambusa arundinacea, between foxtail millet and green bristlegrass, and between rice and tall fescue, Italian ryegrass, sweet vernalgrass, reed canarygrass or Oryza longistaminata. Received 9 August 1999/ Accepted in revised form 12 November 1999     

Mitochondrial dna restriction fragment length polymorphisms infusarium oxysporum f. sp.niveum

Mitochondrial DNA (mtDNA) extracts from 13 isolatesof Fusarium oxysporum f. sp.niveum, including 12 from widely separated geographic regions within the United States and representing the three races, and one race 2 isolate from Israel, were examined for the presence of plasmid DNA and were also subjected to restriction endonucleases analysis. None of the mtDNA from any isolate had a copurifying plasmid. The estimated size of mtDNA fromF. o. f. sp.niveum race 0, calculated as the average of the sum of restriction fragment sizes, was 45.1 ± 2.2 kb. The restriction enzymesBamHI, EcoRI, Hpal, HindIII andMbol resolved 2, 4, 9, 21, and more than 40 fragments, respectively, but no polymorphisms were observed among the 13 isolates with any of these endonucleases. However, PstI digestion showed three distinct polymorphic patterns among the isolates. Each appeared to derive from point mutations that resulted in a change of one or more restriction sites. The most common pattern was present in nine of the isolates (three of race 0, four of race 1, and two of race 2) and included a 1.5 kb fragment. A second polymorphic pattern occurred in three USA isolates (one each of race 0, race 1 and race 2) and was characterized by an apparent replacement of the 1.5 kb fragment by 0.6 and 0.9 kb fragments. The Israeli isolate [ISL-59(73) race 2| had a unique pattern lacking the 1.5 and 2.0 kb fragments present in the common pattern and, instead, had 0.6, 0.9 and 3.0 kb fragments. The mtDNA polymorphisms observed among the USA isolates were not correlated with either pathological race or geographic region of origin.     

Polymerase chain reaction detection and phylogenetic characterization of an agent associated with yellow vine disease of cucurbits

ABSTRACT Diagnosis of yellow vine disease (YVD) in cucurbits, an important disease in the south-central United States, relies on external symptom appearance, phloem discoloration, and the presence of bacterium-like organisms (BLOs) in phloem. Polymerase chain reaction (PCR) amplification of BLO nucleotide sequences was explored as a means to improve diagnostic techniques. PCR, using a primer pair based on sequences of the citrus-greening BLO, amplified a 0.15-kilobase (kb) fragment from the DNA of symptomatic plants, but not from that of asymptomatic plants. Its nucleotide sequence suggested that the DNA amplified was of pro-karyotic origin. A primer pair, designed to amplify nonspecific prokaryotic 16S rDNA, amplified a 1.5-kb DNA fragment in both the symptomatic and asymptomatic plants. The 1.5-kb fragment from the asymptomatic plants corresponded to chloroplast 16S rDNA, and the band from the symptomatic plants was composed of 16S rDNAs from both chloroplasts and a prokaryote. The nucleotide sequence of the prokaryotic DNA was determined and used to design three primers (YV1, YV2, and YV3). Fragments of 0.64 and 1.43 kb were amplified with primers YV1-YV2 and primers YV1-YV3, respectively, from symptomatic plants. Neither primer set yielded fragments from asymptomatic plants, unrelated bacteria, or selected soilborne fungal pathogens of cucurbits. Phylogenetic analysis indicated that the prokaryote is a gamma-3 proteobacterium. The consistent association of the 0.64- and 1.43-kb fragments with symptomatic plants suggests that the gamma-3 proteobacterium may be the causal agent of YVD of cantaloupe, squash, and watermelon.     

First report of blueberry red ringspot disease caused by <Emphasis Type="Italic">Blueberry</Emphasis><Emphasis Type="Italic">red</Emphasis><Emphasis Type="Italic">ringspot</Emphasis><Emphasis Type="Italic">virus</Emphasis> in Japan

Virus-like symptoms—red ringspots on stems and leaves, circular blotches or pale spots on fruit—were found on commercial highbush blueberry (Vaccinium corymbosum) cultivars Blueray, Weymouth, Duke and Sierra in Japan. In PCR testing, single DNA fragments were amplified from total nucleic acid samples of the diseased blueberry bushes using primers specific to Blueberry red ringspot virus (BRRV). Sequencing analysis of the amplified products revealed 95.7–97.7% nucleotide sequence identity with the BRRV genome. This paper is the first report of blueberry red ringspot disease caused by BRRV in Japan. The nucleotide sequence data reported in this paper are available in the GenBank/EMBL/DDBJ database as accessions AB469884 to AB469893 for BRRV isolates from Japan.     

Biotin Induces Sporulation of Mulberry Anthracnose Fungus, Colletotrichum dematium

Compounds in mulberry leaves inducing sporulation of C. dematium, mulberry anthracnose fungus, were detected. Dissolved or suspended aqueous solutions (1%) of 16 amino acids and 10 vitamins occurring in mulberry leaves were applied individually at the margin of the fungal colony growing on PSA plate. Sporulation was induced only where a biotin solution was applied on the mycelium at a concentration of at least 0.01 ppm. This result suggests that biotin, which occurs in mulberry leaves (ca. 0.6 mg/kg of dried leaves), has a role in inducing sporulation of C. dematium. Received 20 August 1999/ Accepted in revised form 16 November 1999     

Two paths of sequence divergence in the citrus tristeza virus complex

ABSTRACT Comparison of a sampling of complementary DNA (cDNA) sequences from the Florida citrus tristeza virus (CTV) isolates T3 and T30 to the sequence of the genome of the Israeli isolate VT showed a relatively consistent or symmetrical distribution of nucleotide sequence identity in both the 5' and 3' regions of the 19.2-kb genome. In contrast, comparison of these sequences to the sequence of isolate T36 showed a dramatic decrease in sequence identity in the 5' proximal 11 kb of the genome. A cDNA probe derived from this region of the T36 genome hybridized to double-stranded RNA (dsRNA) of only 3 of 10 different Florida CTV isolates. In contrast, analogous probes from T3 and T30 hybridized differentially to the seven isolates not selected by the T36 probe. Primers designed from cDNA sequence for polymerase chain reaction (PCR) selectively amplified these 10 isolates, allowing them to be classified as similar to T3, T30, or T36. In contrast, individual cDNA probes derived from the 3' terminal open reading frames of the T3, T30, and T36 genomes all hybridized to dsRNA from all Florida CTV isolates tested, and PCR primers designed from the T36 capsid protein gene sequence amplified successfully from all isolates. Based on these data, we propose the creation of two groups of CTV, exemplified by the VT and T36 isolates, respectively. Isolates in the VT group, which include isolates VT, T3, and T30, have genomic sequence divergence that is relatively constant in proportion and distribution throughout the genome, and candidate isolates for that group could be considered strains of the same virus. The T36 group is differentiated from the VT group by the highly divergent 5' genomic sequence. This 5' region of the CTV genome, thus, can serve as a measure of the extent of sequence divergence and can be used to define new groups and group members in the CTV complex.     

Comparison of rDNA-ITS Sequences between Potato and Tobacco Strains in <Emphasis Type="Italic">Rhizoctonia solani</Emphasis> AG-3

Genetic diversity among 51 isolates of Rhizoctonia solani AG-3, representing potato and tobacco populations, was inferred from the sequences of the internal transcribed spacer (ITS) and 5.8S ribosomal RNA (rRNA) gene. The 5.8S rDNA sequence was completely conserved not only in AG-3, but across all the AG isolates examined, whereas the rDNA-ITS sequence was found to be variable among the isolates. The nucleotide sequence similarity in the ITS 1 region was high (96-100%) for isolates within each of the two populations, but was 91-92% for isolates from different populations. The AG-3 isolates had 56 to 91% sequence similarities in the ITS 1 region with R. solani isolates of the other AGs. Phylogenetic analysis based on the ITS-5.8S rDNA sequence data indicated that the different populations in AG-3 are distantly related to each other. Genetic divergence between the two populations was also supported by the results of DNA-DNA hybridization studies. This study suggests that AG-3 consists of two genetically isolated groups corresponding to separate subgroups: AG-3 PT (potato type) and AG-3 TB (tobacco type). Specific primer sets for the detection of the two AG-3 subgroups were developed from the aligned rDNA-ITS sequences. Received 22 April 1999/ Accepted in revised form 2 July 1999     

β-1,3-D-Glucan Transported from Golgi Apparatus of Japanese Pear Leaves is a Component of Extracellular Polysaccharides Accumulated after AK-toxin I Treatment

This fluorescence and immunoelectron microscopic study showed that β-1,3-D-glucan accumulated only in leaves of a susceptible cultivar of Japanese pear after treatment with a host-specific toxin, AK-toxin I, from Alternate, alternata Japanese pear pathotype. The positive fluorescent reaction of callose was detected only in aniline blue fluorochrome-stained sections from toxin-treated leaves of the susceptible cultivar: positive sites were observed on cell walls of leaf cells. The sites of callose deposition were probably consistent spatially with modified sites on the plasma membrane that were observed only in the toxin-treated leaves of the susceptible cultivar. The toxin-induced modifications, identified as damage to the plasma membrane, were characterized by invagination of the plasmalemma specifically at plasmodesmata and as the concomitant accumulation of extracellular polysaccharides at the invaginated sites. A positive reaction to anti-β-1,3-D-glucan antibody was detected at the polysaccharides, Golgi vesicles, and trans-Golgi network (TGN) of toxin-treated leaves of the susceptible cultivar, but not at Golgi vesicles and TGN of water-treated ones. The cis-, medial and trans-Golgi stacks of toxin-treated leaves of the susceptible cultivar were negative for the antibody. The results showed that the polysaccharides, Golgi vesicles and TGN contained abundant β-1,3-D-glucan and that the glucan was transported from the Golgi apparatus via Golgi vesicles to the modified sites in cells of toxin-treated leaves of the susceptible cultivar. Received 7 March 2002/ Accepted in revised form 10 June 2002