Isolation and characterization of the ATP-binding cassette (ABC) transporter system genes from loofah witches' broom phytoplasma.

A clone containing a 3903 bp EcoRI-restriction fragment was obtained from a lambda(ZAP) genomic library of loofah witches' broom (LfWB) phytoplasma by plaque hybridization using a PCR fragment as a probe. Sequence analysis revealed that this fragment contained three open reading frames (ORFs). The deduced amino acid sequences of ORF 1 and ORF 2 showed a high homology with the ATP-binding proteins of the ABC transporter system genes of prokaryotes and eukaryotes, and encoded proteins with a molecular mass of 36 and 30 kDa, respectively. Based on amino acid sequence similarity, secondary structure, hydrophilicity and a signal peptide sequence at the N-terminus, we predicted that ORF 3 might encode a specific solute-binding prolipoprotein of the ABC transporter system with a molecular mass of 62 kDa. The cleavage site of this prolipoprotein signal peptide was similar to those of gram-positive bacteria. In addition to nutrient uptake, ABC transporter systems of bacteria also play a role in signal transduction, drug-resistance and perhaps virulence. The possible implications of the system to the survival and the pathogenesis of phytoplasma were discussed.     

Cryopreservation for eradication of Jujube witches' broom phytoplasma from Chinese jujube (Ziziphus jujuba)

Here, we report efficient eradication of Jujube witches' broom phytoplasma (Candidatus Phytoplasma ziziphi) from Chinese jujube (Ziziphus jujuba) by cryopreservation. Shoot tips (1.0 mm in size) with 5–6 leaf primordia (LPs) excised from diseased in vitro stock shoots were subject to droplet‐vitrification cryopreservation. Shoot tips following cryopreservation were post‐cultured on a recovery medium for survival. Plantlet regeneration was obtained by micrografting of surviving shoot tips upon in vitro rootstocks. With this protocol, 85% of shoot tips survived following cryopreservation, among which 75% regenerated into whole plantlets and all of them were free of phytoplasma, regardless of the sizes used for cryopreservation. Ultrastructural studies demonstrated that phytoplasma was absent in the apical dome, and leaf primordia (LPs) 1 and 2, while abundance of phytoplasma was present in the lower parts of shoot tips, leaf primordium 3 and older tissues. Histological observations showed that much more damage was found in cells located in the lower part of apical dome, leaf primordium 3 and older tissues than in those at the upper part of apical dome and in the LPs 1 and 2. These cells were most likely to survive and regenerate into phytoplasma‐free plantlets following cryopreservation and micrografting. Ploidy levels analyzed by flow cytometry (FCM) were maintained in plantlets regenerated from cryopreservation followed by micrografting. Results reported here would provide technical support for production of phytoplasma‐free plants and for long‐term storage of germplasm of Chinese jujube.     

Organization of genes of ribosomal RNA from the mushroom Verticillium dahliae

Using yeast probe, a complete ribosomal DNA unit from a plant pathogenic fungus, Verticillium dahliae, was cloned into a plasmid vector pTZ19R. Partial DNA sequence of the clones, when compared to the yeast ribosomal DNA sequence, allowed to establish the physical map of the fungal rDNA. The overall organization was shown to be similar to other fungal rDNAs previously known.     

Organization of the mitochondrial ribosomal RNA genes of maize.

The organisation of the mitochondrial ribosomal RNA genes in maize is described. Each of the rRNAs is encoded by a single gene. The 5S and 18S rRNA genes are close together, and separated from the 26S rRNA gene by 16 kb of DNA. There is no evidence of heterogeneity in this gene arrangement.     

Organization of ribosomal RNA genes in Mycoplasma capricolum

Summary DNA segments carrying rRNA genes of Mycoplasma capricolum have been cloned and characterized by restriction endonuclease mapping, DNA-RNA hybridization and nucleotide sequencing. The M. capricolum genome has two sets of rRNA gene clusters, where the arrangement is in the order of (5)16S-23S-5S(3). The spacer region between 16S and 23S rDNA is extremely rich in AT and does not carry any tRNA genes. Present address: Division of Hematology and Immunology of Internal Medicine, Kanazawa Medical University, Uchinada-Cho, Kahoku-Gun Ishikawa Pref. 920-02, Japan     

Association of mycoplasma-like bodies with potato witches' broom disease from Scotland

Mycoplasma-like bodies were found by electron microscopy of sections of sieve tubes, both from shoots and roots of potato (Solanum tuberosum) plants affected by Scottish witches' broom disease and from graft-inoculated tomato shoots. The bodies were bounded by a unit membrane, contained ribosome-like material and mostly measured 200–800 nm in diameter. Most were oval in cross-section but some had lobes or slender protrusions. Some of the bodies were found in the mouths of sieve pores.     

Reconstruction of ribosomal RNA genes from metagenomic data

Direct sequencing of environmental DNA (metagenomics) has a great potential for describing the 16S rRNA gene diversity of microbial communities. However current approaches using this 16S rRNA gene information to describe community diversity suffer from low taxonomic resolution or chimera problems. Here we describe a new strategy that involves stringent assembly and data filtering to reconstruct full-length 16S rRNA genes from metagenomicpyrosequencing data. Simulations showed that reconstructed 16S rRNA genes provided a true picture of the community diversity, had minimal rates of chimera formation and gave taxonomic resolution down to genus level. The strategy was furthermore compared to PCR-based methods to determine the microbial diversity in two marine sponges. This showed that about 30% of the abundant phylotypes reconstructed from metagenomic data failed to be amplified by PCR. Our approach is readily applicable to existing metagenomic datasets and is expected to lead to the discovery of new microbial phylotypes.     

Organization of the chloroplast ribosomal RNA genes of Euglena gracilis bacillaris

Summary The order of eight of the 29 endonuclease EcoRI-generated fragments of chloroplast DNA was determined. Three sets of rRNA genes aligned sequentially in the same orientation form part of this region. The repeated sets differ in the length and sequence of the spacers among themselves and with the rRNA genes of E. gracilis strain Z.     

Organization and size class homogeneity of ribosomal RNA genes of catfish Heteropneustes fossilis

The ribosomal RNA genes of catfish Heteropneustes fossilis Bloch were examined by Southern blot analysis of genomic DNA digested with restriction enzymes and probed with labelled catfish ribosomal RNA. The major repeat length is 12 kb and about 300 copies per haploid genome are tandemly arranged. The repeat lengths are homogeneous in size in different tissues and individuals. A restriction site polymorphism exists in some of the repeats.     

Organization of the ribosomal RNA genes in Treponema phagedenis and Treponema pallidum.

The genomic DNA fragment which contains ribosomal RNA (rRNA) genes for Treponema phagedenis was cloned into bacteriophage vector lambda EMBL3. A restriction map of the fragment was constructed and the organization of the rRNA genes was determined. The fragment contained at least one copy of the 16S, 23S and 5S sequences and the genes are arranged in the order 16S-23S-5S. Southern hybridization using radiolabeled rRNA gene probes to genomic DNA from T. phagedenis strain Reiter and T. pallidum strain Nichols showed that these organisms have two radioactive fragments which hybridize to the probes in their genome. These results suggest that both pathogenic and non-pathogenic strains of Treponema may carry at least two sets of rRNA genes on their chromosomes.     

Organization of 5S ribosomal RNA genes in tea (Camellia sinensis).

The 5S rRNA genes in the Camellia sinensis (L.) O. Kuntze (tea) genome are arranged as tandem repeat units of 300 and 325 bps. The 2 classes of tandem repeats were discovered by Southern hybridisation of tea genomic DNA with a 5S rRNA gene PCR product.     

Phenylpropanoid amides of serotonin accumulate in witches' broom diseased bamboo

Aciculosporium take (Ascomycota; Clavicipitaceae), causes the witches' broom disease in bamboo, particularly Phyllostachys bambusoides. Since it was observed that endogenous indole-3-acetic acid is reduced in the twigs of the diseased bamboo, the symptoms (bushy appearance) may be induced by reduction in auxin levels. Furthermore, two indolic compounds accumulated in diseased twigs, these being identified as N-p-coumaroylserotonin and N-feruloylserotonin by LC-MS, 1H NMR and 13C NMR spectroscopic analyses. N-p-Coumaroylserotonin possesses antifungal activity against A. take.     

Molecular phylogeny of Collembola inferred from ribosomal RNA genes

The classification of taxa within Collembola (Springtails, Hexapoda) has been controversial. In this study, we combined complete 18S rRNA gene with partial 28S rRNA gene (D7-D10) sequences to investigate the phylogeny of Collembola. About 2500 aligned sites of thirty species representing 29 genera from14 families of Collembola were analyzed, including one species of Neelipleona from which no sequence has been reported previously.The phylogenetic trees were obtained by different methods (maximum parsimony, maximum likelihood, and Bayesian analysis). Our results supported the monophyly of two of the four taxonomic groups of Collembola summarized by Deharveng [Deharveng, L., 2004. Recent advances in Collembola systematics. Pedobiologia 48, 415–433.], namely of Poduromorpha and of Symphypleona. Within Poduromorpha, Neanuridae was monophyletic with high support, but Hypogastruridae was not. Entomobryomorpha was paraphyletic, as the Tomoceroidea (Tomoceridae and Oncopoduridae) was found to be apart from the other entomobryomorphs. In the latter Isotomoidea and Entomobryoidea joined into a group with moderate support. Within Symphypleona, the phylogenetic relationship [(Sminthuridae + Bourletiellidae) + Sminthurididae] was consistent with traditional morphological studies. Neelipleona grouped with Symphypleona in all trees, with moderate support in the ML and Bayesian analyses.