A novel deletion found during cloning of a synthetic palindromic DNA

A 212-bp palindromic DNA comprising two copies of the left end of bacteriophage Mu was assembled from chemically synthesized oligonucleotides and inserted into plasmid pUC9. When cloned and propagated in Escherichia coli, the palindrome was found to be unstable and was generally lost. However, in a few cases, a precise, asymmetric deletion of one half of the insert was observed. This pattern of deletion suggests that the symmetry axis region of the palindrome was involved as recognition site in the deletion process.     

Structural analysis of a beta-thalassemia gene found in Taiwan

The beta-globin gene from a patient with homozygous beta-thalassemia in Taiwan was cloned and extensively sequenced. Four nucleotides in the codon for amino acids, 41 and 42, are deleted. This change generates a frame-shift mutation and a termination codon in the new 59th codon. Some changes in nucleotide sequence were also found in intervening sequences IVS1 and IVS2, and Exon3, and were considered to be sequence polymorphisms.     

Presence of a novel Ehrlichia sp. in Ixodes granulatus found in Okinawa, Japan

Ehrlichia -specific DNA fragments of Ehrlichia omp-1 and groEL genes were found in two I. granulatus ticks which had been collected from wild small mammals in a subtropical zone in Japan. The DNA sequences of groEL and 16SrDNA of the suspected Ehrlichia were clustered into a group of E. chaffeensis , E. muris , and Ehrlichia sp. HF565 found in I. ovatus, but were distinctly different. Therefore the Ehrlichia strain was designated as a novel Ehrlichia sp. 360. The Ehrlichia sp. 360 was detected in I. granulatus but not in any other ticks. This suggests that I. granulatus is a probable vector of Ehrlichia sp. 360 in Japan.     

A novel Au SINE sequence found in a gymnosperm

Although many SINE families have been identified in the animal kingdom, only a few SINE families have been identified in plants, and their distribution is somewhat limited. The Au SINE (Au) has been found discontinuously in basal angiosperms, monocots, and eudicots. In this study, we examined the presence of the Au in gymnosperms and ferns by PCR using internal primers for Au. As a result, we found Au in a gymnosperm species, Ephedra ciliata. Therefore, Au was supposed to be present in the common ancestor of angiosperms and gymnosperms. The Au in E. ciliate was 15 bp shorter than the consensus sequence, which is similar to the Au SINE found in Glycine. However, the 3'end of the Au found in E. ciliate was more similar to the 3'end of the Medicago-type Au than that of the Glycine-type Au. A phylogenetic tree indicated that the Au sequence from E. ciliate is more closely related to the sequence found in Glycine than that found in Medicago/Lotus. These results indicated that Au were present in both angiosperms and gymnosperms.     

A novel pathway of peptide biosynthesis found in methanogenic Archaea

The peptide subunits of the pseudomurein, the cell-wall peptidoglycan of some methanogens, are usually composed of glutamic acid, alanine and lysine. In order to get a more detailed picture of the biosynthetic pathway of the peptide subunit, we performed in vitro assays. Starting from glutamic acid a pentapeptide was obtained in seven steps:

A novel zinc-binding motif found in two ubiquitous deaminase families.

Two families of deaminases, one specific for cytidine, the other for deoxycytidylate, are shown to possess a novel zinc-binding motif, here designated ZBS. We have (1) identified the protein members of these 2 families, (2) carried out sequence analyses that allow specification of this zinc-binding motif, and (3) determined signature sequences that will allow identification of additional members of these families as their sequences become available.     

A novel aminoglycosphingolipid found in Chlorobium limicola f. thiosulfatophilum 6230

An aminolipid from Chlorobium limicola f. thiosulfatophilum has been purified and characterized by thin-layer chromatography, infrared specroscopy, ¹H-NMR, ¹³C-NMR, plasma desorption mass spectrometry, and fast atom bombardment mass spectrometry. The structure is that of an aminosugar (neuraminic acid) attached to a sphingosine backbone with one myristic acid linked to the sphingosine by an amide bond. Related glycosphingolipids and capnoids are found in the Bacterioides/Flavobacteria which are related to the green sulfur bacteria by the criterion of 16S rRNA structure. No aminoglycosphingolipid was found in Chloroflexus aurantiacus.     

Three glucose 6-phosphate dehydrogenase variants found in Japan

Summary Three Japanese glucose 6-phosphate dehydrogenase (G6PD) variants were investigated. G6PD Mediterranean-like had markedly decreased activity, normal electrophoretic mobility, low Km G6P, low Km NADP, increased utilization of all three substrate analogues (2-deoxy-G6P, Gal-6P, and deamino-NADP) and slightly decreased heat stability and slightly biphasic pH curve. G6PD Ogori had markedly decreased activity, but otherwise normal characteristics. G6PD Hofu had moderately decreased activity, normal electrophoretic mobility, slightly reduced Km G6P, normal Km NADP, normal utilization of 2-deoxy-G6P and Gal-6P, but increased utilization of deamino-NADP and normal heat stability as well as normal pH curve.     

Origin of cytoplasm substituted rice cultivars found in Japan

Genetic variation of Japanese rice cultivars were examined. Five of 450 lowland cultivars and another five of 200 upland cultivars were determined as the indica type by using isozyme genotypes and the remainder were of the japonica type. The major characteristics of these indica cultivars, revealed a slender shape of grains, a short apiculus hair length, a positive allele for Ph reaction, and allele-3 for the Pgd1 locus. Three of these indica cultivars showed a non-deletion ORF100, which is essential to the japonica-type plastid. The plastid subtype identity (PS-ID) sequences of these plastids is 6C7A, which is also a japonica-specific repeat unit. Thus, these cultivars were concluded to be naturally generated cytoplasm substituted lines. These plastids were introduced into a indica genetic background from japonica cultivars grown elsewhere. The rest of the indica cultivars revealed a deletion-type ORF100 and plastid subtype 8C8A, both of which are indica-specific. These cultivars carried indica-type allelic constitutions for diagnostic isozyme loci. However, other characters were identical to the cytoplasm-substituted cultivars in Japan. In East and Southeast Asia, cultivars carrying a indica-type nuclear genotype with a japonica-type plastid are restricted to Aus cultivars in the Bengal region. Genetic and historical records suggest that Japanese indica cultivars and the Aus cultivars are closely related. The Aus cultivars acquire necessary genetic constitutions from both indica and japonica cultivars through naturally occurring out-crossing to adapt to a particular cultivation condition in the region. The wide adaptability enabled them to be introduced into a northern region like Japan.     

A novel structural rearrangement of hepatitis delta virus antigenomic ribozyme

A bioinformatic covariation analysis of a collection of 119 novel variants of the antigenomic, self-cleaving hepatitis delta virus (HDV) RNA motif supported the formation of all of the Watson–Crick base pairs (bp) of the catalytic centre except the C19–G81 pair located at the bottom of the P2 stem. In fact, a novel Watson–Crick bp between C19 and G80 is suggested by the data. Both chemical and enzymatic probing demonstrated that initially the C19–G81 pair is formed in the ribozyme (Rz), but upon substrate (S) binding and the formation of the P1.1 pseudoknot C19 switches its base-pairing partner from G81 to G80. As a result of this finding, the secondary structure of this ribozyme has been redrawn. The formation of the C19–G80 bp results in a J4/2 junction composed of four nucleotides, similar to that seen in the genomic counterpart, thereby increasing the similarities between these two catalytic RNAs. Additional mutagenesis, cleavage activity and probing experiments yield an original characterization of the structural features involving the residues of the J4/2 junction.     

A novel CHHC Zn-finger domain found in spliceosomal proteins and tRNA modifying enzymes

We report a previously uncharacterized CHHC Zn-finger domain identified in spliceosomal U11-48K proteins, tRNA methyl-transferases TRM13 and gametocyte specific factors. We show that this domain behaves as an independent folding unit and that it stoichiometrically binds zinc in a one-to-one ratio. Based on the conserved sequence features we predict that this domain may function as a RNA recognition and binding module.     

A lycoperdaceous fungus, Arachnion album (Agaricales, Arachniaceae), newly found in Japan

Arachnion album was collected in Osaka and Hyogo Prefectures, western Honshu, Japan. This is a new record of this genus for Japan. Macro- and microscopic features of the species are described and illustrated based on the Japanese specimens, and comparisons with some related taxa of A. album are given.     

Three novel species of the anamorphic yeast genus Candida in the Candida intermedia clade found in Japan, Thailand and Taiwan

Four strains of yeasts isolated in Japan, Thailand and Taiwan were found to represent three novel species of the genus Candida. The three species are located in a clade including Candida tsuchiyae, Candida thailandica and Candida akabanensis in a tree based on the D1/D2 domain sequences of the large subunit rRNA genes but clearly differentiated from these relative species. Three novel species are proposed for these strains, i. e., Candida berkhoutiae sp. nov., for strains ST-49(T) (=BCC 7749(T)=NBRC 106733(T)=CBS 11722(T)) isolated from insect frass in Thailand and SA13S01 (=NBRC 106053) isolated from soil in Taiwan, Candida ezoensis sp. nov., for strain Y07-1601-2(T) (=NBRC 105019(T)=CBS 11753(T)) isolated from forest soil in Japan, and Candida inulinophila sp. nov., for ST-369(T) (=BCC 15081(T)=NBRC 106735(T)=CBS 11725(T)) isolated from an unidentified wild mushroom from Thailand.