Atomic-level models of the bacterial carboxysome shell

The carboxysome is a bacterial microcompartment that functions as a simple organelle by sequestering enzymes involved in carbon fixation. The carboxysome shell is roughly 800 to 1400 angstroms in diameter and is assembled from several thousand protein subunits. Previous studies have revealed the three-dimensional structures of hexameric carboxysome shell proteins, which self-assemble into molecular layers that most likely constitute the facets of the polyhedral shell. Here, we report the three-dimensional structures of two proteins of previously unknown function, CcmL and OrfA (or CsoS4A), from the two known classes of carboxysomes, at resolutions of 2.4 and 2.15 angstroms. Both proteins assemble to form pentameric structures whose size and shape are compatible with formation of vertices in an icosahedral shell. Combining these pentamers with the hexamers previously elucidated gives two plausible, preliminary atomic models for the carboxysome shell.     

Molecular epidemiological characterization of poultry red mite, Dermanyssus gallinae,in Japan

Dermanyssus gallinae, the poultry red mite, is an obligatory blood-sucking ectoparasite. The genetic diversity of D. gallinae has been examined in some countries, but so far not in Asian countries. Here, we sequenced a part of the mitochondrial cytochrome oxidase subunit I (COI) and16S rRNA genes and nuclear internal transcribed spacers (ITS) region in 239 mite samples collected from 40 prefectures throughout Japan. The COI and 16S rRNA nucleotide sequences were classified into 28 and 26 haplotypes, respectively. In phylogenetic trees, the haplotypes clustered into 2 haplogroups corresponding to haplogroups A and B, which were previously reported. Haplogroups A and B were further subdivided into sub-haplogroups AJ1 and AJ2, and BJ1 and BJ2, respectively. In both trees, the sequences of haplotypes in AJ1 and BJ2 were relatively distant from those reported in other countries, while some sequences in AJ2 and BJ1 were identical to those in Europe. In addition, the ITS sequences were classified into two sequences, and both sequences were closely related to the sequences found in European countries. These findings indicate a possibility of international oversea transmission of D. gallinae.     

Gentian Kobu-sho-associated virus: a tentative, novel double-stranded RNA virus that is relevant to gentian Kobu-sho syndrome

A virus-like dsRNA of about 23 kbp was detected in gentian plants showing Kobu-sho syndrome including stunting, shortened internodes, and tumors on stems, nodes and roots. Nucleotide sequence analysis has suggested that this dsRNA is related to Pestivirus species but not to any other plant viruses. It was protected from externally added RNase, suggesting that the dsRNA is encapsidated. The dsRNA was co-extracted in a crude homogenate of glutaraldehyde-fixed tissue with the virus-like particles that have been associated previously with Kobu-sho syndrome in gentian (Usugi et al. Jpn J Phytopathol 76:21–24, 2010). The RNA sequence was detected in more than 99 % of Kobu-sho gentian individuals but in less than 20 % of apparently healthy gentian individuals from fields affected with Kobu-sho. Thus, we propose naming the virus Gentian Kobu-sho-associated virus.     

An Antibody Against the SecA Membrane Protein of One Phytoplasma Reacts with Those of Phylogenetically Different Phytoplasmas

ABSTRACT Antisera raised against phloem-limited phytoplasmas generally react only with the phytoplasma strain used to produce the antigen. There is a need for an antiserum that reacts with a variety of phytoplasmas. Here, we show that an antiserum raised against the SecA membrane protein of onion yellows phytoplasma, which belongs to the aster yellows 16S-group, detected eight phytoplasma strains from four distinct 16S-groups (aster yellows, western X, rice yellow dwarf, and elm yellows). In immunoblots, approximately 96-kDa SecA protein was detected in plants infected with each of the eight phytoplasmas. Immunohistochemical staining of thin sections prepared from infected plants was localized in phloem tissues. This antiserum should be useful in the detection and histopathological analysis of a wide range of phytoplasmas.     

Structural characterization and hypoglycemic effects of arabinogalactan-protein from the tuberous cortex of the white-skinned sweet potato (Ipomoea batatas L.)

An arabinogalactan-protein (WSSP-AGP) was isolated from the tuberous cortex of the white-skinned sweet potato (WSSP; Ipomoea batatas L.). It consists of 95% (w/w) carbohydrate and 5% (w/w) protein with high contents of hydroxyproline, alanine, and serine. Its sugar composition is α-L-Rha:α-L-Ara:β-D-Gal:β-D-GlcA in a molar ratio of 1.0:4.1:7.6:1.3. Its weight-average molecular weight was estimated to be 126,800 g/mol by high-performance size exclusion chromatography coupled with multiangle laser light scattering. Structural analysis indicated that WSSP-AGP is a (1→3)-β-D-galactan highly branched at O-6 with (1→6)-β-D-galactan, in which the branched chains are substituted at the O-3 position with α-L-Araf-(1→ and α-L-Araf-(1→5)-α-L-Araf-(1→ and at the O-6 position typically with α-L-Rhap-(1→4)-β-D-GlcAp-(1→ as terminating groups. Continuous administration of WSSP-AGP to KKAy mice significantly lowered fasting plasma glucose levels. This indicates that WSSP-AGP plays an important role in the hypoglycemic effects of WSSP.     

A wide range of genetic diversity in pear (<Emphasis Type="Italic">Pyrus ussuriensis</Emphasis> var. <Emphasis Type="Italic">aromatica</Emphasis>) genetic resources from Iwate,Japan revealed by SSR and chloroplast DNA markers

Iwateyamanashi (Pyrus ussuriensis var. aromatica) is one of the Pyrus species which grows wild in Japan. The number of Iwateyamanashi trees has been decreasing, so conservation and evaluation is urgently needed. Over 500 accessions of Pyrus species collected from Iwate in northern Tohoku region are maintained at Kobe University as an Iwateyamanashi germplasm collection. In order to investigate the genetic diversity, five SSR (simple sequence repeat) markers, developed from Japanese and European pear were examined for 86 Pyrus individuals including 58 accessions from Iwate. These SSR loci could discriminate between all the Iwate accessions except for 10 that bear seedless fruit, as well as determine the genetic diversity in Iwateyamanashi germplasms. High levels of variation were detected in 41 alleles and the mean observed heterozygosity across 5 loci was 0.50 for the Iwate accessions. Seedless accessions sharing identical SSR genotype with the local pear variety “Iwatetanenashi” were supposed to have been propagated vegetatively via grafting. In an UPGMA phenogram, Japanese pear varieties (P. pyrifolia) were clustered into two groups with some Iwate accessions including seedless ones. Another 38 Iwate accessions were not clustered clearly, and there was no clear relationship between these accessions and geographical distribution or morphological characters. Allele frequency revealed that the Iwate accessions were genetically more divergent than the Japanese pear varieties. Most Japanese pears possessed a 219 bp deletion at a spacer region between the accD and psaI genes in the chloroplast DNA (cpDNA), but other Pyrus species and two Iwateyamanashi trees did not. In the Iwate accessions, 79.3% had a deletion type cpDNA and others had a standard type cpDNA without deletion. These results are indicative of the wide range of genetic diversity in the Iwate accessions which include Japanese pear varieties. A combination of SSR and cpDNA analyses revealed high heterogeneity in Iwateyamanashi and coexistence of Iwateyamanashi and hybrid progeny with P. pyrifolia. These could be reasons for the wide range of continuous morphological variation described previously.     

Structural characterization and biological activities of an exopolysaccharide kefiran produced by Lactobacillus kefiranofaciens WT-2B(T)

Lactobacillus kefiranofaciens, isolated from kefir grains, produces an extracellular polysaccharide when cultured, not only in PYG10 medium but also in a liquid medium containing a rice hydrolysate that had been previously degraded by treatment with a glucoamylase. The maximum yield of the polysaccharide, using the rice hydrolysate as the medium, was 2.5 g/L after a 7-day culture period at pH 5.0 and 33 degrees C. Compositional analysis, methylation analysis, specific rotation, and (1)H and (13)C NMR spectroscopy revealed that the structures of polysaccharides obtained from these two different culture media are essentially identical. The polysaccharide is composed of a hexasaccharide repeating unit and, thus, is known as kefiran. The weight-average molecular weight and the z-average radius of gyration of a sample, purified from the rice hydrolysate medium, were determined to be 7.6 x 10(5) g/mol and 39.9 nm, respectively, by gel permeation chromatography equipped with a multiangle laser-light-scattering photometer. Changes in blood pressure and serum components were examined in SHRSP/Hos rats, using doses of 100 and 300 mg of kefiran/kg of rat. A suppression in the increase in blood pressure was observed in these rats after 30 days. This activity is discussed in terms of the concentration of serum components of the rat, with emphasis on lipid components such as cholesterols, triglycerides, and free fatty acids.     

Early optical polarization of a gamma-ray burst afterglow

We report the optical polarization of a gamma-ray burst (GRB) afterglow, obtained 203 seconds after the initial burst of gamma-rays from GRB 060418, using a ring polarimeter on the robotic Liverpool Telescope. Our robust (2sigma) upper limit on the percentage of polarization, less than 8%, coincides with the fireball deceleration time at the onset of the afterglow. The combination of the rate of decay of the optical brightness and the low polarization at this critical time constrains standard models of GRB ejecta, ruling out the presence of a large-scale ordered magnetic field in the emitting region.