Characterization of the complete plastome sequence of Korean endemic, Cardamine glechomifolia H.Lév. (Brassicaceae, Brassicales).

In this study, we report the complete plastome sequence of Cardamine glechomifolia H.Lév. 1913 (NCBI acc. no. OP894664). This plastome shows typical quadripartite structure. The plastome size is 154,307 bp, which consists of 84,015 bp large single-copy (LSC), 17,690 bp small single-copy (SSC), and 26,301 bp inverted repeat (IR) regions. The plastome contains 112 genes, including 78 protein-coding, 30 tRNA, and four rRNA genes. The infA gene is pseudogenized. Sixteen genes contain one intron and two genes (clpP and ycf3) have two introns. The phylogenomic analysis conducted in our study reveals that the genus Cardamine, which encompasses C. glechomifolia, exhibits three distinct clades. In order to elucidate the interrelationship among the three clades, it is imperative to conduct additional investigations by augmenting the number of Cardamine samples.

Glutamine-induced production and secretion of Helicobacter pylori gamma-glutamyltranspeptidase at low pH and its putative role in glutathione transport.

Helicobacter pylori increased the gamma-glutamyltranspeptidase (GGT) production under low-pH (maximal at pH 4) and appropriate pCO2 conditions, while the production of GGT mRNA correlated with increased total enzyme activity. At pH 4, the bacterium augmented enzyme production in the presence of glutamine (~10 mM) in the medium, which predominantly occurred after a 6-min time-lag. Monovalent salts such as NaCl or NH4Cl facilitated enzymatic activation in acidic solutions of approximately pH 4.5. In addition, glutathione's gamma-glutamyl moiety cysteinylglycine appeared to be taken up readily by the intact H. pylori, but not by the one pretreated with a potent GGT inhibitor, acivicin, suggesting that the GGT may partake in glutathione uptake by the cell.

Characterization of Bacillus phage-K2 isolated from chungkookjang, a fermented soybean foodstuff.

An investigation of a virulent Bacillus phage-K2 (named Bp-K2) isolated from chungkookjang (a fermented soybean foodstuff) was made. Bp-K2 differed in infectivity against a number of Bacillus subtilis strains including starter strains of chungkookjang and natto, being more infectious to Bacillus strains isolated from the chungkookjang, but much less active against a natto strain. Bp-K2 is a small DNA phage whose genome size is about 21 kb. Bp-K2 is a tailed bacteriophage with an isometric icosahedral head (50 nm long on the lateral side, 80 nm wide), a long contractile sheath (85-90 nm × 28 nm), a thin tail fiber (80-85 nm long, 10 nm wide), and a basal plate (29 nm long, 47 nm wide) with a number of spikes, but no collar. The details of the structures of Bp-K2 differ from natto phage ϕBN100 as well as other known Bacillus phages such as SPO1-like or ϕ 29-like viruses. These data suggest that Bp-K2 would be a new member of the Myoviridae family of Bacillus bacteriophages.

Iso-superoxide dismutase in Deinococcus grandis, a UV resistant bacterium.

Deinococcus grandis possesses two types of superoxide dismutase (SOD, E. C. 1.15.1.1.) that show distinct electrophoretic behavior, one that migrates slowly and the other that migrates rapidly (SOD-1 and SOD-2, respectively). In this study, SOD-1 was uniformly and abundantly detected, regardless of growth phase, whereas SOD-2 was not detected during early growth, but was detectable from the exponential growth phase. In addition, a substantial increase in SOD-2 was observed in cells that were treated with potassium superoxide or UV, which suggests that SOD-2 is an inducible protein produced in response to stressful environments. Insensitivity of SOD-1 to both H(2)O(2) and cyanide treatment suggests that SOD-1 is MnSOD. However, SOD-2 would be FeSOD, since it lost activity in response to H(2)O(2) treatment, but not to cyanide. Localization studies of D. grandis iso-SODs in sucrose-shocked cells suggest that SOD-1 is a membrane-associated enzyme, whereas SOD-2 is a cytosolic enzyme. In conclusion, SOD-1 seems to be an essential constitutive enzyme for viability and SOD-2 appears to be an inducible enzyme that is probably critical for survival upon UV irradiation and oxidative stress.

Molecular cloning and characterization of the alcohol dehydrogenase ADH1 gene of Candida utilis ATCC 9950.

The alcohol dehydrogenase gene (ADH1) of Candida utilis ATCC9950 was cloned and expressed in recombinant Escherichia coli. C. utilis ADH1 was obtained by PCR amplification of C. utilis genomic DNA using two degenerate primers. Amino acid sequence analysis of C. utilis ADH1 indicated that it contained a zinc-binding consensus region and a NAD(P)(+)-binding site, and lacked a mitochondrial targeting peptide. It has a 98 and 73% identity with ADH1s of C. albicans and Saccharomyces cerevisiae, respectively. Amino acid sequence analysis and enzyme characterization with various aliphatic and branched alcohols suggested that C. utilis ADH1 might be a primary alcohol dehydrogenase existing in the cytoplasm and requiring zinc ion and NAD(P)(+) for reaction.

A novel five-subunit-type 2-oxoglutalate:ferredoxin oxidoreductases from Hydrogenobacter thermophilus TK-6.

A thermophilic, chemolithoautotrophic hydrogen-oxidizing bacterium, Hydrogenobacter thermophilus TK-6, fixes carbon dioxide via the reductive TCA cycle. 2-Oxoglutarate:ferredoxin oxidoreductase (OGOR) of this strain is one of the key enzymes of the pathway. OGOR of strain TK-6 has been reported to be a two-subunit-type OGOR and encoded by korAB. A gene cluster, forDABGEF, encoding another OGOR was found 148 bp upstream of korAB in the opposite orientation. Five of the for genes (forDABGE) were required for the expression of the active recombinant enzyme in Escherichia coli. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis of the purified enzyme showed five polypeptides corresponding to the forDABGE gene products, suggesting that the enzyme had a novel five-subunit structure. The recombinant enzyme had high substrate specificity toward 2-oxoglutarate as in the case of the gene products of korAB. Primer extension analysis showed that the korA and forD genes were transcribed from one and two transcriptional initiation sites, respectively. The results also suggested that both gene clusters were expressed in the cells of strain TK-6.

Chemotaxonomic and phylogenetic analyses of Sphingomonas strains isolated from ears of plants in the family Gramineae and a proposal of Sphingomonas roseoflava sp. nov.

Chemotaxonomic and phylogenetic characteristics of Sphingomonas strains isolated from plants of the family Gramineae were investigated. All strains contained the monosaccharide (glucuronic acid) type of glycosphingolipid (GSL-1). Most were found also to contain the oligosaccharide-type glycosphingolipids. Fatty acid and sphingosine profiles of the isolates were identical, although the ratio of the contents varies among the isolates. They all contained ubiquinone Q-10, and the G1C contents were from 66 to 68%. Phylogenetic analysis using 16S rRNA gene base sequences revealed that all the isolates were placed in the phylogenetic group of Sphingomonas paucimobilis in the alpha-4 subclass of Proteobacteria. By DNA-DNA hybridization experiments, the plant isolates were divided into five genotypic groups (groups 1 to 5). The strains of group 5 showed common physiological characteristics and formed pink-yellow colored colonies. Based on these results, Sphingomonas roseoflava sp. nov. was proposed for that homology group.