Deciphering the molecular basis of the broad substrate specificity of alpha-glucosidase from Bacillus sp. SAM1606

The alpha-glucosidase of Bacillus sp. strain SAM1606 is a member of glycosyl hydrolase family 13, and shows an extraordinarily broad substrate specificity and is one of very few alpha-glucosidases that can efficiently hydrolyze the alpha-1,1-glucosidic linkage of alpha,alpha'-trehalose (trehalose). Phylogenetic analysis of family-13 enzymes suggests that SAM1606 alpha-glucosidase may be evolutionally derived from an alpha-1,6-specific ancestor, oligo-1,6-glucosidase (O16G). Indeed, replacement of Pro(273*) and Thr(342*) of B. cereus O16G by glycine and asparagine (the corresponding residues in the SAM1606 enzyme), respectively, was found to cause 192-fold enhancement of the relative catalytic efficiency for trehalose, suggesting that O16G may easily "evolved" into an enzyme with an extended substrate specificity by substitution of a limited number of amino acids, including that at position 273* (an asterisk indicates the amino-acid numbering of the SAM1606 sequence). To probe the role of the amino acid at position 273* of alpha-glucosidase in determination of the substrate specificity, the amino acid at position 273 of SAM1606 alpha-glucosidase was replaced by all other naturally occurring amino acids, and the resultant mutants were kinetically characterized. The results showed that substitution of bulky residues (e.g., isoleucine and methionine) for glycine at this position resulted in large increases in the K(m) values for trehalose and maltose, whereas the affinity to isomaltose was only minimally affected by such an amino-acid substitution at this position. Three-dimensional structural models of the enzyme-substrate complexes of the wild-type and mutant SAM1606 alpha-glucosidases were built to explore the mechanism responsible for these observations. It is proposed that substitution by glycine at position 273* could eliminate steric hindrance around subsite +1 that originally occurred in parental O16G and is, at least in part, responsible for the acquired broad substrate specificity of SAM1606 alpha-glucosidase.     

Participation of a fusogenic protein,glyceraldehyde-3-phosphate dehydrogenase,in nuclear membrane assembly

We found an autoimmune serum, K199, that strongly suppresses nuclear membrane assembly in a cell-free system involving a Xenopus egg extract. Four different antibodies that suppress nuclear assembly were affinity-purified from the serum using Xenopus egg cytosol proteins. Three proteins recognized by these antibodies were identified by partial amino acid sequencing to be glyceraldehyde-3-phosphate dehydrogenase (GAPDH), fructose-1,6-bisphosphate aldolase, and the regulator of chromatin condensation 1. GAPDH is known to be a fusogenic protein. To verify the participation of GAPDH in nuclear membrane fusion, authentic antibodies against human and rat GAPDH were applied, and strong suppression of nuclear assembly at the nuclear membrane fusion step was observed. The nuclear assembly activity suppressed by antibodies was recovered on the addition of purified chicken GAPDH. A peptide with the sequence of amino acid residues 70-94 of GAPDH, which inhibits GAPDH-induced phospholipid vesicle fusion, inhibited nuclear assembly at the nuclear membrane fusion step. We propose that GAPDH plays a crucial role in the membrane fusion step in nuclear assembly in a Xenopus egg extract cell-free system.     

DNA Data Bank of Japan (DDBJ) in XML

The DNA Data Bank of Japan (DDBJ, http://www.ddbj.nig.ac.jp) has collected and released more entries and bases than last year. This is mainly due to large-scale submissions from Japanese sequencing teams on mouse, rice, chimpanzee, nematoda and other organisms. The contributions of DDBJ over the past year are 17.3% (entries) and 10.3% (bases) of the combined outputs of the International Nucleotide Sequence Databases (INSD). Our complete genome sequence database, Genome Information Broker (GIB), has been improved by incorporating XML. It is now possible to perform a more sophisticated database search against the new GIB than the ordinary BLAST or FASTA search.     

Phylogenetic analysis of spotted fever group rickettsiae based on gltA, 17-kDa, and rOmpA genes amplified by nested PCR from ticks in Japan

In order to understand the natural situation of rickettsiae in the ticks in Japan, the rickettsial genes, gltA gene, rOmpA gene, and 17-kDa gene, were amplified from the ticks by nested PCR. The prevalences of rickettsial gltA genes among Haemaphysalis formosensis, H. longicornis, H. megaspinosa, Ixodes ovatus, H. flava, H. kitaokai, and I. persulcatus were 62, 57, 24, 24, 19, 13, and 10%, respectively; 26% (186/722) being the average. The gltA genes amplified from the ticks were classified into 9 genotypes (I to IX) by the difference in nucleotide sequences. Genotype I was detected from 7 species of ticks. Genotype II mainly was detected from H. longicornis and H. formosensis. Genotypes III and VII mainly were detected from H. flava and I. ovatus. The polarization in the distribution of genotypes among regions where the ticks were collected was not clear. Based on the phylogenetic analysis of the three genes presented here, genotypes I, III, and IV (detected from H. formosensis, H. hystricia, and I. ovatus ) are genetically close with each other, but rickettsiae of the same property still have not been isolated from ticks anywhere in the world. These genotypes should be considered as new species among SFG rickettsiae. Genotype II was identical with strain FUJ-98, genetically close to R. japonica which has been isolated from ticks in China. Genotype V was identical with R. felis and strain California 2 isolated from the cat flea. This is the first report on the detection of R. felis from ticks. Genotype VI detected from Ixodes sp. did not seem to belong to genus Rickettsia. Based on the previous antigenic data and the phylogenetic analysis presented here, Genotype VII should be considered a variant of R. helvetica and genotype VIII detected from I. ovatus and I. persulcatus were identical with R. helvetica. Genotype IX detected from I. nipponensis was genetically close to the strains IRS3, IRS4, and IrR/Munich isolated from I. ricinus in Slovakia and German.     

Familial early onset macular degeneration in cynomolgus monkeys (Macaca fascicularis)

The mode of inheritance of macular degeneration was determined with 45 cynomolgus monkeys (18 females and 27 males) who were the offspring of one breeding male with typical macular degeneration. In the first generation, 27 offspring (10 females and 17 males) were born from mating between the macular degeneration-affected founder male and 5 normal female breeders. Among them, 18 monkeys (9 females and 9 males) were judged as having macular degeneration (affected). Next, the distribution of affected offspring was examined with 18 offspring who were born from 3 different mating pairs, normal vs normal, affected vs normal and affected vs affected, when they became 2 years old. All of the 9 monkeys (4 females and 5 males) obtained from the 2 pairs of normal vs normal were normal. On the other hand, 6 affected monkeys (3 females and 3 males) were detected in 8 offspring from the mating pair of affected vs normal, and the single offspring produced by the mating pair of affected vs affected was affected. These results showed that this degeneration must be early onset familial macular degeneration controlled by autosomal dominant gene(s).     

Bone mineral density in chimpanzees,humans, and Japanese macaques

We performed a comparative study of bone mechanical properties in the radii of chimpanzees (Pan troglodytes), humans (Homo sapiens), and Japanese macaques (Macaca fuscata) using peripheral quantitative computed tomography. We investigated: (1)cortical bone area relative to the total periosteal area (PrA); (2) trabecular bone area relative to PrA; (3) cortical bone density; and (4) trabecular bone density. The cortical bone area index for chimpanzees was almost the same as that of Japanese macaques, whereas the equivalent value in humans was about the two-fifths that of the others. Values for the other three properties were constant among these three catarrhine species. Chimpanzees do not particularly resemble humans, but are more similar to digitigrade macaques in terms of bone properties. The constant trabecular bone area index and trabecular density value in these species may suggest that a certain amount of trabecular bone (20–30% of total bone area at the distal 4% level of the forearm) is necessary to achieve normal bone turnover. The physiological metabolism of bone, including cortical bone density, might be conserved in these catarrhines. Electronic Publication     

ML-7 inhibits exocytosis of superoxide-producing intracellular compartments in human neutrophils stimulated with phorbol myristate acetate in a myosin light chain kinase-independent manner

ML-7, (5-iodonaphthalene-1-sulfonyl) homopiperazine, is commonly employed as a myosin light chain kinase (MLCK) inhibitor. In the present study, we demonstrated that ML-7 affects the superoxide (O(2)(-))-producing system of human neutrophils in an MLCK-independent manner. Human neutrophils were stimulated with phorbol myristate acetate (PMA), which does not activate MLCK. ML-7 inhibited extracellular release, but not intracellular production of O(2)(-) in the stimulated cells. Fluorescence microscopy revealed the generation of O(2)(-) at intracellular compartments in the stimulated cells exposed to ML-7. At the electron microscopic level, the reaction product of NADPH oxidase activity was found in intracellular compartments. ML-7 strongly inhibited the association of the oxidant-producing intracellular compartments with the plasma membrane. Furthermore, the upregulation of alkaline phosphatase activity, a marker enzyme of the oxidant-producing intracellular compartments, was also inhibited by ML-7. These findings indicate that ML-7 inhibits the fusion of the oxidant-producing intracellular compartments to the plasma membrane resulting in the inhibition of the extracellular release of O(2)(-) in PMA-stimulated human neutrophils in an MLCK-independent manner.