A detailed biochemical characterization of phosphopantothenate synthetase, a novel enzyme involved in coenzyme A biosynthesis in the Archaea

We have previously reported that the majority of the archaea utilize a novel pathway for coenzyme A biosynthesis (CoA). Bacteria/eukaryotes commonly use pantothenate synthetase and pantothenate kinase to convert pantoate to 4′-phosphopantothenate. However, in the hyperthermophilic archaeon Thermococcus kodakarensis, two novel enzymes specific to the archaea, pantoate kinase and phosphopantothenate synthetase, are responsible for this conversion. Here, we examined the enzymatic properties of the archaeal phosphopantothenate synthetase, which catalyzes the ATP-dependent condensation of 4-phosphopantoate and β-alanine. The activation energy of the phosphopantothenate synthetase reaction was 82.3?kJ?mol^?1. In terms of substrate specificity toward nucleoside triphosphates, the enzyme displayed a strict preference for ATP. Among several amine substrates, activity was detected with β-alanine, but not with γ-aminobutyrate, glycine nor aspartate. The phosphopantothenate synthetase reaction followed Michaelis–Menten kinetics toward β-alanine, whereas substrate inhibition was observed with 4-phosphopantoate and ATP. Feedback inhibition by CoA/acetyl-CoA and product inhibition by 4′-phosphopantothenate were not observed. By contrast, the other archaeal enzyme pantoate kinase displayed product inhibition by 4-phosphopantoate in a non-competitive manner. Based on our results, we discuss the regulation of CoA biosynthesis in the archaea.     

Structural proteins in the egg-shell of the oriental garden cricket, Gryllus mitratus

1. The egg-shell of the oriental garden cricket, Gryllus mitratus, contained at least two different types of structural protein in an approximate ratio of 5:1. The major fraction was extracted in a solvent containing dithiothreitol, EDTA and 8m-urea, and was purified to apparent homogeneity as judged by free-boundary electrophoresis and ultracentrifugation. This was designated SH-fraction and its S-carboxymethyl derivative (CM-fraction) was also prepared. The minor fraction, insoluble in the solvent, was designated insoluble residue. 2. The major fraction was a phosphoprotein, rich in serine (29.8mol% of the total amino acids) and phosphate (nearly equimolar to serine), and O-phosphoserine was identified in its partial acid hydrolysate. The content of cystine was rather low (0.9mol%) in spite of the importance of this amino acid residue in the native form of the protein. The insoluble residue contained only a small amount of phosphorus, and its amino acid composition was clearly different from the major fraction. 3. CM-fraction, a fibrous protein with an average molecular weight of 57500, behaved as a typical polyanion owing to the high content of phosphate. SH-fraction and CM-fraction were precipitable from their aqueous solutions by the addition of bivalent metal cations, and the precipitation of CM-fraction by Ca(2+) and Mg(2+) was studied in detail. 4. When SH-fraction was exposed to air, intermolecular disulphide linkages were formed, yielding a net-like gel that changed its volume with changes in Ca(2+), Mg(2+) and Na(+). 5. The possible role of this protein fraction in maintaining the integrity of the egg-shell, and a comparison of its composition and properties with other egg-shell proteins and other phosphoproteins, are discussed.     

Stimulation of methanotrophic growth in cocultures by cobalamin excreted by rhizobia

Methanotrophs play a key role in the global carbon cycle, in which they affect methane emissions and help to sustain diverse microbial communities through the conversion of methane to organic compounds. To investigate the microbial interactions that cause positive effects on methanotrophs, cocultures were constructed using Methylovulum miyakonense HT12 and each of nine nonmethanotrophic bacteria, which were isolated from a methane-utilizing microbial consortium culture established from forest soil. Three rhizobial strains were found to strongly stimulate the growth and methane oxidation of M. miyakonense HT12 in cocultures. We purified the stimulating factor produced by Rhizobium sp. Rb122 and identified it as cobalamin. Growth stimulation by cobalamin was also observed for three other gammaproteobacterial methanotrophs. These results suggest that microbial interactions through cobalamin play an important role in methane oxidation in various ecosystems.     

Genome wide gene expression in artificially synthesized amphidiploids of Arabidopsis

The merging of two different genomes occurs during the formation of amphidiploids, and the merged regulatory networks have the potential to generate a new gene expression pattern. We examined the genome-wide gene expression of two newly synthesized amphidiploids between Arabidopsis thaliana and the related species Arabidopsis lyrata subsp. lyrata and Arabidopsis halleri subsp. gemmifera. 1,137 (4.7%) and 1,316 (5.4%) of probesets showed differential gene expression in A. thaliana-A. halleri and A. thaliana-A. lyrata hybrids respectively, compared to the mid parent value and of these, 489 were in common. Genes that differed in expression between the parental lines tended to have an expression level in both hybrids differing from the mid parent value. In contrast to protein coding genes, there is little differential expression of transposons. Genes in the categories of chloroplast-targeted and response to stress were overrepresented in the non-additively expressed genes in both amphidiploids. As these genes have the potential to contribute directly to the plant phenotype, we suggest that rapid changes of gene expression in amphidiploids might be important for producing greater biomass.     

Functions of a hemolysin-like protein in the cyanobacterium <Emphasis Type="Italic">Synechocystis</Emphasis> sp. PCC 6803

A glucose-tolerant strain of the cyanobacterium Synechocystis sp. PCC 6803, generally referred to as wild type, produces a hemolysin-like protein (HLP) located on the cell surface. To analyze the function of HLP, we constructed a mutant in which the hlp gene was disrupted. The growth rate of the mutant was reduced when the cells were stressed by treatment with CuSO₄, CdCl₂, ZnCl₂, ampicillin, kanamycin, or sorbitol in liquid medium, suggesting that HLP may increase cellular resistance to the inhibitory effects of these compounds. Uptake assays with ¹⁰⁹Cd²⁺ using the silicone–oil layer centrifugation technique revealed that both wild type and mutant cells were labeled with ¹⁰⁹Cd²⁺ within 1 min. Although the total radioactivity was much higher in the wild-type cells, ¹⁰⁹Cd²⁺ incorporation was clearly much higher in the mutant cells after adsorbed ¹⁰⁹Cd²⁺ was removed from the cell surface by washing with EDTA. These findings suggest that HLP functions as a barrier against the adsorption of toxic compounds.     

Intake of dried bonito broth flavored with dextrin solution induced conditioned place preference in mice

We investigated to determine whether dried bonito broth flavor induces a reinforcing effect using the conditioned place preference (CPP) test. Only dried bonito broth did not induce CPP. Sucrose induced CPP in 20% solution. A 21.86% dextrin solution, with the same calorie content as the 20% sucrose solution, did not induce CPP, but a dextrin solution flavored with dried bonito broth (BD) induced CPP. An AD solution containing the same concentrations of dextrin, NaCl, IMP, GMP, and amino acids as found in BD tended to increase the time spent in the conditioned box but did not significantly. Aromatic compounds, such as citral, vanillin, and menthol flavored AD solutions did not induce CPP, whereas an AD solution supplemented with dried bonito flavoring agent induced CPP. In mice with transected olfactory nerves, CPP was not induced by voluntary intake of BD. These results suggest that the aromatic profile of the dried bonito broth plays an important role in BD-induced CPP.     

On experiences of i2b2 (Informatics for integrating biology and the bedside) database with Japanese clinical patients' data

Informatics for Integrating Biology and the Bedside (i2b2) is a database system to facilitate sharing and reuse of clinical patients' data collected in individual hospitals. The i2b2 provides an ontology based object-oriented database system with highly simple and flexible database schema which enables us to integrate clinical patients' data from different laboratories and different hospitals. 392 patients' data including carcinoma and non-carcinoma specimens from cancer patients are transported from the Integrated Clinical Omics Database (iCOD) to the i2b2 database for a feasibility study to check applicability of i2b2 ontology and database schema on Japanese clinical patients' data. No modification is required for the i2b2 data model to deal with Japanese characters. Some modification of ontology is required to integrate biomedical information extracted from the cancer patients' data. We believe that the i2b2 system will be practical infrastructure to integrate Japanese clinical databases if appropriate disease ontology for Japanese patients is provided.     

Long-term change in coral cover and the effectiveness of marine protected areas in the Philippines: a meta-analysis

Although coral declines have been reported from major reefs of the world, region-specific trends still remain unclear, particularly in areas with high diversity such as the Philippines. We assessed the temporal patterns of the magnitude and trajectory of coral cover change in the Philippines using survey data collected from 317 sites. We examined the rate of change in coral cover in relation to time, effects of bleaching and protection against fishing and assessed the efficacy of marine protected areas (MPAs) using meta-analysis. Results showed an overall increase in coral cover in the Philippines from 1981 to 2010. Protection from fishing contributed to the overall increase in the mean annual rate of change as the coral cover significantly increased within MPAs than outside. The significant differences in the rate of coral cover change through time were influenced by chronic anthropogenic stresses, coinciding with the timing of thermal stress and the establishment of MPAs. The rate of change in coral cover was independent of the level of protection and the age and size of MPA.     

Supersaturation-limited Amyloid Fibrillation of Insulin Revealed by Ultrasonication

Amyloid fibrils form in supersaturated solutions via a nucleation and growth mechanism. We proposed that ultrasonication may be an effective agitation to trigger nucleation that would otherwise not occur under the persistent metastability of supersaturation. However, the roles of supersaturation and effects of ultrasonication have not been elucidated in detail except for limited cases. Insulin is an amyloidogenic protein that is useful for investigating the mechanisms underlying amyloid fibrillation with biological relevance. We studied the alcohol-induced amyloid fibrillation of insulin using various concentrations of 2,2,2-trifluoroethanol and 1,1,1,3,3,3-hexafluoro-2-propanol at pH 2.0 and 4.8. Ultrasonic irradiation effectively triggered fibrillation under conditions in which insulin retained persistent supersaturation. Structural analyses by circular dichroism, Fourier transform infrared spectroscopy, transmission electron microscopy, and atomic force microscopy revealed that the dominant structures of fibrils varied between parallel and antiparallel β-sheets depending on the solvent conditions. pH and alcohol concentration-dependent phase diagrams showed a marked difference before and after the ultrasonic treatment, which indicated that the persistent metastability of supersaturation determined the conformations of insulin. These results indicate the importance of an alternative view of amyloid fibrils as supersaturation-limited crystal-like aggregates formed above the solubility limit.