Satoru Kanai

Molecular analysis of zebrafish photolyase/cryptochrome family: two types of cryptochromes present in zebrafish

Cryptochromes (CRY), members of the DNA photolyase/cryptochrome protein family, regulate the circadian clock in animals and plants. Two types of animal CRYs are known, mammalian CRY and Drosophila CRY. Both CRYs participate in the regulation of circadian rhythm, but they have different light dependencies for their reactions and have different effects on the negative feedback loop which generates a circadian oscillation of gene expression. Mammalian CRYs act as a potent inhibitor of transcriptional activator whose reactions do not depend on light, but Drosophila CRY functions as a light‐dependent suppressor of transcriptional inhibitor.

Molecular Evolution of the Photolyase–Blue-Light Photoreceptor Family

Abstract. The photolyase–blue-light photoreceptor family is composed of cyclobutane pyrimidine dimer (CPD) photolyases, (6-4) photolyases, and blue-light photoreceptors. CPD photolyase and (6-4) photolyase are involved in photoreactivation for CPD and (6-4) photoproducts, respectively. CPD photolyase is classified into two subclasses, class I and II, based on amino acid sequence similarity. Blue-light photoreceptors are essential light detectors for the early development of plants. The amino acid sequence of the receptor is similar to those of the photolyases, although the receptor does not show the activity of photoreactivation. To investigate the functional divergence of the family, the amino acid sequences of the proteins were aligned. The alignment suggested that the recognition mechanisms of the cofactors and the substrate of class I CPD photolyases (class I photolyases) are different from those of class II CPD photolyases (class II photolyases). We reconstructed the phylogenetic trees based on the alignment by the NJ method and the ML method. The phylogenetic analysis suggested that the ancestral gene of the family had encoded CPD photolyase and that the gene duplication of the ancestral proteins had occurred at least eight times before the divergence between eubacteria and eukaryotes.

Identification and functional characterization of a novel barnacle cement protein.

Barnacle attachment to various foreign materials in water is guided by an extracellular multiprotein complex. A 19 kDa cement protein was purified from the Megabalanus rosa cement, and its cDNA was cloned and sequenced. The gene was expressed only in the basal portion of the animal, where the histologically identified cement gland is located. The sequence of the protein showed no homology to other known proteins in the databases, indicating that it is a novel protein. Agreement between the molecular mass determined by MS and the molecular weight estimated from the cDNA indicated that the protein bears no post‐translational modifications. The bacterial recombinant was prepared in soluble form under physiologic conditions, and was demonstrated to have underwater irreversible adsorption activity to a variety of surface materials, including positively charged, negatively charged and hydrophobic ones. Thus, the function of the protein was suggested to be coupling to foreign material surfaces during underwater attachment. Homologous genes were isolated from Balanus albicostatus and B. improvisus, and their amino acid compositions showed strong resemblance to that of M. rosa, with six amino acids, Ser, Thr, Ala, Gly, Val and Lys, comprising 66–70% of the total, suggesting that such a biased amino acid composition may be important for the function of this protein.

Partial sequence of ribulose-1,5-bisphosphate carboxylase/oxygenase and the phylogeny of Prochloron and Prochlorococcus (Prochlorales)

The prochlorophytes, oxygenic photosynthetic prokaryotes having no phycobiliprotein but possessing chlorophylls a and b, have been proposed to have a common ancestry with green chloroplasts, yet this is still controversal. We report here that partial sequence comparisons of the large subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase, including sequence data from two prochlorophytes, Prochlorococcus and Prochloron, indicate that Prochlorococcus is more closely related to a photosynthetic bacterium, Chromatium vinosum (γ-purple bacteria), than to cyanobacteria, while Prochloron is closely related to the prochlorophyte Prochlorothrix and to cyanobacteria. The molecular phylogenetic tree indicates that a common ancestor of Prochlorococcus and γ-purple bacteria branched off from the land plant lineage earlier than Prochloron, Prochlorothrix, and cyanobacteria.

Molecular Evolution of the Domain Structures of Protein Disulfide Isomerases

Abstract. Protein disulfide isomerase (PDI) is an enzyme that promotes protein folding by catalyzing disulfide bridge isomerization. PDI and its relatives form a diverse protein family whose members are characterized by thioredoxin-like (TX) domains in the primary structures. The family was classified into four classes by the number and the relative positions of the TX domains. To investigate the evolution of the domain structures, we aligned the amino acid sequences of the TX domains, and the molecular phylogeny was examined by the NJ and ML methods. We found that all of the current members of the PDI family have evolved from an ancestral enzyme, which has two TX domains in the primary structure. The diverse domain structures of the members have been generated through domain duplications and deletions.

Significance of the conformation of building blocks in curing of barnacle underwater adhesive

Barnacles are a unique sessile crustacean that attach irreversibly and firmly to foreign underwater surfaces. Its biological underwater adhesive is a peculiar extracellular multi‐protein complex. Here we characterize one of the two major proteins, a 52 kDa protein found in the barnacle cement complex. Cloning of the cDNA revealed that the protein has no homolog in the nonredundant database. The primary structure consists of four long sequence repeats. The process of dissolving the protein at the adhesive joint of the animal by various treatments was monitored in order to obtain insight into the molecular mechanism involved in curing of the adhesive bulk. Treatments with protein denaturant, reducing agents and/or chemical‐specific proteolysis in combination with 2D diagonal PAGE indicated no involvement of the protein in intermolecular cross‐linkage/polymerization, including formation of intermolecular disulfide bonds. As solubilization of the proteins required high concentrations of denaturing agents, it appears that both the conformation of the protein as building blocks and non‐covalent molecular interactions between the building blocks, possibly hydrophobic interactions and hydrogen bonds, are crucial for curing of the cement. It was also suggested that the protein contributes to surface coupling by an anchoring effect to micro‐ to nanoscopic roughness of surfaces.

Molecular phylogenetic relationship between two symbiotic photo-oxygenic prokaryotes, Prochloron sp. and Synechocystis trididemni

Abstract Synechocystis trididemni is a photo-oxygenic prokaryotic symbiont in some didemnid ascidians. Although the cells are pink and contain phycoerythrin, they morphologically resemble those of another symbiont of other didemnids, Prochloron didemni, which has no phycobilin pigments but has both chlorophyll a and chlorophyll b. The cytological similarities suggest that they might have evolved from a common ancestor. We examined this hypothesis by comparing nucleotide sequences in gene fragments of the 16S ribosomal RNA (16S rRNA) gene and in the large subunit of Rubisco gene (rbcL). ‘Blast’ search of GenBank showed that the most similar sequences to the 16S rRNA gene and rbcL of S. trididemni were those of Prochloron sp. The percent nucleotide and amino acid identities of the 16S rRNA genes, rbcL and the deduced Rubisco amino acid sequences between Prochloron sp. and S. trididemni were 94%, 90% and 99%, respectively. In trees based on the 16S rRNA gene and rbcL sequences, S. trididemni formed a clade with Prochloron. These data thus support the hypothesis that Prochloron sp. and S. trididemni arose from a common cyanobacterial ancestor and that the ancestor of Prochloron sp. somehow acquired the ability to synthesize chlorophyll b, as well as chlorophyll a, and subsequently lost the ability to synthesize phycobiliproteins.

Molecular Phylogeny of Zooxanthellate Bivalves

The aim of this research was to analyze the phylogenetic relationships of zooxanthellate bivalves belonging to the genera Tridacna, Hippopus, Fragum, and Corculum as well as to the closely related azooxanthellate bivalves belonging to Vasticardium and Fulvia. The small-subunit ribosomal RNA genes (18S rDNAs) from these bivalves were amplified by polymerase chain reaction with universal eukaryotic primers and were then sequenced. The sequence data from each species were analyzed by the neighbor-joining, maximum parsimony, and maximum likelihood methods, and phylogenetic trees were constructed. The results were essentially consistent with the morphological taxonomy of these bivalves. Thus, the zooxanthellate clams branch into two lineages, one composed of the genera Fragum and Corculum in the family Cardiidae, and the other composed of the genera Tridacna and Hippopus in the family Tridacnidae. However, present results indicate that the azooxanthellate clams analyzed (Vasticardium flavum and Fulvia mutica) are more likely to form a clade with the species of Tridacna and Hippopus than with those of Fragum and Corculum. This topology suggests that either the symbiosis with zooxanthellae occurred independently in each of two lineages, Tridacna-Hippopus and Corculum-Fragum, or the symbiosis was established in clams ancestral to the lineages of both the zooxanthellate clams and the azooxanthellate clams Vasticardium and Fulvia, and the latter lost the symbiotic relationship after the symbiotic clam lineages had diverged.

Adenylosuccinate synthetase genes: Molecular cloning and phylogenetic analysis of a highly conserved archaeal gene

Adenylosuccinate synthetase (PurA) catalyzes the first step in the de novo AMP synthesis and has been extensively studied in both Bacteria and Eukarya. We cloned the purA gene from the hyperthermophilic archaeon, Pyrococcus furiosus. The gene appears to be individually transcribed and encodes a protein of 339 amino acids. The amino acid sequence comparison with other archael PurAs found from recent genome analyses indicated that two deletions, one central and the other C-terminal, are a common feature of archaeal PurAs. None of the 21 PurA homologues analyzed from Eukarya and Bacteria exhibited this feature. Amino acid sequences of PurAs in Archaea showed 64% average identities which were significantly higher than the 50% and 55% calculated for Bacteria and Eukarya, respectively. Several residues conserved in PurAs of both Eukarya and Bacteria and shown to be of catalytic importance are missing in the archaeal PurAs. Phylogenetic analysis using PurA as the marker grouped life into 3 domains, hence it was consistent with results derived from 16-18S ribosomal RNA sequences. The topology within the three domains, in general, portrayed the hitherto accepted evolutionary relationship among the organisms utilized. PurA can, thus, serve as an additional marker to evaluate phylogenetic inferences drawn from sequence data from rRNA and other conserved genes. The presence of two unique deletions in both euryarchaeal and crenarchaeal PurAs, but not in those of Bacteria and Eukarya, is a strong evidence confirming the common lineage of these two subdomains of Archaea.

IDENTIFICATION OF NEW MEMBERS OF THE GS ADP-FORMING FAMILY FROM THE DE NOVO PURINE BIOSYNTHESIS PATHWAY

Abstract. Most living organisms can synthesize isosinate from 5-phosphoribosyl 1-pyrophosphate in the de novo purine biosynthesis pathway, which is basically composed of 10 reaction steps. Phosphoribosylglycinamide synthetase (GARS) catalyzes the second step of the pathway. We found that the enzyme shows weak, but significant, sequence similarity to phosphoribosylglycinamide formyltransferase 2 (GART2) and the ATPase domain of phosphoribosylaminoimidazole carboxylase (AIRCA), which catalyze the third and sixth steps of the pathway, respectively. In addition, the three enzymes were similar in amino acid sequence to biotin carboxylase (BC) and carbamoylphosphate synthetase (CPS), which are the members of the GS ADP-forming family. This family has been identified through a tertiary structure comparison and includes glutathione synthetase, d-alanine:d-alanine ligase, BC, succinyl-CoA synthetase β-chain, and phosphoribosylaminoimidazole-succinocarboxamide synthase. Molecular phylogenetic analysis based on a multiple alignment of GARS, GART2, AIRCA, BC, and CPS suggests that GART2 is more closely related to AIRCA than to GARS among the three enzymes from the pathway, though the three enzymes are relatively close to each other within the GS ADP-forming family. Moreover, the analysis showed that archaeal GARS had diverged before the speciation between bacteria and eucarya.