Shinobu Okamoto

Publications of Shinobu Okamoto

• The 2nd DBCLS BioHackathon: interoperable bioinformatics Web services for integrated applications.

  Authors: Toshiaki Katayama, Mark D Wilkinson, Rutger Vos, Takeshi Kawashima, Shuichi Kawashima, Mitsuteru Nakao, Yasunori Yamamoto, Hong-Woo Chun, Atsuko Yamaguchi, Shin Kawano [......] Martin Senger, Jessica Severin, Yasumasa Shigemoto, Hideaki Sugawara, James Taylor, Oswaldo Trelles, Chisato Yamasaki, Riu Yamashita, Noriyuki Satoh, Toshihisa Takagi

  Journal of biomedical semantics. 08/2011; 2:4.

  ABSTRACT: The interaction between biological researchers and the bioinformatics tools they use is still hampered by incomplete interoperability between such tools. To ensure interoperabilityABSTRACT: The interaction between biological researchers and the bioinformatics tools they use is still hampered by incomplete interoperability between such tools. To ensure interoperability initiatives are effectively deployed, end-user applications need to be aware of, and support, best practices and standards. Here, we report on an initiative in which software developers and genome biologists came together to explore and raise awareness of these issues: BioHackathon 2009. Developers in attendance came from diverse backgrounds, with experts in Web services, workflow tools, text mining and visualization. Genome biologists provided expertise and exemplar data from the domains of sequence and pathway analysis and glyco-informatics. One goal of the meeting was to evaluate the ability to address real world use cases in these domains using the tools that the developers represented. This resulted in i) a workflow to annotate 100,000 sequences from an invertebrate species; ii) an integrated system for analysis of the transcription factor binding sites (TFBSs) enriched based on differential gene expression data obtained from a microarray experiment; iii) a workflow to enumerate putative physical protein interactions among enzymes in a metabolic pathway using protein structure data; iv) a workflow to analyze glyco-gene-related diseases by searching for human homologs of glyco-genes in other species, such as fruit flies, and retrieving their phenotype-annotated SNPs. Beyond deriving prototype solutions for each use-case, a second major purpose of the BioHackathon was to highlight areas of insufficiency. We discuss the issues raised by our exploration of the problem/solution space, concluding that there are still problems with the way Web services are modeled and annotated, including: i) the absence of several useful data or analysis functions in the Web service "space"; ii) the lack of documentation of methods; iii) lack of compliance with the SOAP/WSDL specification among and between various programming-language libraries; and iv) incompatibility between various bioinformatics data formats. Although it was still difficult to solve real world problems posed to the developers by the biological researchers in attendance because of these problems, we note the promise of addressing these issues within a semantic framework.

• Genomic structure of an economically important cyanobacterium, Arthrospira (Spirulina) platensis NIES-39.

  Authors: Takatomo Fujisawa, Rei Narikawa, Shinobu Okamoto, Shigeki Ehira, Hidehisa Yoshimura, Iwane Suzuki, Tatsuru Masuda, Mari Mochimaru, Shinichi Takaichi, Koichiro Awai [......] Seiha Omata, Hiromi Takarada, Yoko Katano, Hiroki Kosugi, Satoshi Tanikawa, Kazuko Ohmori, Naoki Sato, Masahiko Ikeuchi, Nobuyuki Fujita, Masayuki Ohmori

  DNA research : an international journal for rapid publication of reports on genes and genomes. 03/2010; 17(2):85-103.

  A filamentous non-N(2)-fixing cyanobacterium, Arthrospira (Spirulina) platensis, is an important organism for industrial applications and as a food supply. Almost the complete genome of A. platensisA filamentous non-N(2)-fixing cyanobacterium, Arthrospira (Spirulina) platensis, is an important organism for industrial applications and as a food supply. Almost the complete genome of A. platensis NIES-39 was determined in this study. The genome structure of A. platensis is estimated to be a single, circular chromosome of 6.8 Mb, based on optical mapping. Annotation of this 6.7 Mb sequence yielded 6630 protein-coding genes as well as two sets of rRNA genes and 40 tRNA genes. Of the protein-coding genes, 78% are similar to those of other organisms; the remaining 22% are currently unknown. A total 612 kb of the genome comprise group II introns, insertion sequences and some repetitive elements. Group I introns are located in a protein-coding region. Abundant restriction-modification systems were determined. Unique features in the gene composition were noted, particularly in a large number of genes for adenylate cyclase and haemolysin-like Ca(2+)-binding proteins and in chemotaxis proteins. Filament-specific genes were highlighted by comparative genomic analysis.

• The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows. The DBCLS BioHackathon Consortium*.

  Authors: Toshiaki Katayama, Kazuharu Arakawa, Mitsuteru Nakao, Keiichiro Ono, Kiyoko F Aoki-Kinoshita, Yasunori Yamamoto, Atsuko Yamaguchi, Shuichi Kawashima, Hong-Woo Chun, Jan Aerts [......] Daron M Standley, Hideaki Sugawara, Toshiyuki Tashiro, Oswaldo Trelles, Rutger A Vos, Mark D Wilkinson, William York, Christian M Zmasek, Kiyoshi Asai, Toshihisa Takagi

  Journal of biomedical semantics. 01/2010; 1(1):8.

  Web services have become a key technology for bioinformatics, since life science databases are globally decentralized and the exponential increase in the amount of available data demands forWeb services have become a key technology for bioinformatics, since life science databases are globally decentralized and the exponential increase in the amount of available data demands for efficient systems without the need to transfer entire databases for every step of an analysis. However, various incompatibilities among database resources and analysis services make it difficult to connect and integrate these into interoperable workflows. To resolve this situation, we invited domain specialists from web service providers, client software developers, Open Bio* projects, the BioMoby project and researchers of emerging areas where a standard exchange data format is not well established, for an intensive collaboration entitled the BioHackathon 2008. The meeting was hosted by the Database Center for Life Science (DBCLS) and Computational Biology Research Center (CBRC) and was held in Tokyo from February 11th to 15th, 2008. In this report we highlight the work accomplished and the common issues arisen from this event, including the standardization of data exchange formats and services in the emerging fields of glycoinformatics, biological interaction networks, text mining, and phyloinformatics. In addition, common shared object development based on BioSQL, as well as technical challenges in large data management, asynchronous services, and security are discussed. Consequently, we improved interoperability of web services in several fields, however, further cooperation among major database centers and continued collaborative efforts between service providers and software developers are still necessary for an effective advance in bioinformatics web service technologies.

• CyanoBase: the cyanobacteria genome database update 2010.

  Authors: Mitsuteru Nakao, Shinobu Okamoto, Mitsuyo Kohara, Tsunakazu Fujishiro, Takatomo Fujisawa, Shusei Sato, Satoshi Tabata, Takakazu Kaneko, Yasukazu Nakamura

  Nucleic acids research. 10/2009;

  CyanoBase (http://genome.kazusa.or.jp/cyanobase) is the genome database for cyanobacteria, which are model organisms for photosynthesis. The database houses cyanobacteria species information,CyanoBase (http://genome.kazusa.or.jp/cyanobase) is the genome database for cyanobacteria, which are model organisms for photosynthesis. The database houses cyanobacteria species information, complete genome sequences, genome-scale experiment data, gene information, gene annotations and mutant information. In this version, we updated these datasets and improved the navigation and the visual display of the data views. In addition, a web service API now enables users to retrieve the data in various formats with other tools, seamlessly.

• Identification of endocrine disruptor biodegradation by integration of structure-activity relationship with pathway analysis.

  Authors: Tadashi Kadowaki, Craig E Wheelock, Tetsuya Adachi, Taku Kudo, Shinobu Okamoto, Nobuya Tanaka, Koichiro Tonomura, Gozoh Tsujimoto, Hiroshi Mamitsuka, Susumu Goto, Minoru Kanehisa

  Environmental science & technology. 01/2008; 41(23):7997-8003.

  We present a SAR method that can predict estrogen-like endocrine disrupting chemical (EDC) activity as well as key biodegradation steps for detoxification. This method is based on a recentWe present a SAR method that can predict estrogen-like endocrine disrupting chemical (EDC) activity as well as key biodegradation steps for detoxification. This method is based on a recent graph-mining algorithm developed by Kudo et al., which generates a set of descriptors from all potent chemical fragments (including rings). This method is novel in that it achieves chemical diversity in the training data set by sampling another data set of larger diversity. The model achieved an 83% accuracy prediction rate, and identified 1291 EDC candidates from the KEGG database. From this set of candidate compounds, bisphenol A was chosen for assay validation and biodegradation pathway analysis. Results showed that bisphenol A exhibited estrogen-like activity and was degraded in three distinct reactions. The prediction model provided information on the mechanism of the ligand-target binding, such as key functional groups involved. We focused on the enzyme commission number, which is useful for analyses of biodegradation pathways. Results identified oxygenases, ether hydrolases, and carbon-halide lyases as being important in the biodegradation pathway. This combined approach provided new information regarding the biodegradation of EDCs, and can potentially be extended to applications with transcriptomic, proteomic, and metabolomic data to provide a quick screen of biological activity and biodegradation pathway(s).

• Complete genomic structure of the bloom-forming toxic cyanobacterium Microcystis aeruginosa NIES-843.

  Authors: Takakazu Kaneko, Nobuyoshi Nakajima, Shinobu Okamoto, Iwane Suzuki, Yuuhiko Tanabe, Masanori Tamaoki, Yasukazu Nakamura, Fumie Kasai, Akiko Watanabe, Kumiko Kawashima [......] Chika Takahashi, Chiharu Minami, Tsunakazu Fujishiro, Mitsuyo Kohara, Midori Katoh, Naomi Nakazaki, Shinobu Nakayama, Manabu Yamada, Satoshi Tabata, Makoto M Watanabe

  DNA research : an international journal for rapid publication of reports on genes and genomes. 01/2008; 14(6):247-56.

  The nucleotide sequence of the complete genome of a cyanobacterium, Microcystis aeruginosa NIES-843, was determined. The genome of M. aeruginosa is a single, circular chromosome of 5,842,795 baseThe nucleotide sequence of the complete genome of a cyanobacterium, Microcystis aeruginosa NIES-843, was determined. The genome of M. aeruginosa is a single, circular chromosome of 5,842,795 base pairs (bp) in length, with an average GC content of 42.3%. The chromosome comprises 6312 putative protein-encoding genes, two sets of rRNA genes, 42 tRNA genes representing 41 tRNA species, and genes for tmRNA, the B subunit of RNase P, SRP RNA, and 6Sa RNA. Forty-five percent of the putative protein-encoding sequences showed sequence similarity to genes of known function, 32% were similar to hypothetical genes, and the remaining 23% had no apparent similarity to reported genes. A total of 688 kb of the genome, equivalent to 11.8% of the entire genome, were composed of both insertion sequences and miniature inverted-repeat transposable elements. This is indicative of a plasticity of the M. aeruginosa genome, through a mechanism that involves homologous recombination mediated by repetitive DNA elements. In addition to known gene clusters related to the synthesis of microcystin and cyanopeptolin, novel gene clusters that may be involved in the synthesis and modification of toxic small polypeptides were identified. Compared with other cyanobacteria, a relatively small number of genes for two component systems and a large number of genes for restriction-modification systems were notable characteristics of the M. aeruginosa genome.

• Prediction of nitrogen metabolism-related genes in Anabaena by kernel-based network analysis.

  Authors: Shinobu Okamoto, Yoshihiro Yamanishi, Shigeki Ehira, Shuichi Kawashima, Koichiro Tonomura, Minoru Kanehisa

  Proteomics. 04/2007; 7(6):900-9.

  Prediction of molecular interaction networks from large-scale datasets in genomics and other omics experiments is an important task in terms of both developing bioinformatics methods and solvingPrediction of molecular interaction networks from large-scale datasets in genomics and other omics experiments is an important task in terms of both developing bioinformatics methods and solving biological problems. We have applied a kernel-based network inference method for extracting functionally related genes to the response of nitrogen deprivation in cyanobacteria Anabaena sp. PCC 7120 integrating three heterogeneous datasets: microarray data, phylogenetic profiles, and gene orders on the chromosome. We obtained 1348 predicted genes that are somehow related to known genes in the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. While this dataset contained previously known genes related to the nitrogen deprivation condition, it also contained additional genes. Thus, we attempted to select any relevant genes using the constraints of Pfam domains and NtcA-binding sites. We found candidates of nitrogen metabolism-related genes, which are depicted as extensions of existing KEGG pathways. The prediction of functional relationships between proteins rather than functions of individual proteins will thus assist the discovery from the large-scale datasets.

• Group 3 sigma factor gene, sigJ, a key regulator of desiccation tolerance, regulates the synthesis of extracellular polysaccharide in cyanobacterium Anabaena sp. strain PCC 7120.

  Authors: Hidehisa Yoshimura, Shinobu Okamoto, Yoichi Tsumuraya, Masayuki Ohmori

  DNA research : an international journal for rapid publication of reports on genes and genomes. 03/2007; 14(1):13-24.

  The changes in the expression of sigma factor genes during dehydration in terrestrial Nostoc HK-01 and aquatic Anabaena PCC 7120 were determined. The expression of the sigJ gene in terrestrial NostocThe changes in the expression of sigma factor genes during dehydration in terrestrial Nostoc HK-01 and aquatic Anabaena PCC 7120 were determined. The expression of the sigJ gene in terrestrial Nostoc HK-01, which is homologous to sigJ (alr0277) in aquatic Anabaena PCC 7120, was significantly induced in the mid-stage of dehydration. We constructed a higher-expressing transformant of the sigJ gene (HE0277) in Anabaena PCC 7120, and the transformant acquired desiccation tolerance. The results of Anabaena oligonucleotide microarray experiments showed that a comparatively large number of genes relating to polysaccharide biosynthesis were upregulated in the HE0277 cells. The extracellular polysaccharide released into the culture medium of the HE0277 cells was as much as 3.2-fold more than that released by the control cells. This strongly suggests that the group 3 sigma factor gene sigJ is fundamental and conducive to desiccation tolerance in these cyanobacteria.

• Genome Informatics 14: 444--445 (2003) Newly Identified Motifs within PAS Domains of

  Authors: Filamentous Cyanobacteria, Rei Narikawa, Shinobu Okamoto, Masahiko Ikeuchi, Masayuki Ohmori

  07/2004;

  Introduction Many cyanobacterial genome projects have been finished or are ongoing. Now, complete genome sequence of Anabaena sp. PCC 7120 (Anabaena)[1] and draft genome sequence of NostocIntroduction Many cyanobacterial genome projects have been finished or are ongoing. Now, complete genome sequence of Anabaena sp. PCC 7120 (Anabaena)[1] and draft genome sequence of Nostoc punctiforme (Nostoc)[3] are available. Phylogenetically, these species are closely related. These species have extremely abundant signal-transduction proteins, especially PAS domain-containing proteins (PAScontaining proteins)[5]. PAS domain is known to be multi-functional domain superfamily with highly conserved 3D structure [6]. We formerly detected 142 and 180 PAS domains in 60 and 84 PAScontaining proteins from Anabaena and Nostoc, respectively. Clutering analysis showed that they were classified into 64 distinct subclasses and 36 "orphans". On the other hand, we detected 35 pairs of PAS-containing proteins that are orthologous to each other between the two species. PAS domains in these orthologous poteins were classified into two groups: orthologous and non-orthologous ones. We interpreted the

• Photoresponsive cAMP signal transduction in cyanobacteria.

  Authors: Masayuki Ohmori, Shinobu Okamoto

  Photochemical & photobiological sciences : Official journal of the European Photochemistry Association and the European Society for Photobiology. 07/2004; 3(6):503-11.

  The molecular mechanism of cAMP-mediated signal transduction from light reception to the physiological response via regulation of gene expression in cyanobacteria is described based on our recentThe molecular mechanism of cAMP-mediated signal transduction from light reception to the physiological response via regulation of gene expression in cyanobacteria is described based on our recent works. Cyanobacteria are known as the organisms that acquired oxygen-evolving, higher plant type photosynthesis. We have found that the cellular cAMP level in the filamentous cyanobacteria Anabaena was oppositely regulated by red and far-red light, i.e., decreasing and increasing, respectively, suggesting that a phytochrome-like red/far-red photoreversible pigment regulates the activity of a certain adenylate cyclase. On the other hand, in the unicellular cyanobacterium Synechocystis cellular cAMP content was increased by blue light irradiation, which led to stimulation of cell motility. The cAMP signaling pathway is known to play an important role in the regulation of various biological activities by altering enzyme activities or controlling gene expression levels in both prokaryotes and eukaryotes. We have isolated genes for adenylate cyclases and cAMP receptor proteins and characterized their molecular properties. Disruption of these genes resulted in the loss of cell motility. It is concluded that the light signal was transmitted by cAMP signal cascade in cyanobacteria.

• Molecular evolution of PAS domain-containing proteins of filamentous cyanobacteria through domain shuffling and domain duplication.

  Authors: Rei Narikawa, Shinobu Okamoto, Masahiko Ikeuchi, Masayuki Ohmori

  DNA research : an international journal for rapid publication of reports on genes and genomes. 05/2004; 11(2):69-81.

  When the entire genome of a filamentous heterocyst-forming N2-fixing cyanobacterium, Anabaena sp. PCC 7120 (Anabaena) was determined in 2001, a large number of PAS domains were detected inWhen the entire genome of a filamentous heterocyst-forming N2-fixing cyanobacterium, Anabaena sp. PCC 7120 (Anabaena) was determined in 2001, a large number of PAS domains were detected in signal-transducing proteins. The draft genome sequence is also available for the cyanobacterium, Nostoc punctiforme strain ATCC 29133 (Nostoc), that is closely related to Anabaena. In this study, we extracted all PAS domains from the Nostoc genome sequence and analyzed them together with those of Anabaena. Clustering analysis of all the PAS domains gave many specific pairings, indicative of evolutionary conservations. Ortholog analysis of PAS-containing proteins showed composite multidomain architecture in some cases of conserved domains and domains of disagreement between the two species. Further inspection of the domains of disagreement allowed us to trace them back in evolution. Thus, multidomain proteins could have been generated by duplication or shuffling in these cyanobacteria. The conserved PAS domains in the orthologous proteins were analyzed by structural fitting to the known PAS domains. We detected several subclasses with unique sequence features, which will be the target of experimental analysis.

• Use of segment-based microarray in the analysis of global gene expression in response to various environmental stresses in the cyanobacterium Anabaena sp. PCC 7120.

  Authors: Naoki Sato, Masayuki Ohmori, Masahiko Ikeuchi, Kousuke Tashiro, C Peter Wolk, Takakazu Kaneko, Katsuhiko Okada, Mikio Tsuzuki, Shigeki Ehira, Hiroshi Katoh, Shinobu Okamoto, Hidehisa Yoshimura, Takatomo Fujisawa, Ayako Kamei, Shizue Yoshihara, Rei Narikawa, Takashi Hamano, Satoshi Tabata, Satoshi Kuhara

  The Journal of general and applied microbiology. 03/2004; 50(1):1-8.

  We prepared microarrays that contain genomic sequences of a heterocyst-forming filamentous cyanobacterium Anabaena sp. PCC 7120. The complete genome of this cyanobacterium codes for about 5,368We prepared microarrays that contain genomic sequences of a heterocyst-forming filamentous cyanobacterium Anabaena sp. PCC 7120. The complete genome of this cyanobacterium codes for about 5,368 protein-coding genes in the main chromosome of 6.4 Mbp. In total, 2,407 DNA segments were selected from the sequencing clones, and amplified by PCR, then spotted on glass slides in duplicate. These microarrays differ from the widely used commercial or custom-made ones for other microorganisms in that each DNA segment was 3-4 kbp long, and contained about 3-4 predicted genes on average. This feature, however, did not decrease the usefulness of the microarrays, since we were able to detect a number of potentially novel genes that are induced in response to nitrogen deprivation, low temperature and drought. In addition, we found some genomic regions in which dozens of contiguous genes are simultaneously regulated. These results suggest that these segment-based microarrays are useful especially for such large genomes as Anabaena, for which the number of genes exceeds either technical or practical limitations.

• The cyanobacterial PilT protein responsible for cell motility and transformation hydrolyzes ATP.

  Authors: Shinobu Okamoto, Masayuki Ohmori

  Plant & cell physiology. 11/2002; 43(10):1127-36.

  The unicellular cyanobacterium, Synechocystis sp. PCC 6803 is motile. A homologue of the PilT protein family, required for twitching motility in Pseudomonas aeruginosa and social gliding motility inThe unicellular cyanobacterium, Synechocystis sp. PCC 6803 is motile. A homologue of the PilT protein family, required for twitching motility in Pseudomonas aeruginosa and social gliding motility in Myxococcus xanthus, was found to be necessarily associated with cyanobacterial motility. The pilT1 (slr0161) mutant shows a pleotropic phenotype, defects in individual cell motility, and an increased number of long surface pili. Furthermore, the mutant loses its ability of natural competency. These findings demonstrate that PilT1 is essential for both cell motility and competency. Since the pilT gene contains a consensus ATP-binding motif (Walker boxes), the PilT protein is suggested for supplying energy for cell motility. The product of pilT1, overproduced in Escherichia coli and purified by Ni-affinity chromatography, hydrolyzes ATP in vitro.

• Regulation of cAMP-mediated photosignaling by a phytochrome in the cyanobacterium Anabaena cylindrica.

  Authors: Masayuki Ohmori, Kazuki Terauchi, Shinobu Okamoto, Masakatu Watanabe

  Photochemistry and photobiology. 07/2002; 75(6):675-9.

  Changes in cellular adenosine 3',5'-cyclic monophosphate (cAMP) content induced by monochromatic light of various wavelengths were determined in the cyanobacterium Anabaena cylindrica. IrradiationChanges in cellular adenosine 3',5'-cyclic monophosphate (cAMP) content induced by monochromatic light of various wavelengths were determined in the cyanobacterium Anabaena cylindrica. Irradiation with monochromatic red light caused a rapid decrease in cAMP content. In contrast, far-red light caused a rapid increase in its content. The effects of red and far-red light were reversible, suggesting the involvement of a prototype phytochrome as the photoreceptor for cAMP-mediated light-responsive signal transduction.

• A cAMP receptor protein, SYCRP1, is responsible for the cell motility of Synechocystis sp. PCC 6803.

  Authors: Hidehisa Yoshimura, Shizue Yoshihara, Shinobu Okamoto, Masahiko Ikeuchi, Masayuki Ohmori

  Plant & cell physiology. 05/2002; 43(4):460-3.

  Disruption of the sycrp1 gene encoding a cyanobacterial cAMP receptor protein makes cells of Synechocystis sp. PCC 6803 non-motile. Electron microscopy showed that the sycrp1-deficient strain had aDisruption of the sycrp1 gene encoding a cyanobacterial cAMP receptor protein makes cells of Synechocystis sp. PCC 6803 non-motile. Electron microscopy showed that the sycrp1-deficient strain had a reduced number of thick pili on the cell surface compared with the wild-type strain. It is suggested that cAMP-SYCRP1 complex controls the biogenesis of pili.

• Characterization of Genes Encoding Multi-domain Proteins in the Genome of the Filamentous Nitrogen-fixing Cyanobacterium Anabaena sp. Strain PCC 7120

  Authors: Masayuki Ohmori, Masahiko Ikeuchi, Naoki Sato, Peter Wolk, Takakazu Kaneko, Teruo Ogawa, Minoru Kanehisa, Susumu Goto, Shuichi Kawashima, Shinobu Okamoto, Hidehisa Yoshimura, Hiroshi Katoh, Takatomo Fujisawa, Shigeki Ehira, Ayako Kamei, Shizue Yoshihara, Rei Narikawa, Satoshi Tabata

  Computational analysis of gene structures in the genome of Anabaena sp. PCC 7120 revealed the presence of a large number of genes encoding proteins with multiple functional domains. This was mostComputational analysis of gene structures in the genome of Anabaena sp. PCC 7120 revealed the presence of a large number of genes encoding proteins with multiple functional domains. This was most evident in the genes for signal transduction pathway and the related systems. Comparison of the putative amino acid sequences of the gene products with those in the Pfam database indicated that GAF and PAS domains which may be involved in signal recognition were extremely abundant in Anabaena: 87 GAF domains in 62 ORFs and 140 PAS domains in 59 ORFs. As for the two-component signal transduction system, 73, 53, and 77 genes for simple sensory His kinases, hybrid His kinases and simple response regulators, respectively, many of which contained additional domains of diverse functions, were presumptively assigned. A total of 52 ORFs encoding putative Hanks-type Ser/Thr protein kinases with various domains such as WD-repeat, GAF and His kinase domains, as well as genes for presumptive protein phosphatases, were also identified. In addition, genes for putative transcription factors and for proteins in the cAMP signal transduction system harbored complex gene structures with multiple domains.

• A phytochrome-like protein AphC triggers the cAMP signaling induced by far-red light in the cyanobacterium Anabaena sp. strain PCC7120.

  Authors: Shinobu Okamoto, Masahiro Kasahara, Asako Kamiya, Yuka Nakahira, Masayuki Ohmori

  Photochemistry and photobiology. 80(3):429-33.

  In the filamentous, nitrogen-fixing cyanobacterium Anabaena sp. PCC7120, red light (630 nm) decreased, whereas far-red light (720 nm) increased cellular adenosine 3',5'-cyclic monophosphate (cAMP)In the filamentous, nitrogen-fixing cyanobacterium Anabaena sp. PCC7120, red light (630 nm) decreased, whereas far-red light (720 nm) increased cellular adenosine 3',5'-cyclic monophosphate (cAMP) content. To find a red and far-red light photoreceptor that triggers the cAMP signal cascade, we disrupted 10 open reading frame having putative chromophore-binding GAF domains. The response of the cellular cAMP concentration to red and far-red light in each open reading frame disruptant was determined. It was found that only the mutant of the gene all2699 failed to respond to far-red light. The open reading frame named as aphC encoded a protein with 920 amino acids including GAF domains similar to those involved in Cph2, a photoreceptor of Synechocystis sp. PCC6803. To determine which adenylate cyclase (AC) is responsible for far-red light signal, we disrupted all AC genes and found that CyaC was the candidate. The enzymatic activity of CyaC might be controlled by a far-red light photoreceptor through the phosphotransfer reaction. The site-specific mutant of the Asp59 residue of the receiver (R1) domain of CyaC lost its light-response capability. It was suggested that the far-red light signal was received by AphC and then transferred to the N-terminal response regulator domain of CyaC. Then its catalytic activity was stimulated, which increased the cellular cAMP concentration and drove the subsequent signal transduction cascade.

• Mutational Analysis of Genes Involved in Pilus Structure, Motility and Transformation Competency in the Unicellular Motile CyanobacteriumSynechocystis sp. PCC 6803

  Authors: Shizue Yoshihara, Xiao Xing Geng, Shinobu Okamoto, Kei Yura, Takashi Murata, Mitiko Go, Masayuki Ohmori, Masahiko Ikeuchi

  The relevance of pilus-related genes to motility, pilus structure on the cell surface and competency of natural transformation was studied by gene disruption analysis in the unicellular motileThe relevance of pilus-related genes to motility, pilus structure on the cell surface and competency of natural transformation was studied by gene disruption analysis in the unicellular motile cyanobacterium Synechocystis sp. PCC 6803. The genes disrupted in this study were chosen as related to the pil genes for biogenesis of the type IV pili in a Gram-negative bacterium Pseudomonas aeruginosa . It was found that motility of Synechocystis cells was lost in the mutants of slr0063 , slr1274 , slr1275 , slr1276 , slr1277 and sll1694 together with a simultaneous loss of the thick pili on the cell surface. Competency of the natural transformation was lost in the mutants listed above and slr0197 -disruptant. The gene slr0197 was previously predicted as a competence gene by a search with sequence-independent DNA-binding structure [ Yura et al. (1999) DNA Res . 6: 75]. It was suggested that both DNA uptake for natural transformation and motility are mediated by a specific type IV-like pilus structure, while a putative DNA-binding protein encoded by slr0197 is additionally required for the DNA uptake. Based on the homology with the pil genes in P . aeruginosa , slr0063 , slr1274 , slr1275 , slr1276 , slr1277 and sll1694 were designated pilB1 , pilM , pilN , pilO , pilQ and pilA1 , respectively. The gene slr0197 was designated comA .