Functional genomics aims at uncovering useful information carried on genome sequences and at using it to understand the mechanisms of biological function. Elucidating the unknown biological functions of new genes based upon the genomics rationales will greatly speed up the extensive understanding of biocatalysis and biodegradation in biological world including microorganisms. DNA microarrays generate a system for the simultaneous measurement of the expression level of thousands of genes in a single hybridization assay. Their data mining (transcriptome) strategy has two categories: differential gene expression and coordinated gene expression. Furthermore, measurement of proteins (proteome) generates information on how the transcribed sequences end up as functional characteristics within the cell, and quantitation of metabolites yields information on how the functional proteins act to produce energy and process substrates (metabolome). Various composite functional genomics databases containing genetic, enzymatic and metabolic information have been developed and will contribute to the understanding of the life blue print and the new discoveries and practices in biocatalysis and biodegradation that could enrich their industrial and environmental applications.

Terminal-restriction fragment length polymorphism (T-RFLP) analysis has been optimized by using in vitro model community composed of genomic DNAs of known bacterial strains and has been applied to assess the bacterial community structure in marine sediments. The specific fluorescence-labeled terminal restriction fragments (T-RFs) between 39 and 839 base long specifying each strain were precisely measured for known bacterial strains. The addition of a co-solvent (dimethylsulfoxide or glycerol) into PCR reactions has reduced differential PCR amplification. Comparative bacterial community structure was investigated for pristine and polluted sediments. A complex T-RFLP pattern showing complex bacterial community structure was obtained in the pristine sediment, whereas simple T-RFLP pattern (low bacterial diversity) was shown in polluted sediments where caged aquaculture has been conducted for several years. The results of T-RFLP analysis were compared with that of cloning and sequencing 16S rDNA clones from the same sediments. Sequence analysis of 16S rDNA clones (72) of the pristine sediment revealed a diverse collection of lineages, largely of the class Proteobacteria ($6\%$ alpha subdivision, $46\%$ gamma subdivision, $13\%$ delta subdivision, and $3\%$ epsilon subdivision), Nitrospina $(8\%)$, high G+C gram positive $(8\%)$, Verrucomicrobia $(7\%)$, and Planctomycetes $(6\%)$. In the contaminated sediments, 17 $(59\%)$ of the 16S rDNA clones (29) were related to Campylobacter and symbiont of Rimicaris exoculata belonging to epsilon subdivision of Proteobacteria. The results obtained indicated that T-RFLP analysis is a rapid and precise technique for comparative bacterial community analysis.

There are a number of ways in which environmental microbiology and microbial ecology will benefit from DNA micro array technology. These include community genome arrays, SSU rDNA arrays, environmental functional gene arrays, population biology arrays, and there are clearly more different applications of microarray technology that can be applied to relevant problems in environmental microbiology. Two types of the applications, bacterial identification chip and functional gene detection chip, will be presented. For the bacterial identification chip, a new approach employing random genome fragments that eliminates the disadvantages of traditional DNA-DNA hybridization is proposed to identify and type bacteria based on genomic DNA-DNA similarity. Bacterial genomes are fragmented randomly, and representative fragments are spotted on a glass slide and then hybridized to test genomes. Resulting hybridization profiles are used in statistical procedures to identify test strains. Second, the direct binding version of microarray with a different array design and hybridization scheme is proposed to quantify target genes in environmental samples. Reference DNA was employed to normalize variations in spot size and hybridization. The approach for designing quantitative microarrays and the inferred equation from this study provide a simple and convenient way to estimate the target gene concentration from the hybridization signal ratio.

Ralstonia eutrupha JMP134 is a well-known soil bacterium which can metabolite diverse aromatic compounds and xenobiotics, such as phenol, 2,4-dichlorophenoxy acetic acid (2, 4-D), and trichloroethylene (TCE), etc. Phenol is degraded through chromosomally encoded phenol degradation pathway. Phenol is first metabolized into catechol by a multicomponent phenol hydroxylase, which is further metabolized to TCA cycle intermediates via a meta-cleavage pathway. The nucleotide sequences of the genes for the phenol hydroxylase have previously been determined, and found to composed of eight genes phlKLMNOPRX in an operon structure. The phlR, whose gene product is a NtrC-like transcriptional activator, was found to be located at the internal region of the structural genes, which is not the case in most bacteria where the regulatory genes lie near the structural genes. In addition to this regulatory gene, we found other regulatory genes, the phlA and phlR2, downstream of the phlX. These genes were found to be overlapped and hence likely to be co-transcribed. The protein similarity analysis has revealed that the PhlA belongs to the GntR family, which are known to be negative regulators, whereas the PhlR2 shares high homology with the NtrC-type family of transcriptional activators like the PhlR. Disruption of the phlA by insertional mutation has led to the constitutive expression of the activity of phenol hydroxylase in JMP134, indicating that PhlA is a negative regulator. Possible regulatory mechanisms of phenol metabolism in R. eutropha JMP134 has been discussed.

Fruit fly, Drosophila melanogaster has developed efficient immune mechanisms to prevent microbial infection, which are consisted of cellular and humoral responses. During the systemic or local infection, two distinct pathways (Toll and Imd) play major roles in antimicrobial peptide synthesis. The Toll pathway is required to defend Gram-positive bacterial and fungal infections, whereas the Imd pathway is important in Gram-negative bacterial infection. We have shown that the infection of the opportunistic Gram-negative bacterium, Pseudomonas aeruginosa strain PA14 (PA14) into fly dorsal thorax can kill the flies within 48 h ($100\%$ mortality) in our optimized infection condition, suggesting that the PA14 strain can cause disease progress in fly model system. We found that flies carrying a constitutively activated mutant form of the Toll receptor $(Tl^{10b})$ showed increased resistance to P. aeruginosa infection and that flies carrying mutations in the Toll signaling pathway as well as in the Imd signaling pathway was more susceptible to PA14 infection. All these results imply that the Toll pathway might be important in the resistance to this pathogenic Gram-negative bacterial infection.

Understanding the molecular pathogenesis of the multifaceted host-pathogen interaction is critical in the development of improved treatment and prevention, as well as elucidating how certain bacteria can circumvent host defenses, multiply in the host, and cause such extensive damage. Disease caused by infection with V. vulnificus is remarkable for the invasive nature of the infection, ensuing severe tissue damage, and rapidly fulminating course. The characterization of somatic as well as secreted products of V. vulnificus has yielded a large list of putative virulence attributes, whose known functions are easily imagined to explain the pathology of disease. These putative virulence factors include a carbohydrate capsule, lipopolysaccharide, a cytolysin/hemolysin, elastolytic metalloprotease, iron sequestering systems, lipase, and pili. However, only few among the putative virulence factors has been confirmed to be essential for virulence by the use of molecular Koch's postulates. This presentation describes molecular biological characterization of the virulence factors contributing to survival as well as to toxigenesis of V. vulnificus.

The role of a TolC homologue in the virulence of Vibrio vulnificus, a marine bacterium causing serious wound infection and fulminant septicemia in persons with underlying conditions, has been studied. TolC, an outer membrane protein, has been implicated in a variety of bacterial functions including export of diverse molecules ranging from large proteins to antibiotics. A homologue of the tolC gene of V. cholerae, which has been shown to be required for bile resistance, cytotoxicity and colonization of this organism, was identified in the partially determined genome sequence of V. vulnificus. To determine the role of TolC in the virulence of V. vulnificus, a TolC-deficient (TD) mutant was isolated by in vivo allelic exchange. Compared with the parent strain, the TD mutant was more sensitive to bile, and much less virulent in mice challenged subcutaneously. This mutant was noncytotoxic to the HEp-2 cells, but its metalloprotease and cytolysin activities in the culture supernatant were comparable to the parent strain. In addition, the resistance of the TD mutant to human serum bactericidal activity as well as its growth in either human or murine blood was not affected. Collectively, our data suggest that TolC may be involved in colonization and/or spread of V. vulnificus to the blood stream, probably by secreting a cytotoxin other than the cytolysin.

While the biosynthetic gene cluster encoding the pigmented antibiotic actinorhodin is present in the two closely related bacterial species, Streptomyces lividans and Streptomyces coelicolor, it normally is expressed only in S. coelicolor---generating the deep blue colonies responsible for the S. coelicolor name. However, multiple copies of the afsR2 gene, which activates actinorhodin synthesis, result in the ability of S. lividansto also synthesize large amounts of actinorhodin. Here we report that the phenotypic property that historicially distinguishes these two Streptomycesspecies is determined conditionally by the carbon source used for culture. Whereas growth on glucose repressed actinorhodin production in S. lividans, culture on solid media containing glycerol as the sole carbon source dramatically increased the expression of afsR2 mRNA---leading to extensive actinorhodin synthesis by S. lividansand obliterating its phenotypic distinction from S. coelicolor. afsR2 transcription under these conditions was developmentally regulated, rising sharply at the time of aerial mycelium formation and coinciding temporally with the onset of actinorhodin production. Our results, which identify media-dependent parallel pathways that regulate actinorhodin synthesis in S. lividans, demonstrate carbon source control of actinorhodin production through the regulation of afsR2 mRNA synthesis. The nucleotide sequences of afsR2 revealed two putative important domains; the domain containing direct repeats in the middle and the domain homologous to sigma factor sequence in the C-terminal end. In this work, we constructed various sized afsR2-derivatives and compared the actinorhodin stimulating effects in S. lividans TK21. The experimental data indicate that the domain homologous to sigma factor sequence in the C-terminal end of afsR2 plays a critical role as an antibiotic stimulating function. In addition, we also observed that the single copy integration of afsR2 regulatory gene into S. lividans TK21 chromosome significantly activates antibiotic overproduction.

Heat shock proteins (HSPs) are induced in most living cells by mild heat treatment, ethanol, heavy metal ions and hypoxia. In yeast Saccharomyces cerevisiae, mild heat pretreatment strongly induces Hsp104 and thus provide acquired thermotolerance. The ability of hsp104 deleted mutant $({\triangle}hsp104)$ to acquire tolerance to extreme temperature is severely impaired. In providing thermotolerance, two ATP binding domains are indispensible, as demonstrated in ClpA and ClpB proteases of E. coli. The mechanisms by which Hsp104 protects cells from severe heat stress are not yet completely elucidated. We have investigated regulation of mitochondrial metabolic pathways controlled by the functional Hsp104 protein using $^{13}C_NMR$ spectroscopy and observed that the turnover rate of TCA cycle was enhanced in the absence of Hsp104. Production of ROS, which are toxic to kill cells radiply via oxidative stress, was also examined by fluorescence assay. Mitochondrial dysfunction was manifested in increased ROS levels and higher sensitivity for oxidative stress in the absence of Hsp104 protein expressed. Finally, we have identified mitochondrial complex I and Ferritin as binding protein(s) of Hsp104 by yeast two hybrid experiment. Based on these observations, we suggest that Hsp104 protein functions as a protector of oxidative stress via either keeping mitochondrial integrity, direct binding to mitochonrial components or regulating metal-catalyzed redox chemistry.

Oligotrophic bacteria isolated from forest soil showed a specific community consisting of various taxonomic groups compared with those in other soil or aquatic habitats. Based on the cell shape, the isolates were divided into four groups: regular rod, curved/spiral rod, irregular rod, and prosthecate bacteria. The cellular fatty acids 60 oligotrophic isolates were analyzed. At the dendrogram based on cellular fatty acid composition, four clusters(I-IV) were separated at a euclidian distance of about 50. Based on the 16S rDNA sequence analysis, the two representative strains(MH256 and MA828) of cluster 3 showed the close relation to genera, Xathomonas/Stenotrophomonas, but were not included in these genera. The isolates with Q-10 were also studied. They are corresponded to the two large groups in Proteobacteria alpha subdivision. One was incorporated in the genus Bradyrhizobium cluster, which also includes Agromonas, a genus for oligotrophic bacteria. The strains of the other group showed high similarity to the genus Agrobacterium. We attempted to screening of bioactive compounds from oligotrophs which was isolated from forest soil. The active compounds were analyzed by mass and NMR spectrum, one of them identified as crisamicin A. Another one designated as SAPH is a new compound. The results indicate that there were possibilities for finding new compounds from the rare microorganisms such as oligotrophs.

The revolution in molecular biology has given us greatly increased ability to obtain and to modify biological resources and to use them for the benefit of all humankind. The sequencing and the associated analysis of gene functions for a growing number of genomes will have an unprecedented effect on the uses of biological resources and the need for access to them. To investigate the diversity of microbial community in swamp, molecular systematic methods were applied. By amplified rDNA restriction analysis (ARDRA) and rDNA partial sequence analysis, $75\%$ of the isolates were known species. In case of uncultured analysis, almost all the selected clones were new species candidate. Especially archea and uncultured bacterial analyses, all clones were new taxon candidates. As for the eukaryotic diversity, several yeast form cultures were isolated from various samples of swamp. Among them, about $60\%$ of the isolates were easily identified. In case of a new species candidate, most strain were included in hymenomycetal yeasts.

The oceans cover about $71\%$ of the Earth's crust and contain nearly 300,000 described species. Free-living bacteria in the sea and symbiotic bacteria of marine invertebrates are proving to be valuable sources of useful bioactive compounds. Marine sponges, in particular, which contain diverse communities of bacteria, produce many classes of compounds that are unique to the marine environment. Uncultured microorganisms are commonly believed to represent $99.9\%$ of the whole microbial community. They have been investigated for the possibility of isolating and over-expressing genes in viable microorganisms. Strict symbiotic species that have been adapted to the host are candidate unculturable species. With the enormous potential for discovery, development, and market value of marine derived compounds, supply of the products is a major limiting factor for further development.

The diversity of epiphytic bacterial communities on deciduous oak tree (Quercus dentate Thunb.) leaves was examined both in the natural forest area with a clean air and in the industrial estate to assess effects of acidic deposition to the phyllosphere using 16S rDNA sequence data. In addition, acid-tolerant epiphytic bacterial communities were compared. A total of 78 epiphytic and 444 acid-tolerant clones were obtained from clone libraries, resulting in 20 and 17 phylotypes by analysis of restriction fragment length polymorphism (RFLP) for PCR-amplified 16S rDNA products. A low bacterial diversity in both areas was found. As tree leaves grow older, bacterial diversities were slightly increased in the level of subphylum. The community structure of epiphytic bacteria in both areas in April consisted of only two subphyla, $\beta-and\;\gamma-Proteobacteria$. In August two additional subphyla in both areas were found, but the composition was a little different, Acidobacteria and Cytophaga-Flexibacter-Bacteroids (CFB) group in the industrial estate and a -Proteobacteria and CFB group in the natural area, respectively. Acidobacteria could be an indicator of epiphytic bacteria for acidic deposition on plant leaves, whereas a -Proteobacteria be one of epiphytic bacteria that naturally survive on leaves that are not affected by acidic deposition. The acid-tolerant bacterial communities in April were composed of two subphyla, $\gamma-Proteobacteria$ and Low G+C gram-positive bacteria in both areas, and in August a-Proteobacteria was added to the community just in the natural forest area. The direct influence of acidic deposition on the acid-tolerant bacterial phylogenetic composition could not be detected in higher taxonomic levels such as subphylum, but at narrower or finer levels it could be observed by a detection of Xanthomonadales group of $\gamma-Proteobacteria$ just in the industrial estate.

Gene therapy is to treat and cure diseases by an introduction of therapeutic genes in defective cells or tissues of human body. Gene delivery system, gene expression system, and therapeutic gene are three core elements for gene therapy. The efficient delivery of therapeutic genes and appropriate gene expression are the crucial issues for therapeutic outcome of gene delivery. Because it can be used in common for the treatment and cure of various diseases, gene delivery system is the most important core element for a successful gene therapy. Viruses are naturally evolved to transfer their genomes into host cells efficiently. This ability has made vectorologists exploit viruses as attractive vehicles for the delivery of therapeutic genes. Viral vectors based on adenovirus (Ad) and adeno-associated virus (AAV) have been often used for gene delivery in laboratory. Ad and AAV vectors derived from human DNA viruses differ greatly in their life cycle, expression level and duration of transgenes, immunogenicity, and vector preparation. Both vectors can be used as effective tools for gene therapy and more recently in functional genomics. Here, the characteristics of Ad and AAV vectors are discussed.

Genetic materials including DNA plasmid are effective delivery vehicle to express interesting gene efficiently and safely not to generate replication competent virus. Moreover, it has advantages to design a better vector and to simplify manufacturing and storage condition. To understand a possible pathogenic mechanism by a flavivirus, West Nile virus (WNV), WNV genome sequence was aligned to other pathogenic viral genome. Interestingly, WNV capsid (Cp) amino acid sequence has some homology to HIV-l Vpr protein. These proteins induce apoptosis in human cell lines as well as in vivo and cell cycle arrest. Therefore, DNA plasmid carrying apoptosis-inducing and cell cycle arresting viral proteins including a HIV-1 Vpr and a WNV Cp protein can be useful for anti-cancer therapeutic applications. This WNV Cp protein is an early expressed protein which can be a reasonable target antigen (Ag) for vaccine design. Immunization of a DNA construct encoding WNV Cp protein induces a strong Ag-specific humoral and Th1-type immune responses in animal. Therefore, DNA plasmid encoding apoptotic viral proteins can be useful tool for therapeutic and prophylactic applications.

This work was initiated to develope a recombinant oral poliovaccine (OPV), which is highly advanced in safety (minimizing VAPP) by introducing Type 2,3 poliovirus epitopes into our RPS-Vax system. We have introduced several potential vaccine epitopes of poliovirus Type 2, and 3 into RPS-Vax system, resulting in production of recombinant polioviruses. Any of these chimeric viruses, however, were not detected for their foreign gene expression by serotype-specific mouse antiserum. We have designed several folding units to stabilize the introduced vaccine protein and attached short epitope-concatamer or epitope-multimer to them, followed by production of chimeric viruses. Only those who have an HIV-1 Tat-mediated folding unit were nicely detected for the introduced foreign proteins by anti-Tat antiserum and type-specific peptide-induced antisera. Nevertheless, introduced epitopes were not detected in Western blot experiment with each serotype-specific antiserum. None of the mice inoculated with these chimeric viruses showed preventative immunity when challenged with Lansing and Leon wildtype 2 and 3 poliovirus, and the antiserum did not show neutralizing capacity in vitro. Conformational epitope covering B/C loop region of type 2 and 3 were newly designed by computer modeling, and introduced into the RPS-Vax vector system, followed by production of chimeric viruses. Introduced epitope regions were nicely detected by anti-Tag23 mAb or peptide antibody, but still not detected by poliovirus antiserum. Nevertheless, neutralizing antibody was detected in the Tg-PVR mice even when inoculated once with these chimeric viruses. Also, the immunized mice showed perfect preventative immunity against the wild Type poliovirus Lancing or Leon. When boosted appropriately, those chimeric virus-inoculated Tg-PVR mice produced equivalent amounts of neutralizing antibody to those in Sabin 2/3-immunized mice. These data strongly suggest that our recombinant poliovirus (RPS-PV2 and RPS-PV3) can be used as a safe and effective rec-OPV instead of any preexisting poliovaccine.

Yeast cells respond to condition of amino acid starvation by synthesizing GCN4, a typical eukaryotic transcriptional activator, which regulates the expression of many amino acids biosynthetic genes. By introducing point mutations in the DNA binding domain of GCN4, mutants with normal DNA binding activity but defective in transcriptional activity were isolated to identify unknown proteins that could suppress the mutant phenotype under an amino acid depletion condition. As a result, SSB(Stress-Seventy B) subfamily proteins were identified as suppressors of mutant GCN4. SSB proteins were known as a member of yeast hsp70 family that probably aids passage of nascent chain through ribosomes. Among them, the mechanism of suppression by SSB2 on the defective GCN4 mutant strains is under investigation. Gcn4p directly interacts with Ssb2p through the basic DNA binding domain of GCN4. It suggests the possibility that physical interaction might induce the transcriptional activation of Gcn4p.

Bacteriophage lambda integrase carries out the site-specific recombination of lambda. Integrase contains two DNA binding domains with distinct sequence specificity, namely arm-type binding and core-type binding domains. The amino-terminal arm-binding domain is structurally related to the three-stranded $\beta-sheet$ family of DNA-binding domains. Integrase binding to the high affinity arm-type site by the amino-terminal domain facilitates Int binding to the low affinity core-type site, where the cleavage and strand exchange occurs. The amino-terminal domain of Int also modulates the core-binding and catalysis through intramolecular domain-domain interaction and/or intermolecular interactions between Int monomers. In addition, the amino-terminal domain interacts cooperatively with excisionase during excision. This indicates that amino-terminal domain of Int plays an important role in formation of proper higher-order nucleoprotein structure required for lambda site-specific recombination.

Schizosaccharomyces pombe is suited for the study of cytokinesis as it divides by forming a septum in the middle of the cell at the end of mitosis. To enhance our understanding of the cytokinesis, we have carried out a genetic screen for temperature-sensitive S. pombe mutants that show defects in septum formation and cell division. Here we present the isolation and characterization of a new temperature-sensitive mutant, sun1(septum uncontrolled), which undergoes uncontrolled septation during cell division cycle at restrictive temperature $(37^{\circ}C)$. In sun1 mutant, actin ring and septum are positioned at random locations and angles, and nuclear division cycle continues. These observations suggest that the sun] gene product is required for the proper placement of the actin ring as well as precise septation. The sun] mutant is monogenic recessive mutation unlinked to previously known various cdc genes of S. pombe. In a screen for $sunl^+$ gene to complement the sun] mutant, we have cloned a gene, $susl^+$(suppressor of sun1 mutant), that encodes a protein of 689 amino acids. The predicted amino acid sequence of $susl^+$ gene is similar to the human hMadlp and Saccharomyces cerevisiae Mad1p, a component of the spindle checkpoint in eukaryotic cells. The null mutant of $susl^+$ gene grows normally at various temperatures and has the increased sensitivity to anti-microtubule drug, while $susl^+$ mutant shows no sensitivity to microtubule destabilizing drugs. The putative S. pombe Sus1p directly interacts with S. pombe Mad2p in yeast two-hybrid assays. These data suggest that the newly isolated susr gene encodes S. pombe Mad1p and suppresses sun] mutant defective in controlled septation in a cell division cycle.

The assemblies of our partial genomic sequence data of Sphingomonas chungbukensis DJ77, with the total size of 877,928 bp, was done by TIGR Assembler. The total size of our current obtained contigs was about 0.73 Mb. A comparative genome analysis between our uncompleted genome and the other completed genomes was performed by taking advantage of the availability of multiple complete genomes in COGs database (Clusters of Orthologous Groups of proteins) to produce the genomic prediction of our S. chungbukensis DJ77. This analysis based on homologues search among completed genomes provides good initial step to our better assigning putative function to predicted coding sequences.

Substantial genomic diversity has been expected among clinical isolates of H. pylori. We have suggested that the two complete H. pylori genomes already sequenced may be insufficient for providing a discriminatory tool for typing clinical isolates as well as an insight into the genomic diversity, which enable to establish strategy for control of H. pylori infection. In this study, we determine the nucleotide sequence of the entire genome of Korean strain 51 and compare it with two reported genomic sequences to suggest validity for extensive genomic sequencing of H. pylori. The genome of H. pylori 51 consists of a circular chromosome with a size of 1,591,297 bp, which is corresponding to $95.4\%\;and\;96.8\%$ of the 26695 and J99 chromosome length, respectively. We predict that there are 1,454 open reading frames (ORFs) in 51, representing $91.4\%\;and\;97.2\%$ of the reported numbers of ORF of 26695 and J99, respectively. In contrast to 26695 and J99 that have 123 and 65 strain-specific genes, respectively, of the 1,454 genes, only 39 genes are unique to 51. Differences in genomic organization between 51 and each foreign strain were greater than between 2 foreign strains in pair wise entire sequence alignments by BLASTN. Particularly, the extent of genomic rearrangement observed between 51 and 26695 is higher than between 51 and J99. Multiple sequence alignment of orthologous genes among 3 strains showed that 51 is genetically closer to 26695 rather than J99. Phylogenetic analysis of nonsynonymous and synonymous mutation indicated J99 has the longest branch length in the unrooted phylogenetic tree, suggesting that J99 has higher mutation rate than the other 2 strains.

We have developed GComp as an analysis tool for comparative analysis of microbial genomes. Thetool uses BLAST or FASTA as a preprocessing program for local alignments, parses the homology search results, and generates tables and files to show homology relationship between two genomes at a glance. The interface for graphical representation of the comparative genomic analysis has been also implemented. Through analysis of a few pairs of microbial genome sequences, the program has been proved to be practically useful and a few additional features have been devised and designed, which will be added in the further development.

Light is an environmental signal that regulates photomovement and main energy source of photosynthesis in the cyanobacterium Synechocystis sp. PCC 6803 (Syn6803). Syn6803 is a popular model system for study of plant functional genomics. In this report, we adopted 2D gel based proteomics study to investigate proteins related with the light absorption and photo-protection in Syn6803. More than 700 proteins were detected on the SDS-gels stained with silver nitrate. Several proteins showing different expression level under various light conditions were identified with MALDI-TOF Mass spectrometry. As a comparison, we also conducted ICAT-based proteome study using WT and cphl (cyanobacterial phytochrome 1) mutant. A cphl deletion led to changes in the expression of proteins involved in translation, photosynthesis including photosystem and CO2 fixation, and cellular regulation. We are currently involved in TAP-tagging method to study protein-protein interactions in search for the molecular component involved in the light signal transduction of Syn6803 photomovement.