ProteinCprotein interactions (PPIs) play crucial roles in protein function for a variety of biological processes. genome sequence of has drastically changed the strategy for studying genetic systems in cyanobacteria.2 Gene identification and functional assignment have been accelerated utilizing the genome sequence. The genome sequence has also allowed systematic analyses of gene regulation and function on the genomic level. Microarray and proteome analyses have made it possible to monitor the expression of a substantial proportion of genes at both transcriptional and translational levels.3,4 Genetic analyses, such as targeted disruption or random tagging analysis, have suggested many functional links between gene products.2 Two genome databases, CyanoBase and CyanoMutants, have been established and act as centralized information resources.5,6 Based on these material and information resources, provides an ideal model system for genetic studies of photosynthetic organisms. Although a large quantity of data has been accumulated through functional analyses of the genome, many of these analyses were driven by the predicted functions of the annotated genes. Therefore, a limited amount of information is available for unannotated genes. One of the effective approaches to obtain information regarding the function of these uncharacterized proteins is an analysis of proteinCprotein interactions (PPIs). Since nearly half of the predicted gene products of remain unannotated, a systematic approach for analysis of PPIs is needed. We conducted a large-scale analysis of PPIs using a yeast two-hybrid (YTH) system. YTH analysis is 27208-80-6 one of the well-established methods to detect binary protein interactions and is feasible for large-scale analysis. Large-scale YTH screens have been conducted in a wide range of organisms and have provided several important biological and bioinformatics platforms for the study of protein networks in different organisms.7C13 These analyses have also successfully placed functionally uncharacterized proteins in their biological context. In this study, we applied the YTH approach to three major target gene groups. For the initial screening, we selected genes of two-component signal transducers in order to evaluate our YTH screening system, as well as to elucidate the two-component signal transduction pathways in The two-component signal transduction system generally consists of a histidine kinase (Hik) and a response regulator (Rre), and signal transduction is achieved by phosphorylation as a result of the interaction between cognate pairs of Hiks and Rres. Since the interactions of Hiks and Rres are binary, these two-component signal transducers are suitable targets for evaluation using the YTH screening system. On the chromosome, 44 putative genes for Hiks and 42 genes for Rres are predicted.1,14,15 In contrast to the and genomes, in which most of the genes for cognate pairs of Hiks and Rres are located close to each other, many of the genes for Hiks and Rres in are distributed randomly in the chromosome. Among 44 genes for Hiks on the chromosome, 14 are located in the vicinity of genes for potential cognate Rres, whereas other 30 are not located near any genes for Rres.15 Therefore, identification of PPIs between two-component signal transducers will provide valuable information to elucidate the cognate pairs of Hiks and Rres and signal transduction pathways in genes whose homologues are conserved in the genome with the aim to obtain interaction information that is applicable to plant genes of cyanobacterial origin as well as genes. Chloroplasts are descendants of free-living cyanobacteria that became endsymbionts. In the course of the evolutionary processes that transformed the cyanobacterial symbiont into an organelle, chloroplasts have donated many genes to nuclear chromosomes.16 Martin et al.17 reported that approximately 1700 of 9369 genes that were investigated are of cyanobacterial origin and these encompass all 27208-80-6 functional categories. PPI information on genes conserved in plants 27208-80-6 would provide useful insights for functional analysis of plant Rabbit Polyclonal to PSEN1 (phospho-Ser357) genes of cyanobacterial origin, since has been used as a model for analysis of these plant genes. For the third screening 27208-80-6 group, we selected genes of unknown function in order to obtain interaction data that could be used to predict function. Since approximately 60% of the genes of unknown function have putative orthologues in at.