The sequence determination of the entire genome of the Synechocystis sp. strain PCC6803 was completed. The total length of the genome finally confirmed was 3,573,470 bp, including the previously reported sequence of 1,003,450 bp from map position 64% to 92% of the genome. The entire sequence was assembled from the sequences of the physical map-based contigs of cosmid clones and of lambda clones and long PCR products which were used for gap-filling. The accuracy of the sequence was guaranteed by analysis of both strands of DNA through the entire genome. The authenticity of the assembled sequence was supported by restriction analysis of long PCR products, which were directly amplified from the genomic DNA using the assembled sequence data. To predict the potential protein-coding regions, analysis of open reading frames (ORFs), analysis by the GeneMark program and similarity search to databases were performed. As a result, a total of 3,168 potential protein genes were assigned on the genome, in which 145 (4.6%) were identical to reported genes and 1,257 (39.6%) and 340 (10.8%) showed similarity to reported and hypothetical genes, respectively. The remaining 1,426 (45.0%) had no apparent similarity to any genes in databases. Among the potential protein genes assigned, 128 were related to the genes participating in photosynthetic reactions. The sum of the sequences coding for potential protein genes occupies 87% of the genome length. By adding rRNA and tRNA genes, therefore, the genome has a very compact arrangement of protein- and RNA-coding regions. A notable feature on the gene organization of the genome was that 99 ORFs, which showed similarity to transposase genes and could be classified into 6 groups, were found spread all over the genome, and at least 26 of them appeared to remain intact. The result implies that rearrangement of the genome occurred frequently during and after establishment of this species.

A novel v-erb-B-related gene, c-erb-B-2, which has been identified in the human genome, maps to human chromosome 17 at q21 (ref. 40), and seems to encode a polypeptide with a kinase domain that is highly homologous with, but distinct from, that of the epidermal growth factor (EGF) receptor. The c-erb-B-2 gene is conserved in vertebrates and it has been suggested that the neu gene, detected in a series of rat neuro/glioblastomas, is, in fact, the rat c-erb-B-2 gene. Amplification of the c-erb-B-2 gene in a salivary adenocarcinoma and a gastric cancer cell line MKN-7 suggests that its over-expression is sometimes involved in the neoplastic process. To determine the nature of the c-erb-B-2 protein, we have now molecularly cloned complementary DNA for c-erb-B-2 messenger RNA prepared from MKN-7 cells. Its sequence shows that the c-erb-B-2 gene encodes a possible receptor protein and allows an analysis of the similarity of the protein to the EGF receptor and the neu product. As a consequence of chromosomal aberration in MKN-7 cells, a 4.6-kilobase (kb) normal transcript and a truncated 2.3-kb transcript of c-erb-B-2 are synthesized at elevated levels. The latter transcript presumably encodes only the extracellular domain of the putative receptor.

No abstract

The erbB gene of an avian erythroblastosis virus, AEV-H, was determined to be 1812 nucleotides long and was predicted to code for a protein of 67,638 daltons. Unexpectedly, a sequence of 285 amino acids in the middle of the protein showed a significant homology (38%) with the sequence in the carboxy terminus of p60src. The nucleotide sequence of a mutant of AEV-H, td-130, which induces sarcomas but not erythroblastosis in chicken, was also analyzed. A deletion of 169 nucleotides was identified in the 3' half of the erbB gene, indicating that the gene codes for a truncated protein with the predicted molecular weight of 46,667. These findings suggest that the homologous domain of erbB protein with its N-terminal portion is sufficient for the transformation of fibroblasts and that one-third of the carboxy-terminal domain has a key role for the transformation of erythroid cells.

The contiguous sequence of 1,003,450 bp spanning map positions 64% to 92% of the genome of Synechocystis sp. strain PCC6803 has been deduced. Computer analysis of the sequence predicts that this region contains at least 818 potential ORFs, in which 255 (31%) were either genes that had already been identified or their homologues, 84 (10%) were homologues to registered hypothetical genes, and 149 (18%) showed weak similarities to reported genes. The remaining 330 ORFs showed no apparent similarity to any reported genes or carried no significant protein motifs. The potential ORFs as a whole occupied 86% of the sequenced region, implying compact arrangement of genes in the genome. As to the structural RNA genes, one rRNA operon consisting of 5,028 bp and at least 11 species of tRNA genes were identified. It is noteworthy that 10 out of the 11 tRNA species showed significant sequence similarities to tRNAs reported in plant chloroplasts. As other notable unique sequences, three classes of IS-like elements each with characteristics typical of IS elements were identified, and a typical unit of WD(Trp-Asp)-repeats which have only been detected in the regulatory proteins of eukaryotes was identified within the large 5,079-bp ORF located at map position 69%.

CyanoBase (http://www.kazusa.or.jp/cyano/) is a database containing genomic information on the cyanobacterium Synechocystis sp. strain PCC6803. It furnishes an annotation to each of the 3168 protein genes deduced from the entire nucleotide sequence of this genome. Information on the genome can be directly accessed through three different menus: a clickable physical map of the genome, a gene classification list, and a keyword search menu, all of which are accessible from the main page of the database. The entry page for a gene annotation contains the following information: the location of the gene on the genome, the nucleotide and deduced amino acid sequence of the gene, the result of a similarity search, and the classification of the deduced gene product according to its function. This page has reverse-links to the local physical map and gene classification list so that relevant genes can be searched in terms of their location on the genome and their function. In addition, the main page of CyanoBase provides engines for similarity searches between a query sequence and the entire genome sequence and for keyword searches, in addition to numerous links to pages containing related information.

In this series of projects of sequencing human cDNA clones which correspond to relatively long and nearly full-length transcripts, we newly determined the sequences of 80 clones, and predicted the coding sequences of the corresponding genes, named KIAA0201 to KIAA0280. Among the sequenced clones, 68 were obtained from human immature myeloid cell line KG-1 and 12 from human brain. The average size of the clones was 5.3 kb, and that of distinct ORFs in clones was 2.8 kb, corresponding to a protein of approximately 100 kDa. Computer search against the public databases indicated that the sequences of 22 genes were unrelated to any reported genes, while the remaining 58 genes carried sequences which show some similarities to known genes. Protein motifs that matched those in the PROSITE motif database were found in 25 genes and significant transmembrane domains were identified in 30 genes. Among the known genes to which significant similarity was shown, the genes that play key roles in regulation of developmental stages, apoptosis and cell-to-cell interaction were included. Taking into account of both the search data on sequence similarity and protein motifs, at least seven genes were considered to be related to transcriptional regulation and six genes to signal transduction. When the expression profiles of the cDNA clones were examined with different human tissues, about half of the clones from brain (5 of 11) showed significant tissue-specificity, while approximately 80% of the genes from KG-1 were expressed ubiquitously.

Many drugs of abuse and most neuropharmacological agents regulate G protein-coupled receptors (GPCRs) in the central nervous system (CNS)_ENREF_1. The striatum, in which dopamine D1 and D2 receptors are enriched, is strongly innervated by the ventral tegmental area (VTA), which is the origin of dopaminergic cell bodies of the mesocorticolimbic dopamine system_ENREF_3 and plays a central role in the development of psychiatric disorders_ENREF_4. Here we report the comprehensive and anatomical transcript profiling of 322 non-odorant GPCRs in mouse tissue by quantitative real-time PCR (qPCR), leading to the identification of neurotherapeutic receptors exclusively expressed in the CNS, especially in the striatum. Among them, GPR6, GPR52, and GPR88, known as orphan GPCRs, were shown to co-localize either with a D2 receptor alone or with both D1 and D2 receptors in neurons of the basal ganglia. Intriguingly, we found that GPR52 was well conserved among vertebrates, is Gs-coupled and responsive to the antipsychotic drug, reserpine. We used three types of transgenic (Tg) mice employing a Cre-lox system under the control of the GPR52 promoter, namely, GPR52-LacZ Tg, human GPR52 (hGPR52) Tg, and hGPR52-GFP Tg mice. Detailed histological investigation suggests that GPR52 may modulate dopaminergic and glutamatergic transmission in neuronal circuits responsible for cognitive function and emotion. In support of our prediction, GPR52 knockout and transgenic mice exhibited psychosis-related and antipsychotic-like behaviors, respectively. Therefore, we propose that GPR52 has the potential of being a therapeutic psychiatric receptor. This approach may help identify potential therapeutic targets for CNS diseases.