Hideo Takahashi

Glutamyl-tRNA mediates a switch in RNA polymerase use during chloroplast biogenesis.

Chloroplast genes of higher plants are transcribed by two types of RNA polymerase that are encoded by nuclear (NEP (nuclear‐encoded plastid RNA polymerase)) or plastid (PEP (plastid‐encoded plastid RNA polymerase)) genomes. NEP is largely responsible for the transcription of housekeeping genes during early chloroplast development. Subsequent light‐dependent chloroplast maturation is accompanied by repression of NEP activity and activation of PEP. Here, we show that the plastid‐encoded transfer RNA for glutamate, the expression of which is dependent on PEP, directly binds to and inhibits the transcriptional activity of NEP in vitro. The plastid tRNAGlu thus seems to mediate the switch in RNA polymerase usage from NEP to PEP during chloroplast development.

DNA Microarray Analysis of Plastid Gene Expression in an Arabidopsis Mutant Deficient in a Plastid Transcription Factor Sigma, SIG2

The plastid genome of higher plants contains more than one hundred genes for photosynthesis, gene expression, and other processes. Plastid transcription is done by two types of RNA polymerase, PEP and NEP. PEP is a eubacteria-type RNA polymerase that is essential for chloroplast development. In Arabidopsis thaliana, six sigma factors (SIG1-6) are encoded by the nuclear genome, and postulated to determine the transcription specificity of PEP. In this study, we constructed a DNA microarray for all of the plastid protein-coding genes, and analyzed the effects of the sig2 lesion on the global plastid gene expression. Of the 79 plastid protein genes, it was found that only the psaJ transcript was decreased in the mutant, whereas transcripts of 47 genes were rather increased. Since many of the up-regulated genes are under the control of NEP, it was suggested that the NEP activity was increased in the sig2-1 mutant.

Site-specific recombinases as tools for heterologous gene integration

Site-specific recombinases are the enzymes that catalyze site-specific recombination between two specific DNA sequences to mediate DNA integration, excision, resolution, or inversion and that play a pivotal role in the life cycles of many microorganisms including bacteria and bacteriophages. These enzymes are classified as tyrosine-type or serine-type recombinases based on whether a tyrosine or serine residue mediates catalysis. All known tyrosine-type recombinases catalyze the formation of a Holliday junction intermediate, whereas the catalytic mechanism of all known serine-type recombinases includes the 180° rotation and rejoining of cleaved substrate DNAs. Both recombinase families are further subdivided into two families; the tyrosine-type recombinases are subdivided by the recombination directionality, and the serine-type recombinases are subdivided by the protein size. Over more than two decades, many different site-specific recombinases have been applied to in vivo genome engineering, and some of them have been used successfully to mediate integration, deletion, or inversion in a wide variety of heterologous genomes, including those from bacteria to higher eukaryotes. Here, we review the recombination mechanisms of the best characterized recombinases in each site-specific recombinase family and recent advances in the application of these recombinases to genomic manipulation, especially manipulations involving site-specific gene integration into heterologous genomes.

Microarray profiling of plastid gene expression in a unicellular red alga, Cyanidioschyzon merolae

Plastid genomes of red algae contain more genes than those of green plant lineages, and it is of special interest that four transcription factors derived from ancestral cyanobacteria are encoded therein. However, little is known about transcriptional regulation of the red algal plastid genome. In this study, we constructed a red algal plastid DNA microarray of Cyanidioschyzon merolae covering almost all protein coding genes, and found that plastid genes are differentially activated by illumination. Run-on transcription assays using isolated plastids confirmed that activation takes place at the transcriptional level. In bacteria and plants, sigma factors determine the genes that are to be transcribed, and four plastid sigma factors (Cm_SIG1–4) encoded in the nuclear genome of C. merolae may be responsible for differential gene expression of the plastid genome. We found that transcripts for all Cm_SIG genes accumulated transiently after a shift from dark to light, whereas only the Cm_SIG2 transcript was increased after a shift from low to high light, suggesting that Cm_SIG2 is a sigma factor that responds to high light. Phylogenetic analysis of plastid sigma factors suggested that sigma factors of red and green algal plastids and the group 1 sigma factors of cyanobacteria form a monophyletic group.

SigC, the Group 2 Sigma Factor of RNA Polymerase, Contributes to the Late-stage Gene Expression and Nitrogen Promoter Recognition in the Cyanobacterium Synechocystis sp. Strain PCC 6803

We examined the role of SigC (Sll0184), a sigma factor of RNA polymerase (RNAP), in a unicellular cyanobacterium, Synechocystis sp. strain PCC 6803. On the inactivation of sigC, which is an Escherichia coli rpoD homolog, cells were viable but had a low survival rate in the stationary phase of growth under normal physiological conditions, indicating that SigC is a group 2 type sigma factor. In analyses of transcript and protein levels using the sigC knockout strain, it was found that expression of glnB, a nitrogen key regulatory gene, is controlled by SigC in the stationary phase. Primer extension revealed that the glnB nitrogen promoter (P2) was specifically recognized by SigC in the stationary phase under conditions of nitrogen starvation. In vitro studies with purified enzymes indicated effective transcription, on supercoiled DNA templates, from P2 by SigC-RNAP with NtcA which is an activator for nitrogen gene transcription. DNase I footprinting also indicated binding and related sites of NtcA and/or RNAP with SigC on the nitrogen promoter. The unique promoter architecture and the mechanism of transcription by RNAP with SigC are also discussed.

ALPHA -TOCOPHEROL PROTECTS PC12 CELLS FROM HYPEROXIA-INDUCED APOPTOSIS

A rat clonal pheochromocytoma cell line (PC12) was cultured under normoxic (21% O2) and hyperoxic (50% O2) conditions. PC12 cells underwent apoptotic cell death when they were cultured in charcoal‐stripped medium in a high‐oxygen atmosphere. Vitamin E homologs, α‐tocopherol (αT), β‐tocopherol (βT), γ‐tocopherol (γT), and δ‐tocopherol (δT), were added to the culture medium to study their biological activities. αT was more effective than γT and δT in preventing hyperoxia‐induced cell death. Addition of exogenous αT to charcoal‐treated medium prevented lactate dehydrogenase (LDH) leakage from PC12 cells and also inhibited the apoptosis, which was accompanied by DNA fragmentation. Additional αT was rapidly concentrated in PC12 cells, suggesting that it exerts antioxidant effects. Our data show that PC12 cell death under high‐oxygen conditions is due to apoptosis and that, among the vitamin E homologs, αT most effectively prevents hyperoxic apoptosis. J. Neurosci. Res. 52:184–191, 1998.

The site‐specific recombination system of actinophage TG1

Actinophage TG1 forms stable lysogens by integrating at a unique site on chromosomes of Streptomyces strains. The phage (attP(TG1)) and bacterial (attB(TG1)) attachment sites for TG1 were deduced from comparative genomic studies on the TG1-lysogen and nonlysogen of Streptomyces avermitilis. The attB(TG1) was located within the 46-bp region in the dapC gene (SAV4517) encoding the putative N-succinyldiaminopimelate aminotransferase. TG1-lysogens of S. avermitilis, however, did not demand either lysine or diaminopimelate for growth, indicating that the dapC annotation of S. avermitilis requires reconsideration. A bioinformatic survey of DNA databases using the fasta program for the attB(TG1) sequence extracted possible integration sites from varied streptomycete genomes, including Streptomyces coelicolor A3(2) and Streptomyces griseus. The gene encoding the putative TG1 integrase (int(TG1)) was located adjacent to the attP(TG1) site. TG1 integrase deduced from the int(TG1) gene was a protein of 619 amino acids having a high sequence similarity to phiC31 integrase, especially at the N-terminal catalytic region. By contrast, sequence similarities at the C-terminal regions crucial for the recognition of attachment sites were moderate or low. The site-specific recombination systems based on TG1 integrase were shown to work efficiently not only in Streptomyces strains but also in heterologous Escherichia coli.

In vitro characterization of the site-specific recombination system based on actinophage TG1 integrase

We have previously shown that, in vivo, the integration system based on the gene encoding the TG1 integrase and the corresponding attBTG1 and attPTG1 sites works well not only in Streptomyces strains, but also in Escherichia coli. Furthermore, the attachment sites for TG1 integrase are distinct from those of ϕC31 integrase. In this report, we expressed TG1 integrase as a GST-TG1 integrase fusion protein and then used affinity separation and specific cleavage to release purified integrase. Conditions for in vitro recombination were established using the purified TG1 integrase and its cognate attPTG1 and attBTG1 sites. TG1 integrase efficiently catalyzed a site-specific recombination between attBTG1 and attPTG1 sites irrespective of their substrate topology. The minimal sequences of attPTG1 and attBTG1 sites required for the substrates of TG1 integrase were demonstrated to be 43 and 39-bp, respectively. These results provide the basic features of the TG1 integrase system to be used as biotechnological tools, as well as to unravel the mechanism of the serine integrase.

Expression of nerve growth factor-induced type 1 plasminogen activator inhibitor (PAI-1) mRNA is inhibited by genistein and wortmannin.

Nerve growth factor (NGF), which acts as a neurotrophic factor in a rat pheochromocytoma cell line (PC12), stimulated type 1 plasminogen activator inhibitor (PAI-1) mRNA expression from 1 to 5 h, after addition at 5 ng/ml. PAI-1 antigen in culture medium, which was measured using an enzyme linked immunosorbent assay (ELISA), was also increased dose dependently by the addition of NGF. Neither epidermal growth factor (EGF), basic fibroblast growth factor (bFGF), phorbol myristate acetate (PMA) nor forskolin increased PAI-1 mRNA expression in PC12 cells. Genistein, an inhibitor of tyrosine protein kinase, completely inhibited NGF induced PAI-1 mRNA in the presence of 100 μM. Wortmannin, a potent and specific inhibitor of phosphatidylinositol 3-kinase (PI-3 kinase), decreased induction of PAI-1 mRNA level at doses of ≥ 10-7 M.

The heat shock protein inhibitor KNK437 induces neurite outgrowth in PC12 cells

The nervous system is highly sensitive to various environmental stresses, such as ischemia. Stress response mechanisms that result in neuroprotection, including the induction of heat shock proteins (HSP), are not well understood. We examined the effect of KNK437, a compound that inhibits the synthesis of inducible heat shock proteins, on neuronal differentiation in rat pheochromocytoma PC12 cells. KNK437 decreased the expression of HSP70, and induced the neurite outgrowth of PC12 cells in the absence of stress stimulation, although with lower efficacy than nerve growth factor (NGF). Neurite outgrowth stimulated by KNK437 and NGF was blocked by inhibitors of ERK mitogen-activated protein (MAP) kinase, p38 MAP kinase, and glycogen synthase kinase 3beta signaling pathways. NGF, and not KNK437, induced acetylcholine esterase (AChE) activity, a functional differentiation marker, indicating that KNK437 utilizes a mechanism distinct from that of NGF. KNK437 enhanced the activity of low dose NGF treatment on neurite outgrowth induction and ERK phosphorylation in PC12 cells, a finding that identifies KNK437 as a possible nerve regeneration agent. This compound may be a useful tool for the investigation of neuronal differentiation and neuroprotection against environmental stress.