Masatsugu Denawa

Perspective factor: a novel indicator for the assessment of journal quality

‘Impact factor (IF)’ has been practically the only indicator to assess journal quality. However, it has various problems associated with citation analysis, such as the effects of ‘different sizes of audience’ and ‘biased citation’. To overcome this, we here propose a new objective index, ‘perspective factor (PF)’, which estimates the journal quality independently of citation analysis. The relationship between IF and PF of life science journals published in 1997, for example, gives a positive correlation when we excluded review journals and extremely high-IF journals, which could not gain comparatively high PF values. Copyright , Beech Tree Publishing.

Identification of a Dual Inhibitor of SRPK1 and CK2 That Attenuates Pathological Angiogenesis of Macular Degeneration in Mice

Excessive angiogenesis contributes to numerous diseases, including cancer and blinding retinopathy. Antibodies against vascular endothelial growth factor (VEGF) have been approved and are widely used in clinical treatment. Our previous studies using SRPIN340, a small molecule inhibitor of SRPK1 (serine-arginine protein kinase 1), demonstrated that SRPK1 is a potential target for the development of antiangiogenic drugs. In this study, we solved the structure of SRPK1 bound to SRPIN340 by X-ray crystallography. Using pharmacophore docking models followed by in vitro kinase assays, we screened a large-scale chemical library, and thus identified a new inhibitor of SRPK1. This inhibitor, SRPIN803, prevented VEGF production more effectively than SRPIN340 owing to the dual inhibition of SRPK1 and CK2 (casein kinase 2). In a mouse model of age-related macular degeneration, topical administration of eye ointment containing SRPIN803 significantly inhibited choroidal neovascularization, suggesting a clinical potential of SRPIN803 as a topical ointment for ocular neovascularization. Thus SRPIN803 merits further investigation as a novel inhibitor of VEGF.

Evidence for lateral gene transfer (LGT) in the evolution of eubacteria-derived small GTPases in plant organelles

The genomes of free-living bacteria frequently exchange genes via lateral gene transfer (LGT), which has played a major role in bacterial evolution. LGT also played a significant role in the acquisition of genes from non-cyanobacterial bacteria to the lineage of “primary” algae and land plants. Small GTPases are widely distributed among prokaryotes and eukaryotes. In this study, we inferred the evolutionary history of organelle-targeted small GTPases in plants. Arabidopsis thaliana contains at least one ortholog in seven subfamilies of OBG-HflX-like and TrmE-Era-EngA-YihA-Septin-like GTPase superfamilies (together referred to as Era-like GTPases). Subcellular localization analysis of all Era-like GTPases in Arabidopsis revealed that all 30 eubacteria-related GTPases are localized to chloroplasts and/or mitochondria, whereas archaea-related DRG and NOG1 are localized to the cytoplasm and nucleus, respectively, suggesting that chloroplast- and mitochondrion-localized GTPases are derived from the ancestral cyanobacterium and α-proteobacterium, respectively, through endosymbiotic gene transfer (EGT). However, phylogenetic analyses revealed that plant organelle GTPase evolution is rather complex. Among the eubacterium-related GTPases, only four localized to chloroplasts (including one dual targeting GTPase) and two localized to mitochondria were derived from cyanobacteria and α-proteobacteria, respectively. Three other chloroplast-targeted GTPases were related to α-proteobacterial proteins, rather than to cyanobacterial GTPases. Furthermore, we found that four other GTPases showed neither cyanobacterial nor α-proteobacterial affiliation. Instead, these GTPases were closely related to clades from other eubacteria, such as Bacteroides (Era1, EngB-1, and EngB-2) and green non-sulfur bacteria (HflX). This study thus provides novel evidence that LGT significantly contributed to the evolution of organelle-targeted Era-like GTPases in plants.

Evolutionary dynamics of spliceosomal intron revealed by in silico analyses of the P-Type ATPase superfamily genes

It has been long debated whether spliceosomal introns originated in the common ancestor of eukaryotes and prokaryotes. In this study, we tested the possibility that extant introns were inherited from the common ancestor of eukaryotes and prokaryotes using in silico simulation. We first identified 21 intron positions that are shared among different families of the P-Type ATPase superfamily, some of which are known to have diverged before the separation of prokaryotes and eukaryotes. Theoretical estimates of the expected number of intron positions shared by different genes suggest that the introns at those 21 positions were inserted independently. There seems to be no intron that arose from before the diversification of the P-Type ATPase superfamily. Namely, the present introns were inserted after the separation of eukaryotes and prokaryotes.

Loss of Sfpq Causes Long-Gene Transcriptopathy in the Brain

Genes specifically expressed in neurons contain members with extended long introns. Longer genes present a problem with respect to fulfilment of gene length transcription, and evidence suggests that dysregulation of long genes is a mechanism underlying neurodegenerative and psychiatric disorders. Here, we report the discovery that RNA-binding protein Sfpq is a critical factor for maintaining transcriptional elongation of long genes. We demonstrate that Sfpq co-transcriptionally binds to long introns and is required for sustaining long-gene transcription by RNA polymerase II through mediating the interaction of cyclin-dependent kinase 9 with the elongation complex. Phenotypically, Sfpq disruption caused neuronal apoptosis in developing mouse brains. Expression analysis of Sfpq-regulated genes revealed specific downregulation of developmentally essential neuronal genes longer than 100 kb in Sfpq-disrupted brains; those genes are enriched in associations with neurodegenerative and psychiatric diseases. The identified molecular machinery yields directions for targeted investigations of the association between long-gene transcriptopathy and neuronal diseases.

Retinoid derivative Tp80 exhibits anti-hepatitis C virus activity through restoration of GI-GPx expression†

Hepatitis C virus (HCV) is a positive‐sense single‐stranded RNA virus with an estimated infection in ∼180 million people worldwide, and its chronic infection leads to development of cirrhosis and hepatocellular carcinoma. Although recent development of direct acting antiviral (DAA) compounds improved anti‐HCV regimens, alternative therapeutic compounds are still demanded due to an expected emergence of escape mutants for those DAAs. In order to identify novel anti‐HCV agents, we conducted chemical library screening for 2086 compounds using HCV Rep‐Feo reporter replicon in Huh7 hepatoma cells. Our screening identified retinoid derivative Tp80, which inhibits replication of HCV Rep‐Feo (genotype 1b) and JFH1 HCV (genotype 2a) with 0.62 μM and 1.0 μM, respectively, of 50% effective concentration (EC50), at which cytotoxicity is not evident for host hepatocytes. Subsequent transcriptome profiling revealed Tp80 exhibits anti‐HCV activity through restoration of gastrointestinal glutathione peroxidase (GI‐GPx), suppression of which is responsible for HCV‐induced oxidative stress to facilitate HCV replication. Furthermore, comparison of Tp80 with other retinoid derivatives revealed Tp80 shows best potency in both GI‐GPx restoration and anti‐HCV activity among compounds we examined. In conclusion, our current study provides Tp80 as a promising candidate of anti‐HCV compound, suppressing host cellular oxidative stress through a restoration of GI‐GPx.

Synthetic ligand promotes gene expression by affecting GC sequence in promoter

A naphthyridine carbamate tetramer (NCT8) is a synthetic compound, which selectively binds to nucleic acids containing CGG/CGG sequence. Although NCT8 is a promising compound for a wide range of DNA and RNA based biotechnology such as modulation of specific gene expression, little is known about its behavior in human cells. In the present study, we investigated the changes induced in gene expression by NCT8. Genes differentially expressed in the presence of NCT8 in HeLa cells were identified by whole-transcriptome analysis. The whole-transcriptome analysis showed that NCT8 significantly induced up-regulation of specific genes, whose promoter region has GC-rich sequence.

Localization of Obg-Hflx and TrmE-Era Super Family Small GTPases in Various Organelles in Plant Cells

P-loop GTPases and related ATPases represent an abundant and remarkable group of proteins in bacteria, which perform essential biological functions. The Obg and Era superfamily comprises a group of ancient GTPases belonging to the TRAFAC (for translation factors) class. GTPases of the Obg/Era superfamily have been reported to be involved in several diverse bacterial functions, including ribosome assembly, DNA repair, sporulation, and morphological development. These GTPase are also conserved in eukaryotes. However, little is known about the biological role of these GTPases in eukaryotic cells. In this study, intensive search on gene and protein databases revealed that Arabidopsis thaliana have 10 (ten) proteins belong to the Obg-Hflx superfamily and 8 (eight) proteins belong to the TrmE-Era superfamily. We found that most bacterial homologues were targeted to chloroplasts (eight) or mitochondria (three) or both (two), whereas other Archaea related proteins were mainly targeted to nucleus (two), retained in the cytoplasm (two), or targeted to cytoplasm and nucleus. Furthermore, many Arabidopsis Obg/Era family genes were found to be essential for plant development in Arabidopsis. These results suggest that members of the GTP-binding Obg/Era family play crucial roles in the biogenesis and/or the functioning of plant organelles, including chloroplasts.