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Biomedical subjects

Takehiro Kusakabe

Publications and source records attributed to Takehiro Kusakabe.

At least 19 recordsLinked to original sources
PubMed2006

The centrosomal protein nephrocystin-6 is mutated in Joubert syndrome and activates transcription factor ATF4.

The molecular basis of nephronophthisis, the most frequent genetic cause of renal failure in children and young adults, and its association with retinal degeneration and cerebellar vermis aplasia in Joubert syndrome are poorly understood. Using positional cloning, we here identify mutations in the gene CEP290 as causing nephronophthisis. It encodes a protein with several domains also present in CENPF, a protein involved in chromosome segregation. CEP290 (also known as NPHP6) interacts with and modulates the activity of ATF4, a transcription factor implicated in cAMP-dependent renal cyst formation. NPHP6 is found at centrosomes and in the nucleus of renal epithelial cells in a cell cycle-dependent manner and in connecting cilia of photoreceptors. Abrogation of its function in zebrafish recapitulates the renal, retinal and cerebellar phenotypes of Joubert syndrome. Our findings help establish the link between centrosome function, tissue architecture and transcriptional control in the pathogenesis of cystic kidney disease, retinal degeneration, and central nervous system development.

Activating Transcription Factor 4↗
PubMed2006

DBTGR: a database of tunicate promoters and their regulatory elements.

The high similarity of tunicates and vertebrates during their development coupled with the transparency of tunicate larvae, their well-studied cell lineages and the availability of simple and efficient transgenesis methods makes of this subphylum an ideal system for the investigation of vertebrate physiological and developmental processes. Recently, the sequencing of two different Ciona genomes has lead to the identification of numerous genes. In order to better understand the regulation of these genes, a database was created containing information on regulation of tunicate genes collected from literature. It includes for instance information regarding the minimal promoter length, the transcription factors involved and their binding sites, as well as the localization of the gene expression. Additionally, binding sites for characterized transcription factors were predicted based on published in vitro recognition sites. Comparison of the promoters of homologous genes in different species is also provided to allow identification of conserved cis elements. At the time of writing, information about 184 promoters, containing 73 identified binding sites and >2000 newly predicted binding sites is available. This database is accessible at http://dbtgr.hgc.jp.

Animals↗
PubMed2005

Evolution of constrained gonadotropin-releasing hormone ligand conformation and receptor selectivity.

Gonadotropin-releasing hormone (GnRH) is the central regulator of reproduction in vertebrates. GnRHs have recently been identified in protochordates and retain the conserved N- and C-terminal domains involved in receptor binding and activation. GnRHs of the jawed vertebrates have a central achiral amino acid (glycine) that favors a type II' beta-turn such that the N- and C-terminal domains are closely apposed in binding the GnRH receptor. However, protochordate GnRHs have a chiral amino acid in this position, suggesting that they bind their receptors in a more extended form. We demonstrate here that a protochordate GnRH receptor does not distinguish GnRHs with achiral or chiral amino acids, whereas GnRH receptors of jawed vertebrates are highly selective for GnRHs with the central achiral glycine. The poor activity of the protochordate GnRH was increased >10-fold at vertebrate receptors by replacement of the chiral amino acid with glycine or a d-amino acid, which favor the type II' beta-turn. Structural analysis of the GnRHs using ion mobility-mass spectrometry and molecular modeling showed a greater propensity for a type II' beta-turn in GnRHs with glycine or a d-amino acid, which correlates with binding affinity at vertebrate receptors. These findings indicate that the substitution of glycine for a chiral amino acid in GnRH during evolution allows a more constrained conformation for receptor binding and that this subtle single amino acid substitution in a site remote from the ligand functional domains has marked effects on its structure and activity.

Amino Acid Sequence↗
PubMed2005

Nephrocystin-5, a ciliary IQ domain protein, is mutated in Senior-Loken syndrome and interacts with RPGR and calmodulin.

Nephronophthisis (NPHP) is the most frequent genetic cause of chronic renal failure in children. Identification of four genes mutated in NPHP subtypes 1-4 (refs. 4-9) has linked the pathogenesis of NPHP to ciliary functions. Ten percent of affected individuals have retinitis pigmentosa, constituting the renal-retinal Senior-Loken syndrome (SLSN). Here we identify, by positional cloning, mutations in an evolutionarily conserved gene, IQCB1 (also called NPHP5), as the most frequent cause of SLSN. IQCB1 encodes an IQ-domain protein, nephrocystin-5. All individuals with IQCB1 mutations have retinitis pigmentosa. Hence, we examined the interaction of nephrocystin-5 with RPGR (retinitis pigmentosa GTPase regulator), which is expressed in photoreceptor cilia and associated with 10-20% of retinitis pigmentosa. We show that nephrocystin-5, RPGR and calmodulin can be coimmunoprecipitated from retinal extracts, and that these proteins localize to connecting cilia of photoreceptors and to primary cilia of renal epithelial cells. Our studies emphasize the central role of ciliary dysfunction in the pathogenesis of SLSN.

Amino Acid Sequence↗
PubMed2005

Decoding cis-regulatory systems in ascidians.

Ascidians, or sea squirts, are lower chordates, and share basic gene repertoires and many characteristics, both developmental and physiological, with vertebrates. Therefore, decoding cis-regulatory systems in ascidians will contribute toward elucidating the genetic regulatory systems underlying the developmental and physiological processes of vertebrates. cis-Regulatory DNAs can also be used for tissue-specific genetic manipulation, a powerful tool for studying ascidian development and physiology. Because the ascidian genome is compact compared with vertebrate genomes, both intergenic regions and introns are relatively small in ascidians. Short upstream intergenic regions contain a complete set of cis-regulatory elements for spatially regulated expression of a majority of ascidian genes. These features of the ascidian genome are a great advantage in identifying cis-regulatory sequences and in analyzing their functions. Function of cis-regulatory DNAs has been analyzed for a number of tissue-specific and developmentally regulated genes of ascidians by introducing promoter-reporter fusion constructs into ascidian embryos. The availability of the whole genome sequences of the two Ciona species, Ciona intestinalis and Ciona savignyi, facilitates comparative genomics approaches to identify cis-regulatory DNAs. Recent studies demonstrate that computational methods can help identify cis-regulatory elements in the ascidian genome. This review presents a comprehensive list of ascidian genes whose cis-regulatory regions have been subjected to functional analysis, and highlights the recent advances in bioinformatics and comparative genomics approaches to cis-regulatory systems in ascidians.

Animals↗
PubMed2004

Computational discovery of DNA motifs associated with cell type-specific gene expression in Ciona.

Temporally and spatially co-expressed genes are expected to be regulated by common transcription factors and therefore to share cis-regulatory elements. In the ascidian Ciona intestinalis, the whole-genome sequences and genome-scale gene expression profiles allow the use of computational techniques to investigate cis-elements that control transcription. We collected 5' flanking sequences of 50 tissue-specific genes from genome databases of C. intestinalis and a closely related species Ciona savignyi. We searched for DNA motifs over-represented in upstream regions of a group of co-expressed genes. Several motifs were distributed predominantly in upstream regions of photoreceptor, pan-neuronal, or muscle-specific gene groups. One muscle-specific motif, M2, was distributed preferentially in regions from -200 to -100 bp relative to the translational start sites. Promoters of muscle-specific genes of C. intestinalis were isolated, connected with a green fluorescent protein gene (GFP), and introduced into C. intestinalis embryos. In muscle cells, these promoters specifically drove GFP expression, which mutations of the M2 sites greatly reduced. When M2 sites were located upstream of a basal promoter, the reporter GFP was specifically expressed in muscle cells. These results suggest the validity of our computational prediction of cis-regulatory elements. Thus, bioinformatics can help identify cis-regulatory elements involved in chordate development.

Animals↗
PubMed2004

Localization of mRNAs encoding alpha and beta subunits of soluble guanylyl cyclase in the brain of rainbow trout: comparison with the distribution of neuronal nitric oxide synthase.

Detailed distribution of mRNAs encoding alpha and beta subunits of soluble guanylyl cyclase (sGC) was examined in the brain of rainbow trout by in situ hybridization. In addition, distribution of nitric oxide synthase (NOS) was mapped in adjacent parallel sections by neuronal NOS (nNOS) immunocytochemistry and NADPH-diaphorase (NADPHd) histochemistry. Following application of digoxigenin-labeled riboprobes for sGC alpha and beta subunit mRNAs, we found comparatively intense hybridization signals in the telencephalon, preoptic area, thalamus, hypothalamus, pretectum and tegmentum. Both nNOS immunocytochemistry and NADPHd histochemistry showed extensive distribution of nitroxergic neurons in various brain areas, although various degrees of dissociation of nNOS immunoreactivity (ir) and NADPHd staining were detected. In comparison with sGC subunit mRNAs, nNOS signals were more widely distributed in many neurons, including parvocellular neurons in the preoptic area, nucleus anterior tuberis in the hypothalamus, periventricular neurons in the optic tectum, most of the rhombencephalic neurons and pituitary cells. However, wide overlaps of sGC mRNA-containing neurons and nNOS-positive neurons were observed in the olfactory bulb, telencephalon, preoptic area, thalamus, hypothalamus, pretectum, optic tectum, tegmentum and cerebellum. The widespread overlapping in sGC subunit mRNAs and nNOS distribution suggests a role for sGC in various neuronal functions, such as processing of olfactory and visual signals and neuroendocrine function, possibly via NO/cGMP signaling in the brain of rainbow trout.

Animals↗
PubMed2004

Identification of neuron-specific promoters in Ciona intestinalis.

We isolated 5' flanking regions of four genes, Ci-Galphai1, Ci-arr, Ci-vAChTP, and Ci-vGAT, each of which is expressed in distinct sets of neurons in the central nervous system of the ascidian Ciona intestinalis, and we examined their function by introducing green fluorescent protein (GFP)-fusion constructs into Ciona embryos. The reporter gene driven by the 5' flanking region of Ci-Galphai1, Ci-arr, and Ci-vAChTP recapitulated the endogenous gene expression patterns, while that of Ci-vGAT can drive GFP expression in particular subsets of neurons expressing the endogenous gene. Deletion analysis revealed that the Ci-Galphai1 promoter consists of multiple regulatory modules controlling the expression in different types of cells. The GFP fluorescence enabled visualization of cell bodies and axons of different sets of neurons in ascidian larvae. These promoters can be a powerful tool for studying molecular mechanisms of neuronal development as well as neuron networks and functions in ascidians.

Amino Acid Sequence↗
PubMed2003

Structure, expression, and cluster organization of genes encoding gonadotropin-releasing hormone receptors found in the neural complex of the ascidian Ciona intestinalis.

Gonadotropin-releasing hormone (GnRH) controls reproductive functions in vertebrates. In the present study, two distinct homologues (Ci-GnRHR1 and Ci-GnRHR2) of the vertebrate GnRH receptor (GnRHR) were identified by cDNA cloning from the neural complex of the ascidian Ciona intestinalis. The Ci-GnRHR1 and Ci-GnRHR2 genes are closely linked to each other and form a cluster with another GnRHR-like gene in the genome. Ci-GnRHR1 and Ci-GnRHR2 are more closely related to vertebrate GnRHRs than to the GnRHR-related protein of Drosophila. The phylogenetic analysis indicates that vertebrates and urochordates independently acquired multiple GnRHRs by gene duplications that occurred during the evolution of each lineage. A voltage clamp of Xenopus oocytes injected with synthetic Ci-GnRHR1 mRNA revealed inward currents in response to an ascidian form of GnRH, suggesting that Ci-GnRHR1 is a bona-fide GnRHR. Expression patterns of Ci-GnRHR1 and Ci-GnRHR2 suggest that a GnRH signaling system is involved in regulation of neuronal and reproductive processes as well as in other physiological functions in ascidians.

Amino Acid Sequence↗
PubMed2003

Targeted knockdown of an opsin gene inhibits the swimming behaviour photoresponse of ascidian larvae.

The sequencing of the ascidian Ciona intestinalis genome was completed at the end of 2002. Effective targeted gene knockdown in this model chordate would greatly enhance understanding of how the genes affect the function of the neurons that underlie behaviour. We show here that antisense morpholinos (MOs) are effective and specific translational inhibitors in C. intestinalis larvae. The larvae developed from eggs injected with a Ci-opsin1 MO lost their photoresponse, which affected their swimming behaviour. Immunohistochemical analysis showed that the expression of Ci-opsin1, the visual pigments in the photoreceptor of the ocellus, had been lost in the larvae with the Ci-opsin1 MO. The inhibition of the photic behaviour of the knockdown larvae is solely due to the suppression of the synthesis of the visual pigments in the photoreceptors. These are the first results showing the knockdown of an ascidian gene and the elucidation of that gene's role in ascidian larval behaviour.

Animals↗
PubMed2003

Origin of the vertebrate visual cycle: genes encoding retinal photoisomerase and two putative visual cycle proteins are expressed in whole brain of a primitive chordate.

The absorption of light by rhodopsin leads to the cis-to-trans isomerization of the chromophore to generate all-trans-retinal. In the visual cycle, the resultant all-trans-retinal is converted back into the 11-cis-retinal. In the mammalian eye, the retinal pigment epithelium (RPE) plays an essential role in the visual cycle. We have identified cDNA clones encoding three putative visual cycle proteins, homologs of mammalian retinal G-protein-coupled receptor (RGR), cellular retinaldehyde-binding protein (CRALBP) and beta-carotene 15,15'-monooxygenase (BCO)/RPE65 in a primitive chordate, ascidian Ciona intestinalis. The mRNAs for these proteins are specifically expressed in the central nervous system during embryonic development. In the larva, the transcripts were widely distributed in the brain vesicle and visceral ganglion. Since visual pigment, Ci-opsin1, is solely expressed in photoreceptor cells, the visual cycle in this primitive chordate may take place in two compartments, which are coupled into a cycle by the direct flow of retinoids though the intercellular matrix. The Ci-opsin3, an ascidian homolog of mammalian RGR, was expressed in HEK 293S cells and purified after binding of retinal. The chromophore of Ci-opsin3 is in an all-trans-retinal and it is isomerized to an 11-cis-form upon absorption of light. Mammalian CRALBP and BCO/RPE65 are believed to play critical roles in the process of reisomerization of all-trans-retinoid to 11-cis-retinoid in RPE. The present data suggest that isomerization of all-trans-retinoid to 11-cis-retinoid occurs in the brain vesicle and visceral ganglion of a primitive chordate.

Amino Acid Sequence↗
PubMed2003

Origin of the vertebrate visual cycle: II. Visual cycle proteins are localized in whole brain including photoreceptor cells of a primitive chordate.

The visual cycle system in a primitive chordate, ascidian Ciona intestinalis, was studied by whole-mount in situ hybridization and by whole-mount immunohistochemistry. Three visual cycle proteins, Ciona homologue of RGR (Ci-opsin3), CRALBP (Ci-CRALBP), and BCO/RPE65 (Ci-BCO/RPE65) were widely distributed in the brain vesicle and visceral ganglion. To identify the visual cycle system in a primitive chordate, we compared the localization of photoreceptor-specific proteins (visual pigment and arrestin) and visual cycle proteins (Ci-opsin3 and Ci-CRALBP). The ascidian visual cycle is composed of two cellular compartments, the photoreceptors and the brain vesicle, but some photoreceptor cells also contain visual cycle proteins.

Animals↗
PubMed2002

Ciona intestinalis cDNA projects: expressed sequence tag analyses and gene expression profiles during embryogenesis.

Ascidians are primitive chordates. Their fertilized egg develops quickly into a tadpole-type larva, which consists of a small number but distinct types of cells, including those of epidermis, central nervous system with two sensory organs, endoderm and mesenchyme in the trunk, and notochord and muscle in the tail. This configuration of the ascidian tadpole is thought to represent the most simplified and primitive chordate body plan. In addition, the free-swimming and non-feeding larvae metamorphose into sessile and filter-feeding adults. The genome size of Ciona intestinalis is estimated to be about 160 Mb, and the number of genes approximately 15,500. The present Ciona cDNA projects focused on gene expression profiles of fertilized eggs, 32-110-cell stage embryos, tailbud embryos, larvae, and young adults. Expressed sequence tags (ESTs) of the 5'-most end and 3'-most end of more than 3000 clones were determined at each developmental stage, and the clones were categorized into independent clusters using the 3'-end sequences. Nearly 1000 clusters of them were then analyzed in detail of their sequences against a BLASTX search. This analysis demonstrates that, on average, half of the clusters showed proteins with sequence similarities to known proteins and the other half did not show sequence similarities to known proteins. Genes with sequence similarities were further categorized into three major subclasses, depending on their functions. Furthermore, the expression profiles of all of the clusters were analyzed by whole-mount in situ hybridization. This analysis highlights gene expression patterns characteristic to each developmental stage. As a result, the present study provides many new molecular markers for each of the tissues and/or organs that constitutes the Ciona tailbud embryo. This sequence information will be used for further comparative genome studies to explore molecular mechanisms involved in the formation of one of the most primitive chordate body plans. All of the data fully characterized may be viewed at the web site http://ghost.zool.kyoto-u.ac.jp.

Animals↗
PubMed2002

Gene expression profiles in tadpole larvae of Ciona intestinalis.

A set of 12,779 expressed sequence tags (ESTs), both the 5'-most and 3'-most ends, derived from Ciona intestinalis tadpole larvae was categorized into 3521 independent clusters, from which 1013 clusters corresponding to 9424 clones were randomly selected to analyze genetic information and gene expression profiles. When compared with sequences in databases, 545 of the clusters showed significant matches (P < E-15) with reported proteins, while 153 showed matches with putative proteins for which there is not enough information to categorize their function, and 315 had no significant sequence similarities to known proteins. Sequence-similarity analyses of the 545 clusters in relation to the biological functions demonstrated that 407 of them have functions that many kinds of cells use, 104 are associated with cell-cell communication, and 34 are transcription factors or other gene-regulatory proteins. Sequence prevalence distribution analysis demonstrated that more than one-half of the mRNAs are rare mRNAs. All of the 1013 clusters were subjected to whole-mount in situ hybridization to analyze the gene expression profile in the tadpole larva. A total of 361 clusters showed expression specific to a certain tissue or organ: 96 showed epidermis-specific expression, 60 were specific to the nervous system, 108 to endoderm, 34 to mesenchyme, 5 to trunk lateral cells, 4 to trunk ventral cells, 23 to notochord, 28 to muscle, and 3 to siphon rudiments. In addition, 190 clusters showed expression in multiple tissues. Moreover, nervous system-specific genes showed intriguing expression patterns dependent on the cluster. The present study highlights a broad spectrum of genes that are used in the formation of one of the most primitive chordate body plans as well as for the function of various types of tissue and organ and also provides molecular markers for individual tissues and organs constituting the Ciona larva.

Amphibians↗
PubMed2002

Central nervous system-specific expression of G protein alpha subunits in the ascidian Ciona intestinalis.

Heterotrimeric G proteins play crucial roles as mediators of signaling by many extracellular stimuli. The receptors that activate G proteins constitute the largest and most diverse family of cell surface molecules involved in signal transmission of metazoan cells. To investigate G protein signaling in the central nervous system (CNS) of chordates, we isolated cDNA fragments encoding five different G protein alpha subunits (CiGalpha(x), CiGalpha(q), CiGalpha(i1a), CiGalpha(i1b), and CiGalpha(i2)) from larvae of the ascidian, a simple chordate, Ciona intestinalis. In situ hybridization analysis revealed that each isoform had distinct patterns of spatial distribution in embryos. Among them, CiGalpha(i1a) and CiG alpha(i1b) mRNAs were specifically expressed in the CNS of the larva, whereas CiGalpha(q) transcripts were expressed in small parts of the trunk epidermis and the tip of the tail, but not in the CNS. The CiGalpha(x) expression was widely observed throughout the trunk and tail of the embryos, and the signals were stronger in the epidermis, mesenchyme, and tail muscle cells. Comparison of cDNA sequences and the exon-intron organization indicate that CiGalpha(i1a) and CiGalpha(i1b) are produced by alternative splicing of transcripts from a single gene, CiGalpha(i1). In the cleavage and gastrula stages, transcripts of CiGalpha(i1) were widely distributed in embryos, and the expression then became restricted to the CNS of tailbud embryos and larvae. An exhaustive search has failed to find transducin-type alpha subunits in C. intestinalis. Since CiGalpha(i1) is expressed in the ocellus, CiGalpha(i1) may mediate signals from Ci-opsin1, a visual pigment of the ocellus photoreceptor cells.

Alternative Splicing↗
PubMedDate not supplied

Origin of the vertebrate visual cycle: III. Distinct distribution of RPE65 and beta-carotene 15,15'-monooxygenase homologues in Ciona intestinalis.

We previously identified three genes that encode putative visual cycle proteins that are homologues of retinal G-protein coupled receptor (Ci-opsin3), cellular retinaldehyde-binding protein (Ci-CRALBP) and beta-carotene 15,15'-monooxygenase (Ci-BCO) in the ascidian Ciona intestinalis. Ci-opsin3 and Ci-CRALBP are localized in both ocellus photoreceptor cells and surrounding non-photoreceptor cells in the brain vesicle of the larva. In the present study, we investigated the possible role and evolutionary origin of the BCO/RPE65 family in the visual cycle by analyzing Ci-BCO localization by immunohistochemistry and by identifying a novel gene that encodes a homologue of retinal pigment epithelium-specific 65 kDa protein (Ci-RPE65) in C. intestinalis. In situ hybridization and expressed sequence tag (EST) profiles consistently suggest that Ci-RPE65 is not significantly expressed in the ocellus and brain vesicle of the larva. Ci-RPE65 is expressed in the neural complex, a photoreceptor organ of the adult ascidian, at a level comparable to that of Ci-opsin3 and Ci-CRALBP. Ci-RPE65 is also expressed in various adult tissues, including the gill, body wall and intestine, suggesting that Ci-RPE65 plays a role in addition to that in the visual cycle. In contrast, Ci-BCO is predominantly localized in ocellus photoreceptor cells of the larva. The larval visual cycle seems to use Ci-opsin3 as a photo-isomerase. Our results also suggest that the RPE65-dependent visual cycle is used in the adult photoreceptors of a primitive chordate.

Amino Acid Sequence↗