A genomewide survey of developmentally relevant genes in Ciona intestinalis. V. Genes for receptor tyrosine kinase pathway and Notch signaling pathway

Protein kinases and protein phosphatases encoded in the Ciona robusta genome

Protein kinases (PKs) and protein phosphatases (PPs) regulate the phosphorylation of proteins that are involved in a variety of biological processes. To study such biological processes systematically, it is important to know the whole repertoire of PKs and PPs encoded in a genome. In the present study, we surveyed the genome of an ascidian (Ciona robusta or Ciona intestinalis type A) to comprehensively identify the genes that encoded PKs and PPs. Because ascidians belong to the sister group of vertebrates, a comparison of the whole repertoire of PKs and PPs of ascidians with those of vertebrates may help to delineate the complements of these proteins that were present in the last common ancestor of these two groups of animals. Our results show that the repertory of PPs was much more expanded in vertebrates than the repertory of PKs. We also showed that approximately 75% of PKs and PPs were expressed during development from eggs to larvae. Thus, the present study provides catalogs for PKs and PPs encoded in the ascidian genome. These catalogs will be useful for systematic studies of biological processes that involve phosphorylation and for evolutionary studies of the origin of vertebrates.

Quantitative Dissection of the Proximal Ciona brachyury Enhancer

A major goal in biology is to understand the rules by which cis-regulatory sequences control spatially and temporally precise expression patterns. Here we present a systematic dissection of the proximal enhancer for the notochord-specific transcription factor brachyury in the ascidian chordate Ciona. The study uses a quantitative image-based reporter assay that incorporates a dual-reporter strategy to control for variable electroporation efficiency. We identified and mutated multiple predicted transcription factor binding sites of interest based on statistical matches to the JASPAR binding motif database. Most sites (Zic, Ets, FoxA, RBPJ) were selected based on prior knowledge of cell fate specification in both the primary and secondary notochord. We also mutated predicted Brachyury sites to investigate potential autoregulation as well as Fos/Jun (AP1) sites that had very strong matches to JASPAR. Our goal was to quantitatively define the relative importance of these different sites, to explore the importance of predicted high-affinity versus low-affinity motifs, and to attempt to design mutant enhancers that were specifically expressed in only the primary or secondary notochord lineages. We found that the mutation of all predicted high-affinity sites for Zic, FoxA or Ets led to quantifiably distinct effects. The FoxA construct caused a severe loss of reporter expression whereas the Ets construct had little effect. A strong Ets phenotype was only seen when much lower-scoring binding sites were also mutated. This supports the enhancer suboptimization hypothesis proposed by Farley and Levine but suggests that it may only apply to some but not all transcription factor families. We quantified reporter expression separately in the two notochord lineages with the expectation that Ets mutations and RBPJ mutations would have distinct effects given that primary notochord is induced by Ets-mediated FGF signaling whereas secondary notochord is induced by RBPJ/Su(H)-mediated Notch/Delta signaling. We found, however, that ETS mutations affected primary and secondary notochord expression relatively equally and that RBPJ mutations were only moderately more severe in their effect on secondary versus primary notochord. Our results point to the promise of quantitative reporter assays for understanding cis-regulatory logic but also highlight the challenge of arbitrary statistical thresholds for predicting potentially important sites.

JNK Mediates Differentiation, Cell Polarity and Apoptosis During Amphioxus Development by Regulating Actin Cytoskeleton Dynamics and ERK Signalling

c-Jun N-terminal kinase (JNK) is a multi-functional protein involved in a diverse array of context-dependent processes, including apoptosis, cell cycle regulation, adhesion, and differentiation. It is integral to several signalling cascades, notably downstream of non-canonical Wnt and mitogen activated protein kinase (MAPK) signalling pathways. As such, it is a key regulator of cellular behaviour and patterning during embryonic development across the animal kingdom. The cephalochordate amphioxus is an invertebrate chordate model system straddling the invertebrate to vertebrate transition and is thus ideally suited for comparative studies of morphogenesis. However, next to nothing is known about JNK signalling or cellular processes in this lineage. Pharmacological inhibition of JNK signalling using SP600125 during embryonic development arrests gastrula invagination and causes convergence extension-like defects in axial elongation, particularly of the notochord. Pharynx formation and anterior oral mesoderm derivatives like the preoral pit are also affected. This is accompanied by tissue-specific transcriptional changes, including reduced expression of six3/6 and wnt2 in the notochord, and ectopic wnt11 in neurulating embryos treated at late gastrula stages. Cellular delamination results in accumulation of cells in the gut cavity and a dorsal fin-like protrusion, followed by secondary Caspase-3-mediated apoptosis of polarity-deficient cells, a phenotype only partly rescued by co-culture with the pan-Caspase inhibitor Z-VAD-fmk. Ectopic activation of extracellular signal regulated kinase (ERK) signalling in the neighbours of extruded notochord and neural cells, possibly due to altered adhesive and tensile properties, as well as defects in cellular migration, may explain some phenotypes caused by JNK inhibition. Overall, this study supports conserved functions of JNK signalling in mediating the complex balance between cell survival, apoptosis, differentiation, and cell fate specification during cephalochordate morphogenesis.

Cell geometry, signal dampening, and a bimodal transcriptional response underlie the spatial precision of an ERK-mediated embryonic induction

Precise control of lineage segregation is critical for the development of multicellular organisms, but our quantitative understanding of how variable signaling inputs are integrated to activate lineage-specific gene programs remains limited. Here, we show how precisely two out of eight ectoderm cells adopt neural fates in response to ephrin and FGF signals during ascidian neural induction. In each ectoderm cell, FGF signals activate ERK to a level that mirrors its cell contact surface with FGF-expressing mesendoderm cells. This gradual interpretation of FGF inputs is followed by a bimodal transcriptional response of the immediate early gene, Otx, resulting in its activation specifically in the neural precursors. At low levels of ERK, Otx is repressed by an ETS family transcriptional repressor, ERF2. Ephrin signals are critical for dampening ERK activation levels across ectoderm cells so that only neural precursors exhibit above-threshold levels, evade ERF repression, and "switch on" Otx transcription.

A Nearly Complete Genome of Ciona intestinalis Type A (C. robusta) Reveals the Contribution of Inversion to Chromosomal Evolution in the Genus Ciona

Since its initial publication in 2002, the genome of Ciona intestinalis type A (Ciona robusta), the first genome sequence of an invertebrate chordate, has provided a valuable resource for a wide range of biological studies, including developmental biology, evolutionary biology, and neuroscience. The genome assembly was updated in 2008, and it included 68% of the sequence information in 14 pairs of chromosomes. However, a more contiguous genome is required for analyses of higher order genomic structure and of chromosomal evolution. Here, we provide a new genome assembly for an inbred line of this animal, constructed with short and long sequencing reads and Hi-C data. In this latest assembly, over 95% of the 123 Mb of sequence data was included in the chromosomes. Short sequencing reads predicted a genome size of 114-120 Mb; therefore, it is likely that the current assembly contains almost the entire genome, although this estimate of genome size was smaller than previous estimates. Remapping of the Hi-C data onto the new assembly revealed a large inversion in the genome of the inbred line. Moreover, a comparison of this genome assembly with that of Ciona savignyi, a different species in the same genus, revealed many chromosomal inversions between these two Ciona species, suggesting that such inversions have occurred frequently and have contributed to chromosomal evolution of Ciona species. Thus, the present assembly greatly improves an essential resource for genome-wide studies of ascidians.

FGF signaling repertoire of the indirect developing hemichordate Ptychodera flava

Fibroblast growth factors (FGFs) are a group of ligands that play multiple roles during development by transducing signals through FGF receptors (FGFRs) to downstream factors. At least 22 FGF ligands and 4 receptors have been identified in vertebrates, while six to eight FGF ligands and a single FGFR are present in invertebrate chordates, such as tunicates and amphioxus. The chordate FGFs can be categorized into at least seven subfamilies, and the members of which expanded during the evolution of early vertebrates. In contrast, only one FGF and two FGFRs have been found in sea urchins. Thus, it is unclear whether the FGF subfamilies duplicated in the lineage leading to the chordates, or sea urchins lost several fgf genes. Analyses of the FGF signaling repertoire in hemichordates, which together with echinoderms form the closest group to the chordates, may provide insights into the evolution of FGF signaling in deuterostomes. In this study, we identified five FGFs and three FGFRs from Ptychodera flava, an indirect-developing hemichordate acorn worm. Phylogenetic analyses revealed that hemichordates possess a conserved FGF8/17/18 in addition to several putative hemichordate-specific FGFs. Analyses of sequence similarity and protein domain organizations suggested that the sea urchin and hemichordate FGFRs arose from independent lineage-specific duplications. Furthermore, the acorn worm fgf and fgfr genes were demonstrated to be expressed during P. flava embryogenesis. These results set the foundations for further functional studies of FGF signaling in hemichordates and provided insights into the evolutionary history of the FGF repertoire.

Gene regulatory systems that control gene expression in the Ciona embryo

Transcriptional control of gene expression is one of the most important regulatory systems in animal development. Specific gene expression is basically determined by combinatorial regulation mediated by multiple sequence-specific transcription factors. The decoding of animal genomes has provided an opportunity for us to systematically examine gene regulatory networks consisting of successive layers of control of gene expression. It remains to be determined to what extent combinatorial regulation encoded in gene regulatory networks can explain spatial and temporal gene-expression patterns. The ascidian Ciona intestinalis is one of the animals in which the gene regulatory network has been most extensively studied. In this species, most specific gene expression patterns in the embryo can be explained by combinations of upstream regulatory genes encoding transcription factors and signaling molecules. Systematic scrutiny of gene expression patterns and regulatory interactions at the cellular resolution have revealed incomplete parts of the network elucidated so far, and have identified novel regulatory genes and novel regulatory mechanisms.

Insulin-like genes in ascidians: findings in Ciona and hypotheses on the evolutionary origins of the pancreas

Insulin plays an extensively characterized role in the control of sugar metabolism, growth and homeostasis in a wide range of organisms. In vertebrate chordates, insulin is mainly produced by the beta cells of the endocrine pancreas, while in non-chordate animals insulin-producing cells are mainly found in the nervous system and/or scattered along the digestive tract. However, recent studies have indicated the notochord, the defining feature of the chordate phylum, as an additional site of expression of insulin-like peptides. Here we show that two of the three insulin-like genes identified in Ciona intestinalis, an invertebrate chordate with a dual life cycle, are first expressed in the developing notochord during embryogenesis and transition to distinct areas of the adult digestive tract after metamorphosis. In addition, we present data suggesting that the transcription factor Ciona Brachyury is involved in the control of notochord expression of at least one of these genes, Ciona insulin-like 2. Finally, we review the information currently available on insulin-producing cells in ascidians and on pancreas-related transcription factors that might control their expression.

Transcriptome dynamics in early embryos of the ascidian, Ciona intestinalis

Maternally provided mRNAs and proteins direct early development and activate the zygotic genome. Using microarrays, we examined the dynamics of transcriptomes during the early development of a basal chordate, Ciona intestinalis. Microarray analysis of unfertilized eggs, as well as 8-, and 16- and 32-cell embryos revealed that nearly half of the genes encoded in the genome were expressed maternally, and that approximately only one-fourth of these genes were expressed at similar levels among eggs obtained from different individuals. Genes encoding proteins involved in protein phosphorylation were enriched in this latter group. More than 90% of maternal RNAs were not reduced before the 16-cell stage when the zygotic developmental program begins. Additionally we obtained gene expression profiles of individual blastomeres from the 8- and 16-cell embryos. On the basis of these profiles, we concluded that the posterior-most localization, which has been reported for over 20 different transcripts, is the only major localization pattern of maternal transcripts. Our data also showed that maternal factors establish only nine distinct patterns of zygotic gene expression at the 16-cell stage. Therefore, one of the main developmental functions of maternally supplied information is to establish these nine distinct expression patterns in the 16-cell embryo. The dynamics of transcriptomes in early-stage embryos provides a foundation for studying how maternal information starts the zygotic program.

Heart genetics in a small package, exploiting the condensed genome of Ciona intestinalis

Defects in the initial establishment of cardiogenic cell fate are likely to contribute to pervasive human congenital cardiac abnormalities. However, the molecular underpinnings of nascent cardiac fate induction have proven difficult to decipher. In this review we explore the participation of extracellular, cellular and nuclear factors in comprehensive specification networks. At each level, we elaborate on insights gained through the study of cardiogenesis in the invertebrate chordate Ciona intestinalis and propose productive lines of future research. In-depth discussion of pre-cardiac induction is intended to serve as a paradigm, illustrating the potential use of Ciona to elucidate comprehensive networks underlying additional aspects of chordate cardiogenesis, including directed migration and subspecification of cardiac and pharyngeal lineages.

Enhancer activity sensitive to the orientation of the gene it regulates in the chordate genome

Enhancers are flexible in terms of their location and orientation relative to the genes they regulate. However, little is known about whether the flexibility can be applied in every combination of enhancers and genes. Enhancer detection with transposable elements is a powerful method to identify enhancers in the genome and to create marker lines expressing fluorescent proteins in a tissue-specific manner. In the chordate Ciona intestinalis, this method has been established with a Tc1/mariner superfamily transposon Minos. Previously, we created the enhancer detection line E[MiTSAdTPOG]15 (E15) that specifically expresses green fluorescent protein (GFP) in the central nervous system (CNS) after metamorphosis. In this study, we identified the causal insertion site of the transgenic line. There are two genes flanking the causal insertion of the E15 line, and the genomic region around the insertion site contains the enhancers responsible for the expression in the endostyle and gut in addition to the CNS. We found that the endostyle and gut enhancers show sensitivity to the orientation of the GFP gene for their enhancer activity. Namely, the enhancers cannot enhance the expression of GFP which is inserted at the same orientation as the E15 line, while the enhancers can enhance GFP expression inserted at the opposite orientation. The CNS enhancer can enhance GFP expression in both orientations. The DNA element adjacent to the endostyle enhancer is responsible for the orientation sensitivity of the enhancer. The different sensitivity of the enhancers to the orientation of the transgene is a cause of CNS-specific GFP expression in the E15 line.

Establishment of enhancer detection lines expressing GFP in the gut of the ascidian Ciona intestinalis

The gut is a tubular, endodermal organ for digesting food and absorbing nutrients. In this study, we characterized eight enhancer detection lines that express green fluorescent protein (GFP) in the whole or part of the digestive tube of the ascidian Ciona intestinalis. Three enhancer detection lines for the pyloric gland, a structure associated with the digestive tube, were also analyzed. These lines are valuable markers for analyzing the mechanisms of development of the gut. Based on the GFP expression of the enhancer detection lines together with morphological characteristics, the digestive tube of Ciona can be subdivided into at least 10 compartments in which different genetic cascades operate. Causal insertion sites of the enhancer detection lines were identified, and the expression pattern of the genes near the insertion sites were characterized by means of whole-mount in situ hybridization. We have characterized four and two genes that were specifically or strongly expressed in the digestive tube and pyloric gland, respectively. The present data provide the basic information and useful resources for studying gut formation in Ciona.

Transcriptional enhancers in ascidian development

The study of cis-regulatory DNAs that control developmental gene expression is integral to the modeling of comprehensive genomic regulatory networks for embryogenesis. Ascidian embryos provide a unique opportunity for the analysis of cis-regulatory DNAs with cellular resolution in the context of a simple but typical chordate body plan. Here, we review landmark studies that have laid the foundations for the study of transcriptional enhancers, among other cis-regulatory DNAs, and their roles in ascidian development. The studies using ascidians of the Ciona genus have capitalized on a unique electroporation technique that permits the simultaneous transfection of hundreds of fertilized eggs, which develop rapidly and express transgenes with little mosaicism. Current studies using the ascidian embryo benefit from extensively annotated genomic resources to characterize transcript models in silico. The search for functional noncoding sequences can be guided by bioinformatic analyses combining evolutionary conservation, gene coexpression, and combinations of overrepresented short-sequence motifs. The power of the transient transfection assays has allowed thorough dissection of numerous cis-regulatory modules, which provided insights into the functional constraints that shape enhancer architecture and diversification. Future studies will benefit from pioneering stable transgenic lines and the analysis of chromatin states. Whole genome expression, functional and DNA binding data are being integrated into comprehensive genomic regulatory network models of early ascidian cell specification with a single-cell resolution that is unique among chordate model systems.

The maternal genes Ci-p53/p73-a and Ci-p53/p73-b regulate zygotic ZicL expression and notochord differentiation in Ciona intestinalis embryos

I isolated a Ciona intestinalis homolog of p53, Ci-p53/p73-a, in a microarray screen of rapidly degraded maternal mRNA by comparing the transcriptomes of unfertilized eggs and 32-cell stage embryos. Higher expression of the gene in eggs and lower expression in later embryonic stages were confirmed by whole-mount in situ hybridization (WISH) and quantitative reverse transcription-PCR (qRT-PCR); expression was ubiquitous in eggs and early embryos. Knockdown of Ci-p53/p73-a by injection of antisense morpholino oligonucleotides (MOs) severely perturbed gastrulation cell movements and expression of notochord marker genes. A key regulator of notochord differentiation in Ciona embryos is Brachyury (Ci-Bra), which is directly activated by a zic-like gene (Ci-ZicL). The expression of Ci-ZicL and Ci-Bra in A-line notochord precursors was downregulated in Ci-p53/p73-a knockdown embryos. Maternal expression of Ci-p53/p73-b, a homolog of Ci-p53/p73-a, was also detected. In Ci-p53/p73-b knockdown embryos, gastrulation cell movements, expression of Ci-ZicL and Ci-Bra in A-line notochord precursors, and expression of notochord marker gene at later stages were perturbed. The upstream region of Ci-ZicL contains putative p53-binding sites. Cis-regulatory analysis of Ci-ZicL showed that these sites are involved in expression of Ci-ZicL in A-line notochord precursors at the 32-cell and early gastrula stages. These results suggest that p53 genes are maternal factors that play a crucial role in A-line notochord differentiation in C. intestinalis embryos by regulating Ci-ZicL expression.

Ciona genetics

Ascidians, such as Ciona, are invertebrate chordates with simple embryonic body plans and small, relatively non-redundant genomes. Ciona genetics is in its infancy compared to many other model systems, but it provides a powerful method for studying this important vertebrate outgroup. Here we give basic methods for genetic analysis of Ciona, including protocols for controlled crosses both by natural spawning and by the surgical isolation of gametes; the identification and propagation of mutant lines; and strategies for positional cloning.

Eph regulates dorsoventral asymmetry of the notochord plate and convergent extension-mediated notochord formation

BACKGROUND

The notochord is a signaling center required for the patterning of the vertebrate embryonic midline, however, the molecular and cellular mechanisms involved in the formation of this essential embryonic tissue remain unclear. The urochordate Ciona intestinalis develops a simple notochord from 40 specific postmitotic mesodermal cells. The precursors intercalate mediolaterally and establish a single array of disk-shaped notochord cells along the midline. However, the role that notochord precursor polarization, particularly along the dorsoventral axis, plays in this morphogenetic process remains poorly understood.

METHODOLOGY/PRINCIPAL FINDINGS

Here we show that the notochord preferentially accumulates an apical cell polarity marker, aPKC, ventrally and a basement membrane marker, laminin, dorsally. This asymmetric accumulation of apicobasal cell polarity markers along the embryonic dorsoventral axis was sustained in notochord precursors during convergence and extension. Further, of several members of the Eph gene family implicated in cellular and tissue morphogenesis, only Ci-Eph4 was predominantly expressed in the notochord throughout cell intercalation. Introduction of a dominant-negative Ci-Eph4 to notochord precursors diminished asymmetric accumulation of apicobasal cell polarity markers, leading to defective intercalation. In contrast, misexpression of a dominant-negative mutant of a planar cell polarity gene Dishevelled preserved asymmetric accumulation of aPKC and laminin in notochord precursors, although their intercalation was incomplete.

CONCLUSIONS/SIGNIFICANCE

Our data support a model in which in ascidian embryos Eph-dependent dorsoventral polarity of notochord precursors plays a crucial role in mediolateral cell intercalation and is required for proper notochord morphogenesis.

Neuropeptides, hormone peptides, and their receptors in Ciona intestinalis: an update

The critical phylogenetic position of ascidians leads to the presumption that neuropeptides and hormones in vertebrates are highly likely to be evolutionarily conserved in ascidians, and the cosmopolitan species Ciona intestinalis is expected to be an excellent deuterostome Invertebrate model for studies on neuropeptides and hormones. Nevertheless, molecular and functional characterization of Ciona neuropeptides and hormone peptides was restricted to a few peptides such as a cholecystokinin (CCK)/gastrin peptide, cionin, and gonadotropin-releasing hormones (GnRHs). In the past few years, mass spectrometric analyses and database searches have detected Ciona orthologs or prototypes of vertebrate peptides and their receptors, including tachykinin, insulin/relaxin, calcitonin, and vasopressin. Furthermore, studies have shown that several Ciona peptides, including vasopressin and a novel GnRH-related peptide, have acquired ascidian-specific molecular forms and/or biological functions. These findings provided indisputable evidence that ascidians, unlike other invertebrates (including the traditional protostome model animals), possess neuropeptides and hormone peptides structurally and functionally related to vertebrate counterparts, and that several peptides have uniquely diverged in ascidian evolutionary lineages. Moreover, recent functional analyses of Ciona tachykinin in the ovary substantiated the novel tachykininergic protease-assoclated oocyte growth pathway, which could not have been revealed in studies on vertebrates. These findings confirm the outstanding advantages of ascidians in understanding the neuroscience, endocrinology, and evolution of vertebrate neuropeptides and hormone peptides. This article provides an overview of basic findings and reviews new knowledge on ascidian neuropeptides and hormone peptides.

Ciona intestinalis and Oxycomanthus japonicus, representatives of marine invertebrates

The study of marine invertebrates is useful in various biological research fields. However, genetic analyses of these animals are limited, mainly due to difficulties in culturing them, and the genetic resources of marine invertebrates have not been organized. Recently, advances have been made in the study of two deuterostomes, an ascidian Ciona intestinalis and a feather star Oxycomanthus japonicus. The draft genome sequence of Ciona intestinalis has been determined, and its compact genome, which has less redundancy of genes compared with vertebrates, provides us with a useful experimental system for analyzing the functions of genes during development. The life cycle of Ciona intestinalis is approximately 2-3 months, and the genetic techniques including a perfect inland culture system, germline transformation with a transposon Minos, enhancer detection and insertional mutagenesis, have been established. The feather star Oxycomanthus japonicus conserves the characteristics of the basic echinoderm body plan with a segmented mesoderm, which is a fascinating characteristic for understanding the evolution of echinoderms. Oxycomanthus japonicus shows strong regeneration ability and is a suitable subject for analysis of the mechanisms of regeneration. In consideration of these features, the National BioResource Project (NBRP) has started to support the supply of wild-types, transgenic lines and inbred lines of Ciona intestinalis and Oxycomanthus japonicus.

Direct contacts between extracellular membrane-proximal domains are required for VEGF receptor activation and cell signaling

Structural analyses of the extracellular region of stem cell factor (SCF) receptor (also designated KIT) in complex with SCF revealed a sequence motif in a loop in the fourth Ig-like domain (D4) that is responsible for forming homotypic receptor contacts and for ligand-induced KIT activation and cell signaling. An identical motif was identified in the most membrane-proximal seventh Ig-like domain (D7) of vascular endothelial growth factor receptor 1 (VEGFR1), VEGFR2, and VEGFR3. In this report we demonstrate that ligand-induced tyrosine autophosphorylation and cell signaling via VEGFR1 or VEGFR2 harboring mutations in critical residues (Arg726 or Asp731) in D7 are strongly impaired. We also describe the crystal structure of D7 of VEGFR2 to a resolution of 2.7 A. The structure shows that homotypic D7 contacts are mediated by salt bridges and van der Waals contacts formed between Arg726 of one protomer and Asp731 of the other protomer. The structure of D7 dimer is very similar to the structure of D4 dimers seen in the crystal structure of KIT extracellular region in complex with SCF. The high similarity between VEGFR D7 and KIT D4 in both structure and function provides further evidence for common ancestral origins of type III and type V RTKs. It also reveals a conserved mechanism for RTK activation and a novel target for pharmacological intervention of pathologically activated RTKs.

Functional diversity of signaling pathways through G protein-coupled receptor heterodimerization with a species-specific orphan receptor subtype

Gonadotropin-releasing hormones (GnRHs) play pivotal roles in control of reproduction via a hypothalamic-pituitary-periphery endocrine system and nervous systems of not only vertebrates but also invertebrates. GnRHs trigger several signal transduction cascades via GnRH receptors (GnRHRs), members of the G protein-coupled receptor (GPCR) family. Recently, six GnRHs (tunicate GnRH [tGnRH]-3 to tGnRH-8) and four GnRHRs (Ciona intestinalis [Ci]-GnRHR1 to GnRHR-4), including a species-specific paralog, Ci-GnRHR4 (R4) regarded as an orphan receptor or nonfunctional receptor, were identified in the protochordate, C. intestinalis, which lacks the hypothalamic-pituitary system. Here, we show novel functional modulation of GnRH signaling pathways via GPCR heterodimerization. Immunohistochemical analysis showed colocalization of R1 and R4 in test cells of the ascidian ovary. The native R1-R4 heterodimerization was detected in the Ciona ovary by coimmunoprecipitation analysis. The heterodimerization in HEK293 cells cotransfected with R1 and R4 was also observed by coimmunoprecipitation and fluorescent energy transfer analyses. Binding assay revealed that R4 had no affinity for tGnRHs, and the heterodimerization did not alter the binding affinity of R1 to the ligands. The R1-R4 elicited 10-fold more potent Ca2+ mobilization than R1 exclusively by tGnRH-6, although R1-mediated cyclic AMP production was not affected by any of tGnRHs via the R1-R4 heterodimer. Moreover, the R1-R4 heterodimer potentiated translocation of both Ca2+-dependent protein kinase C-alpha (PKCalpha) by tGnRH-6 and Ca2+-independent PKCzeta by tGnRH-5 and tGnRH-6, eventually leading to the upregulation of extracellular signal-regulated kinase (ERK) phosphorylation compared with R1 alone. These results provide evidence that the species-specific GnRHR orphan paralog, R4, serves as an endogenous modulator for the fine-tuning of activation of PKC subtype-selective signal transduction via heterodimerization with R1 and that the species-specific GPCR heterodimerization, in concert with multiplication of tGnRHs and Ci-GnRHRs, participates in functional evolution of neuropeptidergic GnRH signaling pathways highly conserved throughout the animal kingdom.

Origin and evolution of the Notch signalling pathway: an overview from eukaryotic genomes

Background

Of the 20 or so signal transduction pathways that orchestrate cell-cell interactions in metazoans, seven are involved during development. One of these is the Notch signalling pathway which regulates cellular identity, proliferation, differentiation and apoptosis via the developmental processes of lateral inhibition and boundary induction. In light of this essential role played in metazoan development, we surveyed a wide range of eukaryotic genomes to determine the origin and evolution of the components and auxiliary factors that compose and modulate this pathway.

Results

We searched for 22 components of the Notch pathway in 35 different species that represent 8 major clades of eukaryotes, performed phylogenetic analyses and compared the domain compositions of the two fundamental molecules: the receptor Notch and its ligands Delta/Jagged. We confirm that a Notch pathway, with true receptors and ligands is specific to the Metazoa. This study also sheds light on the deep ancestry of a number of genes involved in this pathway, while other members are revealed to have a more recent origin. The origin of several components can be accounted for by the shuffling of pre-existing protein domains, or via lateral gene transfer. In addition, certain domains have appeared de novo more recently, and can be considered metazoan synapomorphies.

Conclusion

The Notch signalling pathway emerged in Metazoa via a diversity of molecular mechanisms, incorporating both novel and ancient protein domains during eukaryote evolution. Thus, a functional Notch signalling pathway was probably present in Urmetazoa.

Early zygotic expression of transcription factors and signal molecules in fully dissociated embryonic cells of Ciona intestinalis: A microarray analysis

Specification of early embryonic cells of animals is established by maternally provided factors and interactions of neighboring cells. The present study addressed a question of autonomous versus non-autonomous specification of embryonic cells by using the Ciona intestinalis embryo, in particular the genetic cascade of zygotic expression of transcription factor genes responsible for notochord specification. To examine this issue, we combined the classic experiment of continuous dissociation of embryonic cells with the modern technique of oligonucleotide-based microarrays. We measured early zygotic expression of 389 core transcription factors genes and 118 major signal molecule genes in embryonic cells that were fully dissociated from the first cleavage. Our results indicated that even if cells are free from contact with neighbors, the major transcription factor genes that have primary roles in embryonic cell specification commence their zygotic expression at the same time as in normal embryos. Dissociation of embryonic cells did not affect extracellular signal-regulated kinases (ERK) activity. Although normal embryos treated with U0126 failed to express Bra and Twist-like-1, dissociated embryonic cells treated with U0126 expressed the genes. These results are discussed in relation to the grade of autonomous versus non-autonomous genetic cascades that are responsible for the specification of early Ciona embryonic cells.

Gene-regulatory networks in the Ciona embryos

Ascidians belong to the subphylum Urochordata or Tunicata, which is the sister group of the vertebrates. The simple architecture of the ascidian larva represents the basic chordate body plan. Recent analyses have shown many instances of developmental mechanisms conserved during evolution, while these studies have also revealed a much larger number of instances of divergence. However, to precisely determine the degree of conservation and divergence, that is, how many ways are used to make tadpole-like larvae, we need a systems-level understanding of development. Because animal development is organized by the genome and the minimal functional unit of development is a cell, comprehensiveness and single-cell resolution are necessary for a systems-biological understanding of the development. In the ascidian Ciona intestinalis, gene-regulatory networks responsible for the embryonic development have been studied on a genome-wide scale and at single-cell resolution. The simplicity and compactness of the genome facilitates genome-wide studies. In the Ciona genome, only approximately 670 transcription factor genes are encoded, and their expression profiles during the embryonic development have been analyzed. Gene-knockdown analyses of the transcription factor genes expressed during the embryonic development have been performed. The simplicity of the embryo permits these analyses to be done at single-cell resolution. Actually, these simple embryos are now being modeled in the computer, which allows us to understand the gene-regulatory networks very precisely in three dimensions.

Actors of the tyrosine kinase receptor downstream signaling pathways in amphioxus

One of the major goals of evo-developmentalists is to understand how the genetic mechanisms controlling embryonic development have evolved to create the current diversity of bodyplans that we encounter in the animal kingdom. Tyrosine kinase receptors (RTKs) are transmembrane receptors present in all metazoans known to control several developmental processes. They act via the activation of various cytoplasmic signaling cascades, including the mitogen-activated protein kinase (MAPK), the PI3K/Akt, and the phospholipase C-gamma (PLCgamma)/protein kinase C (PKC) pathways. In order to address the evolution of these three pathways and their involvement during embryogenesis in chordates, we took advantage of the complete genome sequencing of a key evolutionarily positioned species, the cephalochordate amphioxus, and searched for the complete gene set of the three signaling pathways. We found that the amphioxus genome contains all of the most important modules of the RTK-activated cascades, and looked at the embryonic expression of two genes selected from each cascade. Our data suggest that although the PI3K/Akt pathway may have ubiquitous functions, the MAPK and the PLCgamma/PKC cascades may play specific roles in amphioxus development. Together with data known in vertebrates, the expression pattern of PKC in amphioxus suggests that the PLCgamma/PKC cascade was implicated in neural development in the ancestor of all chordates.

Interaction of notochord-derived fibrinogen-like protein with Notch regulates the patterning of the central nervous system of Ciona intestinalis embryos

The midline organ the notochord and its overlying dorsal neural tube are the most prominent features of the chordate body plan. Although the molecular mechanisms involved in the formation of the central nervous system (CNS) have been studied extensively in vertebrate embryos, none of the genes that are expressed exclusively in notochord cells has been shown to function in this process. Here, we report a gene in the urochordate Ciona intestinalis encoding a fibrinogen-like protein that plays a pivotal role in the notochord-dependent positioning of neuronal cells. While this gene (Ci-fibrn) is expressed exclusively in notochord cells, its protein product is not confined to these cells but is distributed underneath the CNS as fibril-like protrusions. We demonstrated that Ci-fibrn interacts physically and functionally with Ci-Notch that is expressed in the central nervous system, and that the correct distribution of Ci-fibrn protein is dependent on Notch signaling. Disturbance of the Ci-fibrn distribution caused an abnormal positioning of neuronal cells and an abnormal track of axon extension. Therefore, it is highly likely that the interaction between the notochord-based fibrinogen-like protein and the neural tube-based Notch signaling plays an essential role in the proper patterning of CNS.

The molecular phylogeny of eph receptors and ephrin ligands

Background

The tissue distributions and functions of Eph receptors and their ephrin ligands have been well studied, however less is known about their evolutionary history. We have undertaken a phylogenetic analysis of Eph receptors and ephrins from a number of invertebrate and vertebrate species.

Results

Our findings indicate that Eph receptors form three major clades: one comprised of non-chordate and cephalochordate Eph receptors, a second comprised of urochordate Eph receptors, and a third comprised of vertebrate Eph receptors. Ephrins, on the other hand, fall into either a clade made up of the non-chordate and cephalochordate ephrins plus the urochordate and vertebrate ephrin-Bs or a clade made up of the urochordate and vertebrate ephrin-As.

Conclusion

We have concluded that Eph receptors and ephrins diverged into A and B-types at different points in their evolutionary history, such that primitive chordates likely possessed an ancestral ephrin-A and an ancestral ephrin-B, but only a single Eph receptor. Furthermore, ephrin-As appear to have arisen in the common ancestor of urochordates and vertebrates, whereas ephrin-Bs have a more ancient bilaterian origin. Ancestral ephrin-B-like ligands had transmembrane domains; as GPI anchors appear to have arisen or been lost at least 3 times.

Evolvable signaling networks of receptor tyrosine kinases: relevance of robustness to malignancy and to cancer therapy

Robust biological signaling networks evolved, through gene duplications, from simple, relatively fragile cascades. Architectural features such as layered configuration, branching and modularity, as well as functional characteristics (e.g., feedback control circuits), enable fail-safe performance in the face of internal and external perturbations. These universal features are exemplified here using the receptor tyrosine kinase (RTK) family. The RTK module is richly mutated and overexpressed in human malignancies, and pharmaceutical interception of its signaling effectively retards growth of specific tumors. Therapy-induced interception of RTK-signaling pathways and the common evolvement of drug resistance are respectively considered here as manifestations of fragility and plasticity of robust networks. The systems perspective we present views pathologies as hijackers of biological robustness and offers ways for identifying fragile hubs, as well as strategies to overcome drug resistance.

Sequential and combinatorial inputs from Nodal, Delta2/Notch and FGF/MEK/ERK signalling pathways establish a grid-like organisation of distinct cell identities in the ascidian neural plate

The ascidian neural plate has a grid-like organisation, with six rows and eight columns of aligned cells, generated by a series of stereotypical cell divisions. We have defined unique molecular signatures for each of the eight cells in the posterior-most two rows of the neural plate - rows I and II. Using a combination of morpholino gene knockdown, dominant-negative forms and pharmacological inhibitors, we tested the role of three signalling pathways in defining these distinct cell identities. Nodal signalling at the 64-cell stage was found to be required to define two different neural plate domains - medial and lateral - with Nodal inducing lateral and repressing medial identities. Delta2, an early Nodal target, was found to then subdivide each of the lateral and medial domains to generate four columns. Finally, a separate signalling system along the anteroposterior axis, involving restricted ERK1/2 activation, was found to promote row I fates and repress row II fates. Our results reveal how the sequential integration of three signalling pathways - Nodal, Delta2/Notch and FGF/MEK/ERK - defines eight different sub-domains that characterise the ascidian caudal neural plate. Most remarkably, the distinct fates of the eight neural precursors are each determined by a unique combination of inputs from these three signalling pathways.

Gene expression profile during the life cycle of the urochordate Ciona intestinalis

Recent whole-genome studies and in-depth expressed sequence tag (EST) analyses have identified most of the developmentally relevant genes in the urochordate, Ciona intestinalis. In this study, we made use of a large-scale oligo-DNA microarray to further investigate and identify genes with specific or correlated expression profiles, and we report global gene expression profiles for about 66% of all the C. intestinalis genes that are expressed during its life cycle. We succeeded in categorizing the data set into 5 large clusters and 49 sub-clusters based on the expression profile of each gene. This revealed the higher order of gene expression profiles during the developmental and aging stages. Furthermore, a combined analysis of microarray data with the EST database revealed the gene groups that were expressed at a specific stage or in a specific organ of the adult. This study provides insights into the complex structure of ascidian gene expression, identifies co-expressed gene groups and marker genes and makes predictions for the biological roles of many uncharacterized genes. This large-scale oligo-DNA microarray for C. intestinalis should facilitate the understanding of global gene expression and gene networks during the development and aging of a basal chordate.

Microarray analysis of zygotic expression of transcription factor genes and cell signaling molecule genes in early Ciona intestinalis embryos

In ascidians, specification of embryonic cells takes place very early at the 16-, 32- and 64-cell stages, and this developmental event involves zygotic expression of various genes, some encoding transcription factors and some encoding cell signaling molecules. Previous studies have demonstrated that approximately 50 transcription factor genes and 25 signaling molecule genes commence their zygotic expression by the 64-cell stage of Ciona intestinalis embryos. With the aid of oligonucleotide-based microarray, we examined the zygotic expression profiles of developmental genes in early Ciona embryos. Although the microarray method had a tendency to barely detect zygotic expression of genes that are expressed maternally, the present results confirmed the results of previous studies. In addition, the present analysis demonstrated the zygotic expression of four genes that were not identified in previous studies, and this result was confirmed by whole-mount in situ hybridization. Our results therefore provide further information on the developmental genes that are zygotically expressed in early Ciona embryos, and demonstrate that the microarray is a powerful tool for future studies of the gene regulatory network in Ciona, a basal chordate with a body plan similar to that of vertebrates.

A genomic view of the sea urchin nervous system

The sequencing of the Strongylocentrotus purpuratus genome provides a unique opportunity to investigate the function and evolution of neural genes. The neurobiology of sea urchins is of particular interest because they have a close phylogenetic relationship with chordates, yet a distinctive pentaradiate body plan and unusual neural organization. Orthologues of transcription factors that regulate neurogenesis in other animals have been identified and several are expressed in neurogenic domains before gastrulation indicating that they may operate near the top of a conserved neural gene regulatory network. A family of genes encoding voltage-gated ion channels is present but, surprisingly, genes encoding gap junction proteins (connexins and pannexins) appear to be absent. Genes required for synapse formation and function have been identified and genes for synthesis and transport of neurotransmitters are present. There is a large family of G-protein-coupled receptors, including 874 rhodopsin-type receptors, 28 metabotropic glutamate-like receptors and a remarkably expanded group of 161 secretin receptor-like proteins. Absence of cannabinoid, lysophospholipid and melanocortin receptors indicates that this group may be unique to chordates. There are at least 37 putative G-protein-coupled peptide receptors and precursors for several neuropeptides and peptide hormones have been identified, including SALMFamides, NGFFFamide, a vasotocin-like peptide, glycoprotein hormones and insulin/insulin-like growth factors. Identification of a neurotrophin-like gene and Trk receptor in sea urchin indicates that this neural signaling system is not unique to chordates. Several hundred chemoreceptor genes have been predicted using several approaches, a number similar to that for other animals. Intriguingly, genes encoding homologues of rhodopsin, Pax6 and several other key mammalian retinal transcription factors are expressed in tube feet, suggesting tube feet function as photosensory organs. Analysis of the sea urchin genome presents a unique perspective on the evolutionary history of deuterostome nervous systems and reveals new approaches to investigate the development and neurobiology of sea urchins.

Three insulin-relaxin-like genes in Ciona intestinalis

The Ciona intestinalis genome harbors three insulin-like genes: INS-L1, -L2 and -L3. Conserved synteny between the Ciona-human genomes predicts that Ciona INS-Ls are orthologous to the vertebrate insulin-relaxin family, but this relation cannot be inferred from molecular phylogeny. A conserved protein core with six cysteines; typical arrangement of B-, C- and A-protein domains; pro-protein maturation mode; and putative insulin receptor-binding sites were identified in Ciona INS-L proteins. ESTs used to assemble exonic sequences of INS-Ls combined with qRT-PCR analysis provided evidence that the predicted genes are expressed in the developing and adult Ciona. Our results support that Ciona INS-L1 is orthologous to the vertebrate insulin-like/relaxin genes, INS-L2 to insulin genes and INS-L3 to IGF genes. Our analysis also implies that the insulin-like/relaxin ancestor switched receptor type from tyrosine kinase- to GPCR-type, whereas insulin-IGF subfamily retained the tyrosine kinase-type of receptor. We propose that this receptor-switch occurred after the time when urochordates branched from the common chordate lineage, but before the two genome-duplications at the root of the vertebrates.

Effects of U0126 and fibroblast growth factor on gene expression profile in Ciona intestinalis embryos as revealed by microarray analysis

Fibroblast growth factor (FGF) induces the notochord and mesenchyme in ascidian embryos, via extracellular signal-regulated kinase (ERK) that belongs to the mitogen-activated protein kinase (MAPK) family. A cDNA microarray analysis was carried out to identify genes affected by an inhibitor of MAPK/ERK kinase (MEK), U0126, in embryos of the ascidian Ciona intestinalis. Data obtained from the microarray and in situ hybridization suggest that the majority of genes are downregulated by U0126 treatment. Genes that were downregulated in U0126-treated embryos included Ci-Bra and Ci-Twist-like1 that are master regulatory genes of notochord and mesenchyme differentiation, respectively. The plasminogen mRNA was downregulated by U0126 in presumptive endoderm cells. This suggests that a MEK-mediated extracellular signal is necessary for gene expression in tissues whose specification does not depend on cell-to-cell interaction. Among 85 cDNA clusters that were not affected by U0126, 30 showed mitochondria-like mRNA localization in the nerve cord/muscle lineage blastomeres in the equatorial region. The expression level and asymmetric distribution of these mRNA were independent of MEK signaling.

RTK and TGF-beta signaling pathways genes in the sea urchin genome

The Receptor Tyrosine kinase (RTK) and TGF-beta signaling pathways play essential roles during development in many organisms and regulate a plethora of cellular responses. From the genome sequence of Strongylocentrotus purpuratus, we have made an inventory of the genes encoding receptor tyrosine kinases and their ligands, and of the genes encoding cytokines of the TGF-beta superfamily and their downstream components. The sea urchin genome contains at least 20 genes coding for canonical receptor tyrosine kinases. Seventeen of the nineteen vertebrate RTK families are represented in the sea urchin. Fourteen of these RTK among which ALK, CCK4/PTK7, DDR, EGFR, EPH, LMR, MET/RON, MUSK, RET, ROR, ROS, RYK, TIE and TRK are present as single copy genes while pairs of related genes are present for VEGFR, FGFR and INSR. Similarly, nearly all the subfamilies of TGF-beta ligands identified in vertebrates are present in the sea urchin genome including the BMP, ADMP, GDF, Activin, Myostatin, Nodal and Lefty, as well as the TGF-beta sensu stricto that had not been characterized in invertebrates so far. Expression analysis indicates that the early expression of nodal, BMP2/4 and lefty is restricted to the oral ectoderm reflecting their role in providing positional information along the oral-aboral axis of the embryo. The coincidence between the emergence of TGF-beta-related factors such as Nodal and Lefty and the emergence of the deuterostome lineage strongly suggests that the ancestral function of Nodal could have been related to the secondary opening of the mouth which characterizes this clade, a hypothesis supported by functional data in the extant species. The sea urchin genome contains 6 genes encoding TGF-beta receptors and 4 genes encoding prototypical Smad proteins. Furthermore, most of the transcriptional activators and repressors shown to interact with Smads in vertebrates have orthologues in echinoderms. Finally, the sea urchin genome contains an almost complete repertoire of genes encoding extracellular modulators of BMP signaling including Chordin, Noggin, Sclerotin, SFRP, Gremlin, DAN and Twisted gastrulation. Taken together, these findings indicate that the sea urchin complement of genes of the RTK and TGF-beta signaling pathways is qualitatively very similar to the repertoire present in vertebrates, and that these genes are part of the common genetool kit for intercellular signaling of deuterostomes.

Formation and evolution of the chordate neurotrophin and Trk receptor genes

Neurotrophins are structurally related neurotrophic polypeptide factors that regulate neuronal differentiation and are essential for neuronal survival, neurite growth and plasticity. It has until very recently been thought that the neurotrophin system appeared with the vertebrate species, but identification of a cephalochordate neurotrophin receptor (Trk), and more recently neurotrophin sequences in several genomes of deuterostome invertebrates, show that the system already existed at the stem of the deuterostome group. Comparative genomics supports the hypothesis that two whole genome duplications produced many of the vertebrate gene families, among those the neurotrophin and Trk families. It remains to be proven to what extent the whole genome duplications have driven macroevolutionary change, but it appears certain that the formation of the multi-gene copy neurotrophin and Trk receptor families at the stem of vertebrates has provided a foundation from which the various functions and pleiotropic effects produced by each of the four extant neurotrophins have evolved.

Neuroendocrinology of protochordates: Insights from Ciona genomics

The genome for two species of Ciona is available making these tunicates excellent models for studies on the evolution of the chordates. In this review most of the data is from Ciona intestinalis, as the annotation of the C. savignyi genome is not yet available. The phylogenetic position of tunicates at the origin of the chordates and the nature of the genome before expansion in vertebrates allows tunicates to be used as a touchstone for understanding genes that either preceded or arose in vertebrates. A comparison of Ciona, a sea squirt, to other model organisms such as a nematode, fruit fly, zebrafish, frog, chicken and mouse shows that Ciona has many useful traits including accessibility for embryological, lineage tracing, forward genetics, and loss- or gain-of-function experiments. For neuroendocrine studies, these traits are important for determining gene function, whereas the availability of the genome is critical for identification of ligands, receptors, transcription factors and signaling pathways. Four major neurohormones and their receptors have been identified by cloning and to some extent by function in Ciona: gonadotropin-releasing hormone, insulin, insulin-like growth factor, and cionin, a member of the CCK/gastrin family. The simplicity of tunicates should be an advantage in searching for novel functions for these hormones. Other neuroendocrine components that have been annotated in the genome are a multitude of receptors, which are available for cloning, expression and functional studies.

The amphioxus T-box gene, AmphiTbx15/18/22, illuminates the origins of chordate segmentation

Amphioxus and vertebrates are the only deuterostomes to exhibit unequivocal somitic segmentation. The relative simplicity of the amphioxus genome makes it a favorable organism for elucidating the basic genetic network required for chordate somite development. Here we describe the developmental expression of the somite marker, AmphiTbx15/18/22, which is first expressed at the mid-gastrula stage in dorsolateral mesendoderm. At the early neurula stage, expression is detected in the first three pairs of developing somites. By the mid-neurula stage, expression is downregulated in anterior somites, and only detected in the penultimate somite primordia. In early larvae, the gene is expressed in nascent somites before they pinch off from the posterior archenteron (tail bud). Integrating functional, phylogenetic and expression data from a variety of triploblast organisms, we have reconstructed the evolutionary history of the Tbx15/18/22 subfamily. This analysis suggests that the Tbx15/18/22 gene may have played a role in patterning somites in the last common ancestor of all chordates, a role that was later conserved by its descendents following gene duplications within the vertebrate lineage. Furthermore, the comparison of expression domains within this gene subfamily reveals similarities in the genetic bases of trunk and cranial mesoderm segmentation. This lends support to the hypothesis that the vertebrate head evolved from an ancestor possessing segmented cranial mesoderm.

Origin and Molecular Evolution of Receptor Tyrosine Kinases with Immunoglobulin-Like Domains

Receptor tyrosine kinases (RTKs) are involved in the control of fundamental cellular processes in metazoans. In vertebrates, RTK could be grouped in distinct classes based on the nature of their cognate ligand and modular composition of their extracellular domain. RTK with immunoglobulin-like domains (IG-like RTK) encompass several RTK classes and have been found in early metazoans, including sponges. Evolution of IG-like RTK is characterized by extended molecular and functional diversification, which prompted us to study their evolutionary history. For that purpose, a nonredundant data set including annotated protein sequences of IG-like RTK (n = 85) was built, representing 19 species ranging from sponges to humans. Phylogenetic trees were generated from alignment of conserved regions using maximum likelihood approach. Molecular phylogeny strongly suggests that IG-like RTK diversification occurred according to a complex scenario. In particular, we propose that specific cis duplications of a common ancestor to both platelet-derived growth factor receptor (class III) and vascular endothelial growth factor receptor (class V) families preceded two trans duplications. In contrast, other IG-like RTK genes, like Musk and PTK7, apparently did not evolve by duplications, whereas fibroblast growth factor receptors (class IV) evolved through two rounds of trans duplications. The proposed model of IG-like RTK evolution is supported by high bootstrap values and by the clustering of genes encoding class III and class V RTKs at specific chromosomal locations in mouse and human genomes.

An integrated database of the ascidian, Ciona intestinalis: towards functional genomics

An integrated genome database is essential for future studies of functional genomics. In this study, we update cDNA and genomic resources of the ascidian, Ciona intestinalis, and provide an integrated database of the genomic and cDNA data by extending a database published previously. The updated resources include over 190,000 ESTs (672,396 in total together with the previous ESTs) and over 1,000 full-insert sequences (6,773 in total). In addition, results of mapping information of the determined scaffolds onto chromosomes, ESTs from a full-length enriched cDNA library for indication of precise 5'-ends of genes, and comparisons of SNPs and indels among different individuals are integrated into this database, all of these results being reported recently. These advances continue to increase the utility of Ciona intestinalis as a model organism whilst the integrated database will be useful for researchers in comparative and evolutionary genomics.

Cataloging transcription factor and major signaling molecule genes for functional genomic studies in Ciona intestinalis

The ascidian Ciona intestinalis provides an excellent experimental system for functional genomic studies because (1) its genome has been sequenced, (2) the transcription factor genes and genes for major signal transduction molecules have been extensively screened and annotated on a genome-wide scale using the molecular phylogenetical method, and (3) their embryonic expression profiles have been almost completely determined. However, the entire genetic structure, including the 5' and 3' untranslated regions and the protein-coding regions, of most gene models used in these prior studies is not always supported by cDNA evidence, and thus, these gene models are potentially imprecise. To facilitate functional genomic studies based on precise gene structures, our present study determined 406 cDNA sequences for 357 transcription factor genes and 112 cDNA sequences for 107 signal transduction molecule genes, greatly improving the previous gene models and revealing transcript variants for 44 genes. Considering these data alongside those of previously characterized genes deposited in the DNA Data Bank of Japan/European Molecular Biology Laboratory/GENBANK databases, 95.6% of the catalogued transcription factor genes (373/390) and 98.3% of the catalogued signal transduction molecule genes (117/119) have now been verified by cDNA sequences. Thus, the present study greatly improves the resources available for functional genomic studies in C. intestinalis.

Conserved synteny between the Ciona genome and human paralogons identifies large duplication events in the molecular evolution of the insulin-relaxin gene family

The aims of the study were to outline the sequence of events that gave rise to the vertebrate insulin-relaxin gene family and the chromosomal regions in which they reside. We analyzed the gene content surrounding the human insulin/relaxin genes with respect to what family they belonged to and if the duplication history of investigated families parallels the evolution of the insulin-relaxin family members. Markov Clustering and phylogenetic analysis were used to determine family identity. More than 15% of the genes belonged to families that have paralogs in the regions, defining two sets of quadruplicate paralogy regions. Thereby, the localization of insulin/relaxin genes in humans is in accordance with those regions on human chromosomes 1, 11, 12, 19q (insulin/insulin-like growth factors) and 1, 6p/15q, 9/5, 19p (insulin-like factors/relaxins) were formed during two genome duplications. We compared the human genome with that of Ciona intestinalis, a species that split from the vertebrate lineage before the two suggested genome duplications. Two insulin-like orthologs were discovered in addition to the already described Ci-insulin gene. Conserved synteny between the Ciona regions hosting the insulin-like genes and the two sets of human paralogons implies their common origin. Linkage of the two human paralogons, as seen in human chromosome 1, as well as the two regions hosting the Ciona insulin-like genes suggests that a segmental duplication gave rise to the region prior to the genome doublings. Thus, preserved gene content provides support that genome duplication(s) in addition to segmental and single-gene duplications shaped the genomes of extant vertebrates.

Ci-Tbx6b and Ci-Tbx6c are key mediators of the maternal effect gene Ci-macho1 in muscle cell differentiation in Ciona intestinalis embryos

Maternally deposited mRNA encoding the Zic family zinc-finger protein Ci-macho1 is a determinant responsible for muscle cell differentiation in Ciona intestinalis embryos. In a previous study, we identified possible Ci-macho1 downstream genes, which include seven transcription factor genes and seven signaling molecule genes (Yagi, K., Satoh, N., Satou, Y., 2004. Identification of downstream genes of the ascidian muscle determinant gene Ci-macho1. Dev. Biol. 274, 478-489), suggesting complex Ci-macho1 downstream cascades. Here, we show that of the Ci-macho1 downstream genes, only Ci-Tbx6b and Ci-Tbx6c promote ectopic differentiation of muscle cells when misexpressed in non-muscle blastomeres. Overexpression of Ci-Tbx6b or Ci-Tbx6c in Ci-macho1 knockdown embryos is able to compensate for the functional loss of Ci-macho1 and promote differentiation of muscle cells. In addition, we show that knockdown of each of Ci-Tbx6b or Ci-Tbx6c suppresses the initiation of muscle protein gene expression, and both gene products appear to recognize a similar binding sequence. However, later expression of muscle protein genes at the tailbud stage is only reduced in Ci-Tbx6b knockdown embryos and undisturbed in Ci-Tbx6c knockdown embryos. Although ectopic expression or knockdown of Ci-ZicL alone does not affect muscle cell differentiation, simultaneous knockdown of Ci-Tbx6b, Ci-Tbx6c, and Ci-ZicL completely abolishes muscle cell differentiation, as in the case of knockdown of Ci-macho1 and Ci-ZicL. These results strongly suggest that muscle cell differentiation in Ciona embryos is controlled by four key factors: maternal macho1 and zygotic Tbx6b, Tbx6c, and ZicL. The two T-box genes are primary mediators of macho1 function, and cooperation between the zygotically expressed transcription factors is indispensable for muscle cell differentiation in Ciona embryos.

Evolution of the Fgf and Fgfr gene families

Fibroblast growth factors (Fgfs) and Fgf receptors (Fgfrs) comprise a signaling system that is conserved throughout metazoan evolution. Twenty-two Fgfs and four Fgfrs have been identified in humans and mice. During evolution, the Fgf family appears to have expanded in two phases. In the first phase, during early metazoan evolution, Fgfs expanded from two or three to six genes by gene duplication. In the second phase, during the evolution of early vertebrates, the Fgf family expanded by two large-scale gen(om)e duplications. By contrast, the Fgfr family has expanded only in the second phase. However, the acquisition of alternative splicing by Fgfrs has increased their functional diversity. The mechanisms that regulate alternative splicing have been conserved since the divergences of echinoderms and vertebrates. The expansion of the Fgf and Fgfr gene families has enabled this signaling system to acquire functional diversity and, therefore, an almost ubiquitous involvement in developmental and physiological processes.

Time course of programmed cell death in Ciona intestinalis in relation to mitotic activity and MAPK signaling

Programmed cell death (PCD) in the ascidian species Ciona intestinalis (Tunicata; Chordata) is investigated from early larvae to juvenile stages, by means of digoxigenin-based terminal deoxynucleotidyl transferase-mediated biotinylated UTP nick end labeling (TUNEL) technique. At first, PCD in the swimming larva affects trunk mesenchyme and central nervous system (CNS), then it participates extensively to metamorphosis, until it is restricted to developing organs of juveniles. Analysis of patterns of cell death and division in the larval CNS question old models on the genesis of the adult C. intestinalis brain. Upon performing immunochemical and functional assays for mitogen-activated protein kinase (MAPK) kinase kinase-1 (MEKK1), MAPK kinase 1/2 (MEK1/2), c-Jun NH2-terminal kinase (JNK), and dual phosphorylated extracellular regulated kinase 1/2 (dpERK1/2), the neurogenic competence of the larval brain appears to rely on a combinatorial regulation of PCD by the mitogen-activated protein kinase signaling cascade. These results show that, in tunicates, PCD consists of a multistep program implicated in growth and patterning with various roles.