Chordate phylogeny and evolution: a not so simple three-taxon problem

Functional characterization of growth hormone releasing hormone and its receptor in amphioxus with implication for origin of hypothalamic-pituitary axis

Growth hormone-releasing hormone (GHRH) has been widely shown to stimulate growth hormone (GH) production via binding to GHRH receptor GHRHR in various species of vertebrates, but information regarding the functional roles of GHRH and GHRHR in the protochordate amphioxus remains rather scarce. We showed here that two mature peptides, BjGHRH-1 and BjGHRH-2, encoded by BjGHRH precursor, and a single BjGHRHR protein were identified in the amphioxus Branchiostoma. japonicum. Like the distribution profiles of vertebrate GHRHs and GHRHRs, both the genes Bjghrh and Bjghrhr were widely expressed in the different tissues of amphioxus, including in the cerebral vesicle, Hatschek's pit, neural tube, gill, hepatic caecum, notochord, testis and ovary. Moreover, both BjGHRH-1 and BjGHRH-2 interacted with BjGHRHR, and triggered the cAMP/PKA signal pathway in a dose-dependent manner. Importantly, BjGHRH-1 and BjGHRH-2 were both able to activate the expression of GH-like gene in the cells of Hatschek's pit. These indicate that a functional vertebrate-like GHRH-GHRHR axis had already emerged in amphioxus, which is a seminal innovation making physiological divergence including reproduction, growth, metabolism, stress and osmoregulation possible during the early evolution of vertebrates.

The oral sensory organs in Bathochordaeus stygius (Tunicata Appendicularia) are unique in structure and homologous to the coronal organ

BACKGROUND

Appendicularia consists of approximately 70 purely marine species that belong to Tunicata the probable sister taxon to Craniota. Therefore, Appendicularia plays a pivotal role for our understanding of chordate evolution. In addition, appendicularians are an important part of the epipelagic marine plankton. Nevertheless, little is known about appendicularian species, especially from deeper water.

RESULTS

Using µCT, scanning electron microscopy, and digital 3D-reconstruction techniques we describe three pairs of complex oral sensory organs in the mesopelagic appendicularian Bathochordaeus stygius. The oral sensory organs are situated at the anterior and lateral margin of the mouth and inside the mouth cavity. A single organ consists of 22-90 secondary receptor cells that project apical cilia through a narrow hole in the epidermis. The receptor cells are innervated by branches of the second brain nerve.

CONCLUSIONS

Based on position, morphology, and innervation we suggest that the oral sensory organs are homologues of the coronal organs in other tunicates. We discuss the hypothesized homology of coronal organs and the lateral line system of primary aquatic vertebrates. The complex oral sensory organs of B. stygius are unique in tunicates and could be adaptations to the more muffled environment of the mesopelagic.

The pericardium of Oikopleura dioica (Tunicata, Appendicularia) contains two distinct cell types and is rotated by 90 degrees to the left

The planktonic Oikopleura dioica belongs to Tunicata, the probable sister taxon to Craniota, and might show plesiomorphic characters, conserved from the common lineage of Tunicata and Craniota. In O. dioica a pericardium in a position similar to other chordates but also to the heart and pericardium of craniates is found. Surprisingly, little is known about the ultrastructure of the pericardium in O. dioica. Here, we show based on electron microscopy that the pericardium is completely lined by a single layer of 16 epithelial cells: 6 epithelial myocardial cells on the left side of the pericardium and 10 peritoneal cells constituting the right side. One of the peritoneal cells, situated at the ventral border between peritoneal cells and myocardial cells has an extension that anchors the pericardium to the basal lamina beneath the latero-ventral epidermis. The primary body cavity of O. dioica appears quite uniformly clear in electron microscopic aspect but several sheets, resembling the basal lamina of the pericardium cross the larger spaces of the body cavity and connect to the pericardial basal lamina. This is the first detailed description of two distinct cell types in the epithelial lining of the pericardium of O. dioica. In comparison with other chordates, we conclude that two cell types can be reconstructed for the last common ancestor of Chordata at least. The position of the pericardium at the intersection of trunk and tail in combination with the basal-lamina like sheets spanning the hemocoel is probably of importance for the function of the circulation of the hemocoelic fluid. Similar to the tail, the axis of the pericardium is shifted through 90 degrees to the left as compared to the main body axis of the trunk and we infer that this shift is an apomorphic character of Appendicularia.

Phylogenetic analysis of phenotypic characters of Tunicata supports basal Appendicularia and monophyletic Ascidiacea

With approximately 3000 marine species, Tunicata represents the most disparate subtaxon of Chordata. Molecular phylogenetic studies support Tunicata as sister taxon to Craniota, rendering it pivotal to understanding craniate evolution. Although successively more molecular data have become available to resolve internal tunicate phylogenetic relationships, phenotypic data have not been utilized consistently. Herein these shortcomings are addressed by cladistically analyzing 117 phenotypic characters for 49 tunicate species comprising all higher tunicate taxa, and five craniate and cephalochordate outgroup species. In addition, a combined analysis of the phenotypic characters with 18S rDNA-sequence data is performed in 32 OTUs. The analysis of the combined data is congruent with published molecular analyses. Successively up-weighting phenotypic characters indicates that phenotypic data contribute disproportionally more to the resulting phylogenetic hypothesis. The strict consensus tree from the analysis of the phenotypic characters as well as the single most parsimonious tree found in the analysis of the combined dataset recover monophyletic Appendicularia as sister taxon to the remaining tunicate taxa. Thus, both datasets support the hypothesis that the last common ancestor of Tunicata was free-living and that ascidian sessility is a derived trait within Tunicata. "Thaliacea" is found to be paraphyletic with Pyrosomatida as sister taxon to monophyletic Ascidiacea and the relationship between Doliolida and Salpida is unresolved in the analysis of morphological characters; however, the analysis of the combined data reconstructs Thaliacea as monophyletic nested within paraphyletic "Ascidiacea". Therefore, both datasets differ in the interpretation of the evolution of the complex holoplanktonic life history of thaliacean taxa. According to the phenotypic data, this evolution occurred in the plankton, whereas from the combined dataset a secondary transition into the plankton from a sessile ascidian is inferred. Besides these major differences, both analyses are in accord on many phylogenetic groupings, although both phylogenetic reconstructions invoke a high degree of homoplasy. In conclusion, this study represents the first serious attempt to utilize the potential phylogenetic information present in phenotypic characters to elucidate the inter-relationships of this diverse marine taxon in a consistent cladistic framework.

A hypothesis on paradoxical privileged portal vein metastasis of hepatocellular carcinoma. Can organ evolution shed light on patterns of human pathology, and vice versa?

Unlike other carcinomas, hepatocellular carcinoma (HCC) metastasizes to distant organs relatively rarely. In contrast, it routinely metastasizes to liver vasculature/liver, affecting portal veins 3-10 times more often than hepatic veins. This portal metastatic predominance is traditionally rationalized within the model of a reverse portal flow, due to accompanying liver cirrhosis. However, this intuitive model is not coherent with facts: 1) reverse portal flow occurs in fewer than 10% of cirrhotic patients, while portal metastasis occurs in 30-100% of HCC cases, and 2) portal vein prevalence of HCC metastasis is also characteristic of HCC in non-cirrhotic livers. Therefore, we must assume that the route for HCC metastatic dissemination is the same as for other carcinomas: systemic dissemination via the draining vessel, i.e., via the hepatic vein. In this light, portal prevalence versus hepatic vein of HCC metastasis appears as a puzzling pattern, particularly in cases when portal HCC metastases have appeared as the sole manifestation of HCC. Considering that other GI carcinomas (colorectal, pancreatic, gastric and small bowel) invariably disseminate via portal vein, but very rarely form portal metastasis, portal prevalence of HCC metastasis appears as a paradox. However, nature does not contradict itself; it is rather our wrong assumptions that create paradoxes. The 'portal paradox' becomes a logical event within the hypothesis that the formation of the unique portal venous system preceded the appearance of liver in evolution of chordates. The analysis suggests that the appearance of the portal venous system, supplying hormones and growth factors of pancreatic family, which includes insulin, glucagon, somatostatin, and pancreatic polypeptide (HGFPF) to midgut diverticulum in the early evolution of chordates (in an Amphioxus-like ancestral animal), promoted differentiation of enterocytes into hepatocytes and their further evolution to the liver of vertebrates. These promotional-dependent interactions are conserved in the vertebrate lineage. I hypothesize that selective homing and proliferation of malignant hepatocytes (i.e., HCC cells) in the portal vein environment are due to a uniquely high concentration of HGFPF in portal blood. HGFPF are also necessary for liver function and renewal and are significantly extracted by hepatocytes from passing blood, creating a concentration gradient of HGFPF between the portal blood and hepatic vein outflow, making post-liver vasculature and remote organs less favorable spaces for HCC growth. It also suggested that the portal vein environment (i.e., HGFPF) promotes the differentiation of more aggressive HCC clones from already-seeded portal metastases, explaining the worse outcome of HCC with the portal metastatic pattern. The analysis also offers new hypothesis on the phylogenetic origin of the hepatic diverticulum of cephalochordates, with certain implications for the modeling of the chordate phylogeny.

An evolutionary perspective on the systems of adaptive immunity

We propose an evolutionary perspective to classify and characterize the diverse systems of adaptive immunity that have been discovered across all major domains of life. We put forward a new function-based classification according to the way information is acquired by the immune systems: Darwinian immunity (currently known from, but not necessarily limited to, vertebrates) relies on the Darwinian process of clonal selection to 'learn' by cumulative trial-and-error feedback; Lamarckian immunity uses templated targeting (guided adaptation) to internalize heritable information on potential threats; finally, shotgun immunity operates through somatic mechanisms of variable targeting without feedback. We argue that the origin of Darwinian (but not Lamarckian or shotgun) immunity represents a radical innovation in the evolution of individuality and complexity, and propose to add it to the list of major evolutionary transitions. While transitions to higher-level units entail the suppression of selection at lower levels, Darwinian immunity re-opens cell-level selection within the multicellular organism, under the control of mechanisms that direct, rather than suppress, cell-level evolution for the benefit of the individual. From a conceptual point of view, the origin of Darwinian immunity can be regarded as the most radical transition in the history of life, in which evolution by natural selection has literally re-invented itself. Furthermore, the combination of clonal selection and somatic receptor diversity enabled a transition from limited to practically unlimited capacity to store information about the antigenic environment. The origin of Darwinian immunity therefore comprises both a transition in individuality and the emergence of a new information system - the two hallmarks of major evolutionary transitions. Finally, we present an evolutionary scenario for the origin of Darwinian immunity in vertebrates. We propose a revival of the concept of the 'Big Bang' of vertebrate immunity, arguing that its origin involved a 'difficult' (i.e. low-probability) evolutionary transition that might have occurred only once, in a common ancestor of all vertebrates. In contrast to the original concept, we argue that the limiting innovation was not the generation of somatic diversity, but the regulatory circuitry needed for the safe operation of amplifiable immune responses with somatically acquired targeting. Regulatory complexity increased abruptly by genomic duplications at the root of the vertebrate lineage, creating a rare opportunity to establish such circuitry. We discuss the selection forces that might have acted at the origin of the transition, and in the subsequent stepwise evolution leading to the modern immune systems of extant vertebrates.

Tunicates: exploring the sea shores and roaming the open ocean. A tribute to Thomas Huxley

This review is a tribute to the remarkable contributions of Thomas Huxley to the biology of tunicates, the likely sister group of vertebrates. In 1851, the great biologist and philosopher published two landmark papers on pelagic tunicates in the Philosophical Transactions of the Royal Society. They were dedicated to the description of the adult anatomy and life cycle of thaliaceans and appendicularians, the pelagic relatives of ascidians. In the first part of this review, we discuss the novel anatomical observations and evolutionary hypotheses made by Huxley, which would have a lasting influence on tunicate biology. We also briefly comment on the more philosophical reflections of Huxley on individuality. In the second part, we stress the originality and relevance of past and future studies of tunicates in the resolution of major biological issues. In particular, we focus on the complex relationship between genotype and phenotype and the phenomenon of developmental system drift. We propose that more than 150 years after Huxley's papers, tunicate embryos are still worth studying in their own right, independently of their evolutionary proximity to vertebrates, as they provide original and crucial insights into the process of animal evolution. Tunicates are still at the forefront of biological research.

High-precision morphology: bifocal 4D-microscopy enables the comparison of detailed cell lineages of two chordate species separated for more than 525 million years

BACKGROUND

Understanding the evolution of divergent developmental trajectories requires detailed comparisons of embryologies at appropriate levels. Cell lineages, the accurate visualization of cleavage patterns, tissue fate restrictions, and morphogenetic movements that occur during the development of individual embryos are currently available for few disparate animal taxa, encumbering evolutionarily meaningful comparisons. Tunicates, considered to be close relatives of vertebrates, are marine invertebrates whose fossil record dates back to 525 million years ago. Life-history strategies across this subphylum are radically different, and include biphasic ascidians with free swimming larvae and a sessile adult stage, and the holoplanktonic larvaceans. Despite considerable progress, notably on the molecular level, the exact extent of evolutionary conservation and innovation during embryology remain obscure.

RESULTS

Here, using the innovative technique of bifocal 4D-microscopy, we demonstrate exactly which characteristics in the cell lineages of the ascidian Phallusia mammillata and the larvacean Oikopleura dioica were conserved and which were altered during evolution. Our accurate cell lineage trees in combination with detailed three-dimensional representations clearly identify conserved correspondence in relative cell position, cell identity, and fate restriction in several lines from all prospective larval tissues. At the same time, we precisely pinpoint differences observable at all levels of development. These differences comprise fate restrictions, tissue types, complex morphogenetic movement patterns, numerous cases of heterochronous acceleration in the larvacean embryo, and differences in bilateral symmetry.

CONCLUSIONS

Our results demonstrate in extraordinary detail the multitude of developmental levels amenable to evolutionary innovation, including subtle changes in the timing of fate restrictions as well as dramatic alterations in complex morphogenetic movements. We anticipate that the precise spatial and temporal cell lineage data will moreover serve as a high-precision guide to devise experimental investigations of other levels, such as molecular interactions between cells or changes in gene expression underlying the documented structural evolutionary changes. Finally, the quantitative amount of digital high-precision morphological data will enable and necessitate software-based similarity assessments as the basis of homology hypotheses.

Identification and functional characterization of viperin of amphioxus Branchiostoma japonicum: Implications for ancient origin of viperin-mediated antiviral response

Viperin, an antiviral protein, has been shown to be active against a wide range of DNA and RNA viruses, but no information is available regarding functional characterization of viperin in invertebrate species. In this study, we clearly demonstrate that amphioxus (Branchiostoma japonicum) viperin, BjVip, has features in common with those of vertebrate viperin, including the presence of the SAM superfamily domain with the characteristic CNYKCGFC motif, syntenic conservation, and predicted 3D structure. Bjvip exhibits a tissue-specific expression with abundant levels in the hepatic cecum, hind-gut, gill and muscle, and following challenge with the viral mimic poly I:C, its expression is significantly up-regulated, suggesting an involvement of BjVip in immune response of amphioxus against viral infection. Importantly, we show that the cells transfected with Bjvip is able to kill LCDV or inhibiting its propagation, and co-incubation of rBjVip with WSSV markedly attenuates its infectivity. Thus, we provide the first evidences that amphioxus viperin, like that of vertebrates, is capable of promoting resistance against viral infection in vitro and in vivo, indicating that viperin-mediated antiviral response already emerged in the primitive chordate. We also prove that amphioxus viperin has evolved under positive selection.

The deuterostome context of chordate origins

Our understanding of vertebrate origins is powerfully informed by comparative morphology, embryology and genomics of chordates, hemichordates and echinoderms, which together make up the deuterostome clade. Striking body-plan differences among these phyla have historically hindered the identification of ancestral morphological features, but recent progress in molecular genetics and embryology has revealed deep similarities in body-axis formation and organization across deuterostomes, at stages before morphological differences develop. These developmental genetic features, along with robust support of pharyngeal gill slits as a shared deuterostome character, provide the foundation for the emergence of chordates.

Identification, expression and regulation of amphioxus G6Pase gene with an emphasis on origin of liver

Vertebrate glucose-6-phosphatase (G6Pase) consists of three isozymes: G6Pase-I, G6Pase-II and G6Pase-III. Despite extensive study on G6Pases in vertebrates, information regarding expression and regulation of G6Pase genes is rather limited in invertebrates. Here we report the identification of G6Pase gene in amphioxus Branchiostoma japonicum, which is abundantly expressed in the digestive diverticulum and ovary in a tissue-specific manner. The phylogenetic and genomic structure analyses reveal that amphioxus G6Pase bears close resemblance to vertebrate G6Pase-III and represents the archetype of vertebrate G6Pase from which the vertebrate G6Pase isoforms may be originated by 2 rounds of genome duplication during vertebrate evolution. We also demonstrate that GH treatment induces a closely similar expression pattern and trend of g6pases in both zebrafish and amphioxus, and that G6Pase activity in amphioxus digestive diverticulum is subjected to regulation of feeding and fasting as observed in vertebrates. Collectively, all these provide functional evidences supporting the notion that the digestive diverticulum is the liver homologue playing a key role in maintaining the glucose homeostasis in amphioxus.

A new vetulicolian from Australia and its bearing on the chordate affinities of an enigmatic Cambrian group

Background

Vetulicolians are one of the most problematic and controversial Cambrian fossil groups, having been considered as arthropods, chordates, kinorhynchs, or their own phylum. Mounting evidence suggests that vetulicolians are deuterostomes, but affinities to crown-group phyla are unresolved.

Results

A new vetulicolian from the Emu Bay Shale Konservat-Lagerstätte, South Australia, Nesonektris aldridgei gen. et sp. nov., preserves an axial, rod-like structure in the posterior body region that resembles a notochord in its morphology and taphonomy, with notable similarity to early decay stages of the notochord of extant cephalochordates and vertebrates. Some of its features are also consistent with other structures, such as a gut or a coelomic cavity.

Conclusions

Phylogenetic analyses resolve a monophyletic Vetulicolia as sister-group to tunicates (Urochordata) within crown Chordata, and this holds even if they are scored as unknown for all notochord characters. The hypothesis that the free-swimming vetulicolians are the nearest relatives of tunicates suggests that a perpetual free-living life cycle was primitive for tunicates. Characters of the common ancestor of Vetulicolia + Tunicata include distinct anterior and posterior body regions – the former being non-fusiform and used for filter feeding and the latter originally segmented – plus a terminal mouth, absence of pharyngeal bars, the notochord restricted to the posterior body region, and the gut extending to the end of the tail.

Electronic supplementary material

The online version of this article (doi:10.1186/s12862-014-0214-z) contains supplementary material, which is available to authorized users.

Structural and functional characterization of a TGFβ molecule from amphioxus reveals an ancient origin of both immune-enhancing and -inhibitory functions

Transforming growth factor beta (TGFβ) is a pleiotropic cytokine with important roles in mediating inflammatory response. TGFβ has been shown to be widely present in invertebrates, but little is known about its functions in immune and inflammatory responses. Moreover, structural and functional insights into TGFβ molecules in invertebrates remain completely lacking. Here we demonstrate the presence of a single TGFβ-like gene in the amphioxus Branchiostoma japonicum, Bjtgfβ, which represents the archetype of vertebrate TGFβ proteins, and displays a higher expression in the hind-gut, hepatic caecum, ovary, and gill. We also show that amphioxus TGFβ exerts both enhancing and suppressing effects on the migration of macrophages like RAW264.7, and the motif WSTD is important for TGFβ in inducing or inhibiting the migration of macrophages. Altogether, these data suggest that amphioxus TGFβ is phylogenetically and functionally similar to vertebrate TGFβ, suggesting an ancient origin of bipolar function of TGFβ proteins.

Evolution of integrin I domains

In humans, an ~200-residue "inserted" I domain, a von Willebrand factor A domain (vWFA), buds out from the β-propeller domain in 9 of 18 integrin α subunits. The vWFA domain is not unique to the α subunit as it is an integral part of all integrin β subunits and many other proteins. The βI domain has always been a component of integrins but the αI domain makes its appearance relatively late, in early chordates, since it is found in tunicates and later diverging species. The tunicate αI domains are distinct from the human collagen and leukocyte recognizing integrin α subunits, but fragments of integrins from agnathastomes suggest that the human-type αI domains arose in an ancestor of the very first vertebrate species. The rise of integrins with αI domains parallels the enormous changes in body plan and systemic development of the chordate line that began some 550 million or more years ago.

Axial systems and their actuation: new twists on the ancient body of craniates

Craniate animals--vertebrates and their jawless sister taxa--have evolved a body axis with powerful muscles, a distributed nervous system to control those muscles, and an endoskeleton that starts at the head and ends at the caudal fin. The body axis undulates, bends, twists, or holds firm, depending on the behavior. In this introduction to the special issue on axial systems and their actuation, we provide an overview of the latest research on how the body axis functions, develops, and evolves. Based on this research, we hypothesize that the body axis of craniates has three primary, post-cranial modules: precaudal, caudal, and tail. The term "module" means a portion of the body axis that functions, develops, and evolves in relative independence from other modules; "relative independence" means that structures and processes within a module are more tightly correlated in function, development, and behavior than the same processes are among modules.

Evolution of air breathing: oxygen homeostasis and the transitions from water to land and sky

Life originated in anoxia, but many organisms came to depend upon oxygen for survival, independently evolving diverse respiratory systems for acquiring oxygen from the environment. Ambient oxygen tension (PO2) fluctuated through the ages in correlation with biodiversity and body size, enabling organisms to migrate from water to land and air and sometimes in the opposite direction. Habitat expansion compels the use of different gas exchangers, for example, skin, gills, tracheae, lungs, and their intermediate stages, that may coexist within the same species; coexistence may be temporally disjunct (e.g., larval gills vs. adult lungs) or simultaneous (e.g., skin, gills, and lungs in some salamanders). Disparate systems exhibit similar directions of adaptation: toward larger diffusion interfaces, thinner barriers, finer dynamic regulation, and reduced cost of breathing. Efficient respiratory gas exchange, coupled to downstream convective and diffusive resistances, comprise the "oxygen cascade"-step-down of PO2 that balances supply against toxicity. Here, we review the origin of oxygen homeostasis, a primal selection factor for all respiratory systems, which in turn function as gatekeepers of the cascade. Within an organism's lifespan, the respiratory apparatus adapts in various ways to upregulate oxygen uptake in hypoxia and restrict uptake in hyperoxia. In an evolutionary context, certain species also become adapted to environmental conditions or habitual organismic demands. We, therefore, survey the comparative anatomy and physiology of respiratory systems from invertebrates to vertebrates, water to air breathers, and terrestrial to aerial inhabitants. Through the evolutionary directions and variety of gas exchangers, their shared features and individual compromises may be appreciated.

Identification, expression of a glycoprotein hormone receptor homolog in the amphioxus Branchiostoma belcheri with implications for origin of vertebrate GpHRs

Amphioxus is phylogenetically located at the most primitive position of the chordate clade. Its endocrine system has been extensively studied; however, key information about the glycoprotein hormone (GpH) and its receptor (GpHR) in the endocrine system remained to be elucidated. In this study, a GpHR homologous gene, BbGpHR-like, has been identified in the amphioxus Branchiostoma belcheri. It contains a 1377bp open reading frame that corresponds to a deduced protein of 458 amino acid residues with a predicted molecular mass of approximately 50kDa. Phylogenetic analysis shows that BbGpHR-like is located at the position between vertebrate and invertebrate, indicating amphioxus B. belcheri is in an evolutionary transitional state between vertebrate and invertebrate in the GpHR lineage. BbGpHR-like has been successfully expressed in Pichia pastoris. Western blot analysis confirmed that the receptor produced a cross-immunoreactivity with human thyrotropin receptor (TSHR), the luteinizing hormone receptor (LHR) and the follicle-stimulating hormone receptor (FSHR). In situ hybridization and immunohistochemical analyses revealed that the BbGpHR-like transcripts and proteins were strongly distributed in the ovaries, testes and/or endostyle. These findings suggest that BbGpHR-like possibly plays an ancient and fundamental role in the control of thyroid hormone synthesis and gametogenesis in chordates. Presumably, the amphioxus BbGpHR-like represents the ancestral form of the GpHR gene prior to its split to the vertebrate paralogs gonadotropin receptor and thyrotropin receptor.

A novel short peptidoglycan recognition protein in amphioxus: identification, expression and bioactivity

Peptidoglycan recognition proteins (PGRPs) are widely distributed in invertebrates and vertebrates, and structure-activity relationship of insect and mammalian PGRPs has been well characterized, but functional and structural insights into PGRPs in other species are rather limited. Here we identified a novel short PGRP gene from the amphioxus Branchiostoma japonicum, named pgrp-s, which possesses a domain combination of ChtBD1 domain-PGRP domain, which is unique to all known PGRPs. Amphioxus pgrp-s was predominantly expressed in the hepatic caecum, hind-gut and muscle in a tissue-specific manner. Recombinant PGRP-S, rPGRP-S, and truncated protein with ChtBD1 domain deleted, rP86/250, both showed affinity to Dap-type PGN, Lys-type PGN and chitin. Consistently, they were also able to bind to Escherichia coli, Staphylococcus aureus and Pichia pastoris. Moreover, both rPGRP-S and rP86/250 had amidase enzymatic activity, capable of hydrolyzing Dap-type and Lys-type PGNs. Like vertebrate PGRPs, rPGRP-S was directly microbicidal, capable of killing E. coli, S. aureus and P. pastoris, whereas rP86/250 only inhibited the growth of E. coli and S. aureus, and its anti-P. pastoris activity was significantly reduced. It is clear that neither the binding of amphioxus PGRP-S nor its amidase enzymatic activity depend on the N-terminal ChtBD1 domain, but its antifungal activity does. Collectively, these data suggested that amphioxus PGRP-S may function as a multivalent pattern recognition receptor, capable of recognizing PGN and chitin, a microbicidal agent, capable of killing bacteria such as E. coli and S. aureus and fungus like P. pastoris, and probably a PGN scavenger, capable of hydrolyzing PGN.

Pikaia gracilens Walcott, a stem-group chordate from the Middle Cambrian of British Columbia

The Middle Cambrian Pikaia gracilens (Walcott) has an iconic position as a Cambrian chordate, but until now no detailed description has been available. Here on the basis of the 114 available specimens we review its anatomy, confirm its place in the chordates and explore with varying degrees of confidence its relationships to both extant and extinct chordates and other deuterostomes. The body of Pikaia is fusiform, laterally compressed and possesses about 100 myomeres. The head is small, bilobed and bears two narrow tentacles. There is no evidence for eyes. Apart from a thin dorsal fin (without finrays) and a series of at least nine bilaterally arranged appendages with possible pharyngeal pores at the anterior end, there are no other external features. In addition to the musculature the internal anatomy includes an alimentary canal, the anterior of which forms a prominent lenticular unit that is almost invariably preserved in positive relief. The cavity is interpreted as pharyngeal, implying that the mouth itself was almost terminal. The posterior extension of the gut is unclear although the anus appears to have been terminal. The most prominent internal structure is a reflectively preserved unit, possibly hollow, termed here the dorsal organ. Although formerly interpreted as a notochord its position and size make this less likely. Its original function remains uncertain, but it could have formed a storage organ. Ventral to the dorsal organ a narrower strand of tissue is interpreted as representing the nerve chord and notochord. In addition to these structures, there is also evidence for a vascular system, including a ventral blood vessel. The position of Pikaia in the chordates is largely based on the presence of sigmoidal myomeres, and the more tentative identification of a notochord. In many other respects, Pikaia differs from the expected nature of primitive chordates, especially as revealed in amphioxus and the Cambrian record (including Cathaymyrus, Haikouichthys, Metaspriggina, Myllokunmingia, and Zhongxiniscus). Whilst the possibility that Pikaia is simply convergent on the chordates cannot be dismissed, we prefer to build a scenario that regards Pikaia as the most stem-ward of the chordates with links to the phylogenetically controversial yunnanozoans. This hypothesis has implications for the evolution of the myomeres, notochord and gills. Finally, the wealth of material of Pikaia indicates that, although by definition there must be some sort of taphonomic imprint, the consistency of preservational details allows a reliable reconstruction of the anatomy and does not significantly erode phylogenetically relevant characters.

Checklist das ascídias (Tunicata, Ascidiacea) do Estado de São Paulo, Brasil

Ascídias são organismos marinhos que, em sua maioria, vivem fixados a substratos consolidados desde as regiões costeiras até às grandes profundidades. Apesar de serem cordados, apresentam um plano corporal adulto muito modificado em função de seu hábito de vida. O Estado de São Paulo é o que apresenta o melhor conhecimento da fauna de ascídias, tanto em termos de sua biodiversidade como em aspectos ecológicos. No estado, a região do município de São Sebastião foi a mais estudada em função da presença do Centro de Biologia Marinha da USP, que atraiu muitos pesquisadores desde a década de 1960. Nos últimos 50 anos houve um crescimento constante no conhecimento da fauna paulista de ascídias, que conta atualmente com 66 espécies registradas. No entanto, ainda existem lacunas importantes, pois o extremo norte e o litoral sul do estado ainda têm uma fauna de ascídias praticamente desconhecida, especialmente aquela relacionada às ilhas costeiras. As regiões mais profundas da plataforma continental e talude também foram pouco exploradas. Há necessidade de formação de recursos humanos para manter a continuidade dos estudos de biodiversidade, pois atualmente não existe nenhum grupo de pesquisa consolidado trabalhando com Ascidiacea no estado.

Cortical cytasters: a highly conserved developmental trait of Bilateria with similarities to Ctenophora

BACKGROUND

Cytasters (cytoplasmic asters) are centriole-based nucleation centers of microtubule polymerization that are observable in large numbers in the cortical cytoplasm of the egg and zygote of bilaterian organisms. In both protostome and deuterostome taxa, cytasters have been described to develop during oogenesis from vesicles of nuclear membrane that move to the cortical cytoplasm. They become associated with several cytoplasmic components, and participate in the reorganization of cortical cytoplasm after fertilization, patterning the antero-posterior and dorso-ventral body axes.

PRESENTATION OF THE HYPOTHESIS

The specific resemblances in the development of cytasters in both protostome and deuterostome taxa suggest that an independent evolutionary origin is unlikely. An assessment of published data confirms that cytasters are present in several protostome and deuterostome phyla, but are absent in the non-bilaterian phyla Cnidaria and Ctenophora. We hypothesize that cytasters evolved in the lineage leading to Bilateria and were already present in the most recent common ancestor shared by protostomes and deuterostomes. Thus, cytasters would be an ancient and highly conserved trait that is homologous across the different bilaterian phyla. The alternative possibility is homoplasy, that is cytasters have evolved independently in different lineages of Bilateria.

TESTING THE HYPOTHESIS

So far, available published information shows that appropriate observations have been made in eight different bilaterian phyla. All of them present cytasters. This is consistent with the hypothesis of homology and conservation. However, there are several important groups for which there are no currently available data. The hypothesis of homology predicts that cytasters should be present in these groups. Increasing the taxonomic sample using modern techniques uniformly will test for evolutionary patterns supporting homology, homoplasy, or secondary loss of cytasters.

IMPLICATIONS OF THE HYPOTHESIS

If cytasters are homologous and highly conserved across bilateria, their potential developmental and evolutionary relevance has been underestimated. The deep evolutionary origin of cytasters also becomes a legitimate topic of research. In Ctenophora, polyspermic fertilization occurs, with numerous sperm entering the egg. The centrosomes of sperm pronuclei associate with cytoplasmic components of the egg and reorganize the cortical cytoplasm, defining the oral-aboral axis. These resemblances lead us to suggest the possibility of a polyspermic ancestor in the lineage leading to Bilateria.

Expression and regulation by thyroid hormone (TH) of zebrafish IGF-I gene and amphioxus IGFl gene with implication of the origin of TH/IGF signaling pathway

Thyroid hormone (TH)/insulin-like growth factor (IGF) signaling pathway has been identified in all the vertebrates, but its evolutionary origin remains elusive. In this study we examined the expression profiles in vitro as well as in vivo of the IGF-I gene of fish Danio rerio (vertebrate) and the IGF-like gene (IGFl) of amphioxus Branchiostoma japonicum (protochordate) following T(3) treatment. Our results showed that T(3) was able to enhance hepatic IGF-I/IGFl gene expression in vitro in both zebrafish and amphioxus in a dose-dependent manner. This T(3)-induced hepatic expression of IGF-I/IGFl genes in both species was significantly inhibited by the T(3)-specific inhibitor DEA, indicating the specificity of IGF-I/IGFl gene regulation by T(3). At 100nM T(3), in both the long (42h) and short (8h) time course experiments, the IGF-I/IGFl gene expression profiles following T(3) treatment in the tissue cultures of both species exhibited closely similar pattern and trend. Moreover, exposure of zebrafish and amphioxus to T(3)in vivo for 72h induced a significant increase in the expression of IGF-I/IGFl genes in both the liver and the hepatic caecum. These data together suggest that amphioxus and zebrafish both share a similar regulatory mechanism of IGF gene expression in response to T(3), providing an evidence for the presence of a vertebrate-like TH/IGF signaling pathway in the protochordate amphioxus.

Walter Garstang: a retrospective

Although, Walter Garstang died over 60 years ago, his work is still cited--sometimes praised, but sometimes belittled. On the negative side, he often appropriated ideas of others without attribution, ignored earlier studies conflicting with his theories, and clung to notions like inheritance of acquired characters, progressive evolution, and saltation after many of his contemporaries were advancing toward the modern synthesis. Moreover, his evolutionary scenarios--especially his derivation of vertebrates from a sessile ascidian--have not been well supported by recent work in developmental genetics and molecular phylogenetics. On the positive side, Garstang firmly established several points of view that remain useful in the age of evolutionary development (evo-devo). He popularized the valid idea that adaptive changes in larvae combined with shifts in developmental timing (heterochrony) could radically change adult morphology and provide an escape from overspecialization. Moreover, his re-statement of the biogenetic law is now widely accepted: namely, that recapitulation results when characters at one stage of development are required for the correct formation of other characters at subsequent stages (his stepping stone model). In other words, ontogeny creates phylogeny because some developmental features are constraints, favoring particular evolutionary outcomes while excluding others. This viewpoint is a useful basis for advancing concepts of homology and for comparing the phylogeny of ontogenies across a series of animals to ascertain the timing and the nature of the underlying ontogenetic changes.

A trypsin homolog in amphioxus: expression, enzymatic activity and evolution

Trypsin has been documented in a variety of species including both vertebrates and invertebrates, but little is known about it in amphioxus, a model organism for insights into the origin and evolution of vertebrates. Here we identified a trypsin gene in Branchiostoma japonicum. The cDNA was 978 bp long with an ORF encoding a deduced protein of 272 amino acids. The deduced protein had an N-terminal signal peptide of 15 amino acids, a 16 activation peptide with the typical cleavage site Arg/Ile, a Tryp_SPc domain with the catalytic triad His(72)-Asp(118)-Ser(215) and the S1 substrate binding residue Asp(209), which are all characteristic of trypsinogens. The recombinant trypsin protein was able to hydrolyse the trypsin prototypic substrate BAEE, which was inhibited by the trypsin-specific inhibitor soybean trypsin inhibitor. Both northern blotting and tissue-section in situ hybridization demonstrated that trypsin gene was expressed in a tissue-specific manner, with most abundant levels in the hepatic caecum, mid-gut and ovary. And the whole mount in situ hybridization showed that it began to express in the middle third of the full-length primitive gut in 2-day larvae, where the hepatic caecum will form later during development. Phylogenetic analysis indicated that both amphioxus and ascidian trypsins are more closer to each other than to vertebrate trypsins, suggesting a continuous evolutionary divergence of vertebrate trypsins after split from protochordate/vertebrate common ancestor.

An ancient molecule with novel function: Alanine aminotransferase as a lipopolysaccharide binding protein with bacteriocidal activity

Alanine aminotransaminase (ALT) has been identified from bacteria to plants to animals including humans. The increase in serum ALT is regarded as an index for clinical diagnosis of liver function in humans. However, ALT elevation is also reported in non-liver injury conditions and in apparently healthy people, suggesting it may play a fundamental role physiologically. Herein we isolated an alt homolog, Amphialt, from Branchiostoma japonicus, an intermediatary species from invertebrates to vertebrates, which encoded a polypeptide of 500 amino acids with more than 62 and 52% sequence identity to vertebrate and invertebrate ALT isoenzymes, respectively. It was constitutively expressed in many tissues including the hepatic caecum, the precursor of liver, and its expression in the caecum was significantly up-regulated by challenge with lipopolysaccharides (LPS). Strikingly, recombinant AmphiALT, with a specific activity of 0.114±0.02U/mg, was capable of specifically binding to the Gram-negative bacteria Escherichia coli and Aeromonas hydrophila and to their conserved molecule LPS, as well as inhibiting the growth of E. coli and causing its lysis. In contrast, AmphiALT did not bind to the Gram-positive bacteria Staphyloccocus aureus and Bacillus subtilis as well as their conserved molecule LTA. In addition, a high homology noted between amphioxus and mammalian ALT sequences suggested a functional conservation of ALT evolutionarily, hinting at the clue that mammalian ALT may also play an antibacterial role similar to that of AmphiALT. Taken together, it is proposed that AmphiALT is an immune-relevant molecule capable of identifying LPS and causing damage to Gram-negative bacteria like E. coli and A. hydrophila. It also bolsters the notion that the hepatic caecum of amphioxus is the precursor of vertebrate liver, acting as a major tissue in acute phase response.

Identification and expression of liver-specific genes after LPS challenge in amphioxus: the hepatic cecum as liver-like organ and "pre-hepatic" acute phase response

Liver is present in all vertebrates and central to many physiological processes including processing of nutrients from ingested food, plasma protein synthesis, hormone production, and detoxification. However, its evolutionary origin remains open to date. Liver is also the principal organ of acute phase response (APR) but when the vertebrate-like APR regulatory network emerges during the chordate evolution is unknown. By combining global genome survey and qRT-PCR data sets, here, we clearly demonstrate the presence of the 58 vertebrate (zebrafish) liver-specific genes in amphioxus (hepatic cecum-specific genes) that are expressed in a tissue-specific manner in the hepatic cecum, the homolog of liver. Among these 58 hepatic cecum-specific genes, 52 genes respond to lipopolysaccharide challenge, which show similar expression profiles in both zebrafish and amphioxus. In addition, searching for binding sites for HNF and APR-associated transcription factors in promoter sequences for all the 58 hepatic cecum-specific genes and the 52 APR-related genes suggests that both HNF factors and APR-associated transcription factors in amphioxus form regulatory networks similar to those observed in zebrafish, regulating the hepatic cecum-specific genes and APR-related genes, respectively, via binding to their binding sites in the promoter regions. These similarities in liver/hepatic cecum-specific genes, APR, and regulatory networks between amphioxus and zebrafish supports the idea that hepatic cecum in amphioxus is the "pre-hepatic" organ homologous to vertebrate liver and acts as an immunological organ, playing an important role in APR.

Ontogeny of the collar cord: neurulation in the hemichordate Saccoglossus kowalevskii

The chordate body plan is characterized by a central notochord, a pharynx perforated by gill pores, and a dorsal central nervous system. Despite progress in recent years, the evolutionary origin of each of theses characters remains controversial. In the case of the nervous system, two contradictory hypotheses exist. In the first, the chordate nervous system is derived directly from a diffuse nerve net; whereas, the second proposes that a centralized nervous system is found in hemichordates and, therefore, predates chordate evolution. Here, we document the ontogeny of the collar cord of the enteropneust Saccoglossus kowalevskii using transmission electron microscopy and 3D-reconstruction based on completely serially sectioned stages. We demonstrate that the collar cord develops from a middorsal neural plate that is closed in a posterior to anterior direction. Transversely oriented ependymal cells possessing myofilaments mediate this morphogenetic process and surround the remnants of the neural canal in juveniles. A mid-dorsal glandular complex is present in the collar. The collar cord in juveniles is clearly separated into a dorsal saddle-like region of somata and a ventral neuropil. We characterize two cell types in the somata region, giant neurons and ependymal cells. Giant neurons connect via a peculiar cell junction that seems to function in intercellular communication. Synaptic junctions containing different vesicle types are present in the neuropil. These findings support the hypotheses that the collar cord constitutes a centralized element of the nervous system and that the morphogenetic process in the ontogeny of the collar cord is homologous to neurulation in chordates. Moreover, we suggest that these similarities are indicative of a close phylogenetic relationship between enteropneusts and chordates.

Antioxidant activities of recombinant amphioxus (Branchiostoma belcheri) apolipoprotein D

Apolipoprotein D (ApoD), a member of lipocalin, has been recently shown to be involved in regulating protection from oxidative stress. The absence of ApoD in mouse and Drosophila can reduce the resistance to oxidative stress and shorten lifespan. However, little information is available regarding the expression in vitro of ApoD and its biochemical properties. Amphioxus (Branchiostoma belcheri) ApoD, BbApoD, is an archetype of vertebrate ApoD proteins. In this study, the prokaryotic expression plasmid pET32a-BbApoD was constructed and recombinant BbApoD expressed in Escherichia coli BL21 and purified. Antioxidation assays showed that the recombinant BbApoD protein had the capacities to scavenge hydroxyl radicals (≥ 240 μg/ml) and to prevent nicking of the supercoiled DNA (≥ 100 μg/ml) in vitro, providing a biochemical evidence for antioxidant role of ApoD. This supports the notion that ApoD is part of the mechanisms regulating protection from oxidative stresses.

Glial versus melanocyte cell fate choice: Schwann cell precursors as a cellular origin of melanocytes

Melanocytes and Schwann cells are derived from the multipotent population of neural crest cells. Although both cell types were thought to be generated through completely distinct pathways and molecular processes, a recent study has revealed that these different cell types are intimately interconnected far beyond previously postulated limits in that they share a common post-neural crest progenitor, i.e. the Schwann cell precursor. This finding raises interesting questions about the lineage relationships of hitherto unrelated cell types such as melanocytes and Schwann cells, and may provide clinical insights into mechanisms of pigmentation disorders and for cancer involving Schwann cells and melanocytes.

Functional specialization of cellulose synthase genes of prokaryotic origin in chordate larvaceans

Extracellular matrices play important, but poorly investigated, roles in morphogenesis. Extracellular cellulose is central to regulation of pattern formation in plants, but among metazoans only tunicates are capable of cellulose biosynthesis. Cellulose synthase (CesA) gene products are present in filter-feeding structures of all tunicates and also regulate metamorphosis in the ascidian Ciona. Ciona CesA is proposed to have been acquired by lateral gene transfer from a prokaryote. We identified two CesA genes in the sister-class larvacean Oikopleura dioica. Each has a mosaic structure of a glycoslyltransferase 2 domain upstream of a glycosyl hydrolase family 6 cellulase-like domain, a signature thus far unique to tunicates. Spatial-temporal expression analysis revealed that Od-CesA1 produces long cellulose fibrils along the larval tail, whereas Od-CesA2 is responsible for the cellulose scaffold of the post-metamorphic filter-feeding house. Knockdown of Od-CesA1 inhibited cellulose production in the extracellular matrix of the larval tail. Notochord cells either failed to align or were misaligned, the tail did not elongate properly and tailbud embryos also exhibited a failure to hatch. Knockdown of Od-CesA2 did not elicit any of these phenotypes and instead caused a mild delay in pre-house formation. Phylogenetic analyses including Od-CesAs indicate that a single lateral gene transfer event from a prokaryote at the base of the lineage conferred biosynthetic capacity in all tunicates. Ascidians possess one CesA gene, whereas duplicated larvacean genes have evolved distinct temporal and functional specializations. Extracellular cellulose microfibrils produced by the pre-metamorphic Od-CesA1 duplicate have a role in notochord and tail morphogenesis.