The Complement System of Agnathans

Agnathans (lamprey and hagfish) are a group of primitive jawless fish. Jawed vertebrates possess adaptive immunity including immunoglobulins, while agnathans lack immunoglobulins but have alternative adaptive immunity in which variable lymphocyte receptors (VLRs) function as antibodies. The complement system consists of many proteins involved in the elimination of pathogens. In mammals, it is activated via the three different pathways, resulting in the generation of C3b followed by the lytic pathway. Complement components including C3, mannose-binding lectin (MBL), and MBL-associated serine proteases (MASP) of the lectin pathway and factor B of the alternative pathway have been identified from lamprey and/or hagfish, while lytic pathway components have not been identified. In mammals, C1q binds to IgM/IgG-antigen complexes and activates the classical pathway in association with C1r and C1s. Lamprey also has C1q (LC1q), but its function differs from that of mammalian C1q. LC1q acts as a lectin and activates C3 in association with MASP via the lectin pathway. Furthermore, LC1q may interact with a secreted type of VLR (VLRB) in complex with antigens and mediate activation of C3, potentially via MASP, leading to cytolysis. Cytolysis is mediated by a newly identified serum protein named lamprey pore-forming protein (LPFP). In conclusion, lamprey has a complement activation pathway, which could be regarded as the classical pathway and also has a cytolytic system that is distinct from the mammalian lytic pathway. Thus, it appears that the complement system of agnathans is very unique and may have developed independently from jawed vertebrates

Genomic view of the evolution of the complement system

The recent accumulation of genomic information of many representative animals has made it possible to trace the evolution of the complement system based on the presence or absence of each complement gene in the analyzed genomes. Genome information from a few mammals, chicken, clawed frog, a few bony fish, sea squirt, fruit fly, nematoda and sea anemone indicate that bony fish and higher vertebrates share practically the same set of complement genes. This suggests that most of the gene duplications that played an essential role in establishing the mammalian complement system had occurred by the time of the teleost/mammalian divergence around 500 million years ago (MYA). Members of most complement gene families are also present in ascidians, although they do not show a one-to-one correspondence to their counterparts in higher vertebrates, indicating that the gene duplications of each gene family occurred independently in vertebrates and ascidians. The C3 and factor B genes, but probably not the other complement genes, are present in the genome of the cnidaria and some protostomes, indicating that the origin of the central part of the complement system was established more than 1,000 MYA

Phylogenomics of vertebrate serpins

Kumar A. Phylogenomics of vertebrate serpins. Bielefeld (Germany): Bielefeld University; 2010.The serpins constitute a superfamily of proteins that fold into a conserved tertiary structure and employ a sophisticated, irreversible suicide-mechanism of inhibition. More than 6000 serpins have been identified, occurring in all three forms of the life - the eukaryotes, the prokaryotes and the archea. Vertebrate serpins can be conveniently classified into six groups (V1 - V6), based on three independent biological features - gene organization, diagnostic amino acid sites and rare indels. In the present work, the phylogenetic relationships of serpins from Nematostella vectensis, Strongylocentrotus purpuratus, Ciona intestinalis, four fish species, frog, chicken and mammals were investigated, using gene architecture analyses and stringent criteria for identification of orthologs. With some deviations, all vertebrate serpin genes fit into one of the six exon/intron gene classes previously identified, dating the existence and maintenance of these gene organizations before or close to the divergence of fishes. Group V1 and V2 gene families underwent rapid adaptive radiation along the lineages leading to mammals as indicated by an up to nine-fold increased number of family members, accompanied by a rapid functional diversification. In contrast, gene groups V3 to V6 display a rather conservative evolution with little changes since the divergence of fishes and the other vertebrates. The orthology assessment indicates that all vertebrates are equipped with a subset of strongly conserved serpins with functions that can be clearly correlated with basic vertebrate-specific physiology. None of serpin genes from C. intestinalis shares a common exon-intron architecture organisation with any of the vertebrate serpin gene classes, nor was it possible to identify orthologs of vertebrates. The lack of gene architecture similarity and the complete absence of orthology between urochordate and vertebrate serpins indicate that major changes with bursts of character acquisition must have occurred during evolution of serpins in the time interval separating urochordates from chordates, indicating massive intron gains or losses and events providing C and N-terminal sequence extensions characteristic for today's vertebrate serpins. Lancelets and sea urchin genomes, in contrast, share one orthologous serpin with vertebrates. Rare genomic characters are used to show that orthologs of neuroserpin, a prominent representative of vertebrate group V3 serpin genes, exist in early diverging deuterostomes and probably also in cnidarians, indicating that the origin of a mammalian serpin can be traced back far in the history of eumetazoans. A C-terminal address code assigning association with secretory pathway organelles is present in all neuroserpin orthologs, suggesting that supervision of cellular export/import routes by antiproteolytic serpins is an ancient trait. Phylogenomic comparisons show that, after establishment of canonical exon-intron patterns in the serpin superfamily at the dawn of vertebrate evolution, multiple intron acquisition events have occurred during diversification of a lineage of actinopterygian fishes. The novel introns were acquired within a limited time interval (on an evolutionary timescale), and no such events were observed in other groups of vertebrates. Examination of the sequences flanking the intron insertion points revealed that the genetic requirements for acquisition of novel introns might be less stringent than previously suggested. Finally, we argue that genome compaction, a phenomenon associated with the fish lineage depicting preferential intron gain, might promote intron acquisition

Evolution, gene regulation and functional analysis of BMP2 in fish

Bone morphogenetic proteins (BMPs) are multifunctional growth factors belonging to the transforming growth factor β (TGFβ) superfamily with a central role in bone formation and mineralization. BMP2, a founding member of this family, has demonstrated remarkable osteogenic properties and is clinically used to promote bone repair and fracture healing. Lack of basic data on factors regulating BMP2 expression and activity have hampered a better understanding of its role in bone formation and bone-related diseases. The objective of this work was to collect new functional data and determine spatiotemporal expression patterns in a fish system aiming towards a better understanding of BMP2 function and regulation. Transcriptional and post-transcriptional regulation of gilthead seabream BMP2 gene was inferred from luciferase reporter systems. Several bone- and cartilage-related transcription factors (e.g. RUNX3, MEF2c, SOX9 and ETS1) were found to regulate BMP2 transcription, while microRNA 20a was shown to affect stability of the BMP2 transcript and thus the mineralogenic capacity of fish bone-derived host cells. The regulation of BMP2 activity through an interaction with the matrix Gla protein (MGP) was investigated in vitro using BMP responsive elements (BRE) coupled to luciferase reporter gene. Although we demonstrated the functionality of the experimental system in a fish cell line and the activation of BMP signaling pathway by seabream BMP2, no conclusive evidence could be collected on a possible interaction beween MGP and BMP2. The evolutionary relationship among the members of BMP2/4/16 subfamily was inferred from taxonomic and phylogenetic analyses. BMP16 diverged prior to BMP2 and BMP4 and should be the result of an ancient genome duplication that occurred early in vertebrate evolution. Structural and functional data suggested that all three proteins are effectors of the BMP signaling pathway, but expression data revealed different spatiotemporal patterns in teleost fish suggesting distinct mechanisms of regulation. In this work, through the collection of novel data, we provide additional insight into the regulation, the structure and the phylogenetic relationship of BMP2 and its closely related family members.O sistema esquelético confere suporte e proteção ao organismo, permite o armazenamento de minerais e desempenha funções hematopoiéticas. Um dos seus principais componentes é o osso, um tecido conectivo especializado e constituído por uma matriz extracelular extensamente mineralizada. O processo de mineralização envolve mecanismos extremamente complexos que estão sujeitos a um rigoroso controlo a nível molecular, no qual estão envolvidas várias proteínas responsáveis pela diferenciação celular e pela síntese de matriz extracelular. Dentro deste conjunto de proteínas, destacam-se alguns fatores de crescimento essenciais ao mecanismo de mineralização tecidular, como é o caso das proteínas morfogenéticas do osso (BMPs). As BMPs pertencem à superfamília de fatores de crescimento de transformação β (TGFβ) e estão envolvidas em vários processos durante a embriogénese, organogénese, proliferação e diferenciação celular e mecanismos de formação óssea. Atualmente estão descritos e caracterizados mais de vinte membros pertencentes a esta família, que foram divididos em várias subfamílias, de acordo com a semelhança da estrutura primária das suas proteínas. A subfamília BMP2/4/16 à qual pertence a BMP2 foi uma das primeiras a ser identificada e caracterizada. A BMP2 é uma das proteínas que possui uma maior capacidade osteogénica e é, desde há muito tempo, considerada um potencial agente terapêutico para o tratamento de doenças relacionadas com o osso, sendo mesmo utilizada em alguns casos clínicos de fraturas ósseas. O conhecimento dos processos de formação óssea, bem como os mecanismos de regulação da BMP2, são por isso de extrema importância para uma melhor compreensão dos processos subjacentes ao desenvolvimento e progressão de algumas doenças ósseas. Assim, a BMP2 tem sido alvo de vários estudos, quer a nível de conhecimento da sua função, quer a nível de mecanismos de ação e processamento. Sabe-se que a BMP2 é uma proteína secretada para a matriz extracelular onde, através de um mecanismo de sinalização molecular, é responsável pela regulação de vários processos. O mecanismo de sinalização inicia-se quando dímeros de BMP2 se ligam aos respetivos recetores, presentes na superfície da célula, ativando assim uma cascata de sinalização molecular. Através de diferentes intermediários intracelulares, envolvidos na cascata de sinalização, a BMP2 é responsável pela regulação transcricional de vários genes-alvo. No entanto, e apesar dos vários estudos que foram feitos nesta área, o conhecimento existente acerca deste assunto é ainda bastante escasso. Neste sentido, o objetivo principal deste trabalho foi a recolha de novos dados funcionais e estruturais, que permitam uma melhor compreensão da função da BMP2. Para tal, e de modo a complementar o conhecimento existente, utilizámos o peixe como modelo alternativo aos sistemas de mamíferos. O peixe é atualmente reconhecido como um modelo válido para estudos do esqueleto de vertebrados para o qual existem já várias ferramentas que permitem análises in silico, in vitro e in vivo. Este trabalho envolveu o estudo da regulação do gene da BMP2 de dourada, tanto a nível transcricional como a nível pós-transcricional. Numa primeira fase, foram identificados potenciais reguladores transcricionais da BMP2 de dourada, através da análise in silico da região reguladora do gene. Dentro dos potenciais reguladores transcricionais, foram identificados vários fatores de transcrição com funções descritas ao nível do osso e da cartilagem, nomeadamente o RUNX3, SOX9, MEF2C e ETS1, que foram posteriormente testados a nível funcional através de ensaios repórter de luciferase. Em paralelo, no decorrer da caracterização de reguladores pós-transcricionais da BMP2, através da análise da região 3’ não traduzida (3’UTR) do seu mRNA, foi possível identificar um local de ligação para o miR-20a, conservado ao longo da evolução. A fim de melhor compreender os mecanismos de ação da BMP2, neste trabalho investigámos também possíveis parceiros desta proteína. A caraterização da interação entre a BMP2 e a proteína Gla da matriz (MGP), um conhecido inibidor da calcificação, foi avaliada através do uso de um sistema de elementos de resposta às BMPs, acoplado a um gene repórter, a luciferase. Embora tenhamos demonstrado a funcionalidade do sistema através da ativação do mecanismo de sinalização celular pela BMP2 de dourada, não foram obtidos dados conclusivos no que diz respeito à interação entre a BMP2 e a MGP. Finalmente, abordamos o aspecto evolutivo dos membros da subfamília BMP2/4/16 através da análise da sua distribuição taxonómica entre vários organismos vertebrados, bem como as relações filogenéticas existentes entre os vários membros desta subfamília. Foi demonstrado que a BMP16 divergiu antes da BMP2 e BMP4 na linhagem dos vertebrados e foi, provavelmente, o resultado de uma duplicação genómica que terá ocorrido ancestralmente. Dados estruturais sugerem uma conservação funcional das três proteínas, facto que foi confirmado pela capacidade de ativação dos mecanismos de sinalização das BMPs. No entanto, e apesar da conservação ao nível da região codante dos genes das BMP2, BMP4 e BMP16, as regiões não traduzidas são substancialmente diferentes, apontando para uma regulação diferencial dos três genes, como é aliás sugerido pelos distintos padrões de expressão observados para a BMP2, BMP4 e BMP16, tanto em linguado como em peixe zebra. Ao longo deste trabalho foram recolhidos novos dados que permitem uma melhor compreensão da função e regulação da BMP2. Foram igualmente obtidas informações relevantes acerca da filogenia molecular dos membros da subfamília das BMP2/4/16 que contribuíram para uma melhor compreensão e interpretação da complexa história evolutiva desta subfamília. No seu conjunto, os resultados deste trabalho contribuem para uma validação do uso dos peixes como um modelo alternativo na investigação de mecanismos moleculares envolvidos no processo de mineralização tecidular.Universidade do Algarve, Departamento de Ciências Biomédica

Handbook of Marine Model Organisms in Experimental Biology

"The importance of molecular approaches for comparative biology and the rapid development of new molecular tools is unprecedented. The extraordinary molecular progress belies the need for understanding the development and basic biology of whole organisms. Vigorous international efforts to train the next-generation of experimental biologists must combine both levels – next generation molecular approaches and traditional organismal biology. This book provides cutting-edge chapters regarding the growing list of marine model organisms. Access to and practical advice on these model organisms have become aconditio sine qua non for a modern education of advanced undergraduate students, graduate students and postdocs working on marine model systems. Model organisms are not only tools they are also bridges between fields – from behavior, development and physiology to functional genomics. Key Features Offers deep insights into cutting-edge model system science Provides in-depth overviews of all prominent marine model organisms Illustrates challenging experimental approaches to model system research Serves as a reference book also for next-generation functional genomics applications Fills an urgent need for students Related Titles Jarret, R. L. & K. McCluskey, eds. The Biological Resources of Model Organisms (ISBN 978-1-1382-9461-5) Kim, S.-K. Healthcare Using Marine Organisms (ISBN 978-1-1382-9538-4) Mudher, A. & T. Newman, eds. Drosophila: A Toolbox for the Study of Neurodegenerative Disease (ISBN 978-0-4154-1185-1) Green, S. L. The Laboratory Xenopus sp. (ISBN 978-1-4200-9109-0)

Evolutionary and Developmental Survey of Genes Involved in Chordate Pigmentation

The pigmentation represents one of the most interesting topics in animal life because it is a decisive factor for the evolutionary success and the conquest of new ecological niches. Through the combination of developmental biology and comparative genomics, some aspects of pigmentary dynamics have been studied. Given Rabs regulate a plethora of trafficking steps, the members belonging to this family are central to the transport of molecules involved in pigmentation. Moreover, comprehending the evolution of Rab family is relevant to understand the establishment of eukaryotic cellular organization and for its implication in many human pathologies. For the first time, I reconstructed the evolutionary scenario of Rab family in eleven species of metazoans, spanning from cnidarians to human. Phylogeny, intron code and synteny conservation prompted me to depict Rab evolution, with a special focus on chordates that exhibit a highly dynamic evolutionary pattern. I clarified the evolution of Rab32/38 subfamily, fundamental in regulation of trafficking related to melanogenesis. It has been clarified the evolutionary history of Rab32/38 genes in deuterostomes and the expression pattern in key species as zebrafish and amphioxus, demonstrating how events as whole-genome duplications have influenced their role during embryogenesis. In order to find new genes involved in pigmentation, I analyzed a Kelch-like member in ascidian Ciona robusta (Cr-Klhl21). My results point at this gene as a marker of pigmented cells, with a dynamic expression profile during embryogenesis: from middle tailbud stage, it is expressed specifically in the otolith. Moreover, Cr-Klhl21 shows an intricate regulatory scenario with the possible intervention of a transcription factors combination (Cr-Mitf, Cr-msxb, Cr-Dmrt). This work contains first data about a Kelch-like member in ascidians, providing new insights in pigmentation or pigment cell specification. This encourages further analyses on its gene regulatory network and possible function

Direct evidence for a membrane deforming motif in endophilin: implications beyond synaptic vesicle recycling

Effective neurotransmission is dependent on fast, reproduceable synaptic vesicle recycling. The synaptic vesicle recycling process is a complex event involving both protein-protein, as well as protein-lipid interactions. A central part of the retrieval process of synaptic vesicles lies in the ability of soluble proteins to deform the plasma membrane into a nascent bud which will eventually reform a fully competent synaptic vesicle upon fission. This process involves clathrin-coat proteins, which form a protein scaffold around the vesicle bud, as well as proteins which have more recently been thought to be involved in generating the high curvature membranes present at the tubular neck of the nascent vesicle bud.Endophilin 1, a protein highly enriched in the pre-synaptic neuronal subcompartment has been implicated in many stages of synaptic vesicle retrieval. The following work represents evidence of a direct role for endophilin in tubular membrane deformation, which may play an important part in the regeneration of synaptic vesicles. This behavior of endophilin complements that of one of its major pre-synaptic binding partners, dynamin, a large GTPase strongly implicated in the fission process of endocytosis. Endophilin forms a coordinated complex with dynamin along membrane tubules, and stabilizes these membrane tubules against the biomechanical changes imparted by dynamin to the membrane in a GTP-dependent manner.The membrane deforming motif in endophilin comprises a putative amphipathic helical region. This motif is conserved in amphiphysin, another major pre-synaptic dynamin binding partner implicated in synaptic vesicle recycling, and in another endophilin-related protein localized to the Golgi complex. Membrane deforming amphipathic helices have since been found in other proteins localized to additional cellular subcompartments, implicating this type of membrane interaction in diverse functions within the cell

Genetic Factors Associated with Anti-Factor H Autoantibodies in Atypical Hemolytic Uremic Syndrome (aHUS)

Atypical hemolytic uremic syndrome (aHUS) is a rare form of thrombotic microangiopathy characterized by renal failure and determined by genetic and acquired defects of alternative pathway (AP) of the complement system. Autoantibodies against factor H (anti-FHs), a regulator of the AP, were reported in 10% of patients, and are associated with the deficiency of factor H related 1 (FHR1), a FH homologous protein. The aim of this thesis was to evaluate the contribution of genetics to the development of anti-FHs in aHUS. Thirty patients affected by aHUS resulted positive for anti-FHs (9.8%) and FHR1 deficiency was present in 83.3% of them. A healthy control also showed anti-FHs in concomitance with FHR1 deficiency documenting that the lack of FHR1 strongly predisposed to anti-FH development also in healthy subjects although this condition was not sufficient for the disease manifestation. The presence of infectious prodromal signs and an age at the disease onset around 8 years indicated that common infections may trigger the development of autoantibodies in subjects with at risk genetic background. Likely pathogenetic variants in complement genes were observed in 37% of our patients with anti-FHs. At variance, common variants in complement genes did not seem to contribute to the disease, as documented by comparing patients with super controls, unaffected subjects carrying FHR1 deficiency. Finally, I report that the HLA-DRB1*11:04 allele could be a predisposing genetic variant for anti-FH associated aHUS. Further works will be necessary to confirm this finding and to explore the presence of other genetic susceptibility factors that, in combination with the HLA-DRB1*11:04 allele and the FHR1 deficiency, could increase the risk for anti-FHs