EST analysis of mRNAs expressed in neurula of Chinese amphioxus

An Overview of Bioinformatics Tools and Resources in Allergy

The rapidly increasing number of characterized allergens has created huge demands for advanced information storage, retrieval, and analysis. Bioinformatics and machine learning approaches provide useful tools for the study of allergens and epitopes prediction, which greatly complement traditional laboratory techniques. The specific applications mainly include identification of B- and T-cell epitopes, and assessment of allergenicity and cross-reactivity. In order to facilitate the work of clinical and basic researchers who are not familiar with bioinformatics, we review in this chapter the most important databases, bioinformatic tools, and methods with relevance to the study of allergens.

EST and transcriptome analysis of cephalochordate amphioxus--past, present and future

The cephalochordates, commonly known as amphioxus or lancelets, are now considered the most basal chordate group, and the studies of these organisms therefore offer important insights into various levels of evolutionary biology. In the past two decades, the investigation of amphioxus developmental biology has provided key knowledge for understanding the basic patterning mechanisms of chordates. Comparative genome studies of vertebrates and amphioxus have uncovered clear evidence supporting the hypothesis of two-round whole-genome duplication thought to have occurred early in vertebrate evolution and have shed light on the evolution of morphological novelties in the complex vertebrate body plan. Complementary to the amphioxus genome-sequencing project, a large collection of expressed sequence tags (ESTs) has been generated for amphioxus in recent years; this valuable collection represents a rich resource for gene discovery, expression profiling and molecular developmental studies in the amphioxus model. Here, we review previous EST analyses and available cDNA resources in amphioxus and discuss their value for use in evolutionary and developmental studies. We also discuss the potential advantages of applying high-throughput, next-generation sequencing (NGS) technologies to the field of amphioxus research.

Molecular characteristics of the tubeworm, Ridgeia piscesae, from the deep-sea hydrothermal vent

Ridgeia piscesae, living around the extremely harsh hydrothermal vent in deep sea, is an ideal model for studying the adaptative mechanism to extreme environment. For insights of its molecular characteristics, a cDNA library of R. piscesae was constructed. A total of 879 expressed sequence tags (ESTs) were sequenced and 199 genes were identified for the first time. They were found to be involved in basal metabolism, adaptation and defense, or signal transduction. Among them, we found 23 various chitin-binding proteins, which are the major component of the chitinous tube that prevents the tubeworms from predators and surrounding extreme environment. Additionally, high polymorphism also exists in other genes, such as myohemerythrin, lysozyme. The gene-expression profile might help to further understand the molecular basis of tubeworm physiology. It will also lay a good foundation for functional studies on the adaptation to extreme environments.

The identification of lymphocyte-like cells and lymphoid-related genes in amphioxus indicates the twilight for the emergence of adaptive immune system

To seek evidence of a primitive adaptive immune system (AIS) before vertebrate, we examined whether lymphocytes or lymphocyte-like cells and the related molecules participating in the lymphocyte function existed in amphioxus. Anatomical analysis by electron microscopy revealed the presence of lymphocyte-like cells in gills, and these cells underwent morphological changes in response to microbial pathogens that are reminiscent of those of mammalian lymphocytes executing immune response to microbial challenge. In addition, a systematic comparative analysis of our cDNA database of amphioxus identified a large number of genes whose vertebrate counterparts are involved in lymphocyte function. Among these genes, several genes were found to be expressed in the vicinity of the lymphocyte-like cells by in situ hybridization and up-regulated after exposure to microbial pathogens. Our findings in the amphioxus indicate the twilight for the emergence of AIS before the invertebrate-vertebrate transition during evolution.

Bbt-TNFR1 and Bbt-TNFR2, two tumor necrosis factor receptors from Chinese amphioxus involve in host defense

Two novel tumor necrosis factor receptors, Bbt-TNFR1 and Bbt-TNFR2, were isolated from Chinese amphioxus, the closest relative to vertebrate. The mRNA of Bbt-TNFR1 encoded a type I membrane protein of 452 amino acids, including four cysteine-rich domains in the extracellular region and a putative TRAF6-binding site at its 154aa long cytoplasmic tail. Bbt-TNFR2 was a 304aa long type I membrane protein, featuring three cysteine-rich domains and a short cytoplasmic tail of just 13 amino acids. Southern blot revealed that Bbt-TNFR1 was a single copy gene, while Bbt-TNFR2 was presented in multiple copies. Sequence comparison indicated that both Bbt-TNFR1 and Bbt-TNFR2 were weakly similar to LT-bR, HVEM, TNFR2, CD40, OX40 and DcR3. Real-time PCR showed that Bbt-TNFR1 and Bbt-TNFR2 were regulated during development and finally had high expression in mucosa-rich tissues in adult stage. Furthermore, up-regulated expression of both genes was also observed in guts after Gram-positive bacteria challenge. However, not like Bbt-TNFR2's slowly and gradually augmentation in the following 48 h, expression of Bbt-TNFR1 dramatically surged up within 4 h and then subsided rapidly. Taking together, Bbt-TNFR1 and Bbt-TNFR2 may involve in the host defense of Chinese amphioxus via distinct fashions.

Expression analysis of immune-relevant genes in the spleen of large yellow croaker (Pseudosciaena crocea) stimulated with poly I:C

A SMART cDNA library from spleen of large yellow croaker (Pseudosciaena crocea) stimulated by poly I:C was constructed. A total of 1039 clones from the library were single-pass sequenced and compared with known sequences in the GenBank database. Of those expressed sequence tags (ESTs), 607 were identified as orthologs of known genes in the GenBank databases by Blast X search. Four hundred and thirty-two did not show significant homology with any known sequences in the public databases. These identified ESTs represented at least 252 different genes, which were categorised into nine groups according to their function. Of the identified genes, 159 genes (63.1%) shared homology with fish genes while 93 (36.9%) showed the highest homology to the genes from other species. Forty-six genes were identified to be involved in immune functions, including complement system components, immunoglobulins, antigen processing and presentation proteins, interferon system proteins, cytokines, and some innate defence molecules. The most frequently occurring genes in this spleen cDNA library were hepcidin precursors represented by 46 ESTs, which were divided into five groups based on their putative amino acid sequences. The expression analysis of selected genes during polyI:C induction was performed by reverse transcription-PCR (RT-PCR), including Mx protein, beta2-microglobulin (beta(2)m), CD2 binding protein 1(CD2BP1), placenta-specific 8 genes, MHC class II associated invariant chain (li) and cytochrome b-245 alpha peptide (Cyba). The results revealed that expression levels of Mx protein, beta(2)m, placenta-specific 8 genes, and Cyba were significantly upregulated at 30h after induction with poly I:C, and the CD2BP1 expression was also induced by polyI:C, suggesting that these genes may be involved in an immune response induced by poly I:C in large yellow croaker.

Transcriptome analysis of Deinagkistrodon acutus venomous gland focusing on cellular structure and functional aspects using expressed sequence tags

Background

The snake venom gland is a specialized organ, which synthesizes and secretes the complex and abundant toxin proteins. Though gene expression in the snake venom gland has been extensively studied, the focus has been on the components of the venom. As far as the molecular mechanism of toxin secretion and metabolism is concerned, we still knew a little. Therefore, a fundamental question being arisen is what genes are expressed in the snake venom glands besides many toxin components?

Results

To examine extensively the transcripts expressed in the venom gland of Deinagkistrodon acutus and unveil the potential of its products on cellular structure and functional aspects, we generated 8696 expressed sequence tags (ESTs) from a non-normalized cDNA library. All ESTs were clustered into 3416 clusters, of which 40.16% of total ESTs belong to recognized toxin-coding sequences; 39.85% are similar to cellular transcripts; and 20.00% have no significant similarity to any known sequences. By analyzing cellular functional transcripts, we found high expression of some venom related genes and gland-specific genes, such as calglandulin EF-hand protein gene and protein disulfide isomerase gene. The transcripts of creatine kinase and NADH dehydrogenase were also identified at high level. Moreover, abundant cellular structural proteins similar to mammalian muscle tissues were also identified. The phylogenetic analysis of two snake venom toxin families of group III metalloproteinase and serine protease in suborder Colubroidea showed an early single recruitment event in the viperids evolutionary process.

Conclusion

Gene cataloguing and profiling of the venom gland of Deinagkistrodon acutus is an essential requisite to provide molecular reagents for functional genomic studies needed for elucidating mechanisms of action of toxins and surveying physiological events taking place in the very specialized secretory tissue. So this study provides a first global view of the genetic programs for the venom gland of Deinagkistrodon acutus described so far and an insight into molecular mechanism of toxin secreting.

All sequences data reported in this paper have been submitted into the public database [GenBank: DV556511-DV565206].

Construction of a BAC library for Chinese amphioxus Branchiostoma belcheri and identification of clones containing Amphi-Pax genes

Amphioxus is a crucial organism for the study of vertebrate evolution. Although a genomic BAC library of Branchiostoma floridae has been constructed, we report here another BAC library construction of its distant relative species Branchiostoma belcheri. The amphioxus BAC library established in present study consists of 45,312 clones arrayed in one hundred and eighteen 384-well plates. The average insert fragment size was 120 kb estimated by Pulsed Field Gel Electrophoresis (PFGE) analysis of 318 randomly selected clones. The representation of the library is about 12 equivalent to the genome, allowing a 99.9995% probability of recovering any specific sequence of interest. We further screened the library with 4 single copied Amphi-Pax genes and identified total of 26 positive clones with average of 6.5 clones for each gene. The result indicates this library is well suited for many applications and should also serve as a useful complemental resource for the scientific community.

The phylogenetic analysis of tetraspanins projects the evolution of cell–cell interactions from unicellular to multicellular organisms

In animals, the tetraspanins are a large superfamily of membrane proteins that play important roles in organizing various cell-cell and matrix-cell interactions and signal pathways based on such interactions. However, their origin and evolution largely remain elusive and most of the family's members are functionally unknown or less known due to difficulties of study, such as functional redundancy. In this study, we rebuilt the family's phylogeny with sequences retrieved from online databases and our cDNA library of amphioxus. We reveal that, in addition to in metazoans, various tetraspanins are extensively expressed in protozoan amoebae, fungi, and plants. We also discuss the structural evolution of tetraspanin's major extracellular domain and the relation between tetraspanin's duplication and functional redundancy. Finally, we elucidate the coevolution of tetraspanins and eukaryotes and suggest that tetraspanins play important roles in the unicell-to-multicell transition. In short, the study of tetraspanin in a phylogenetic context helps us understand the evolution of intercellular interactions.

Identification and characterisation of a homolog of an activation gene for the recombination activating gene 1 (RAG 1) in amphioxus

Expression of recombination activating genes (RAG) involved in the V (D) J recombination is regulated by the RAG1 gene activator (RGA) in mammals. The sequence of a cDNA clone from an amphioxus cDNA library was found to be homologous to that of RGA from mouse stromal cells with 45% identity. The full-length cDNA sequence comprises 1119 bp and encodes a putative protein of 210 amino acid residues. Characterisation of the amino acid sequence revealed that two MtN3 domains and seven transmembrane spans are present in this protein, indicating a potential role as a plasma membrane protein. This gene is expressed in many tissues and at differential developmental stages. A high expression level of RGA is detected in gonad tissues, and gastrula embryo and adult stages. The presence of the RGA gene in amphioxus suggests that the signal pathway required for the expression of RAG could exist in this primitive protochordate. It also implies that in the related molecules, primitive adaptive immunity may have existed in cephalochordate although the complete machinery of VDJ rearrangement may not be formed.

Genes "waiting" for recruitment by the adaptive immune system: the insights from amphioxus

In seeking evidence of the existence of adaptive immune system (AIS) in ancient chordate, cDNA clones of six libraries from a protochordate, the Chinese amphioxus, were sequenced. Although the key molecules such as TCR, MHC, Ig, and RAG in AIS have not been identified from our database, we demonstrated in this study the extensive molecular evidence for the presence of genes homologous to many genes that are involved in AIS directly or indirectly, including some of which may represent the putative precursors of vertebrate AIS-related genes. The comparative analyses of these genes in different model organisms revealed the different fates of these genes during evolution. Their gene expression pattern suggested that the primitive digestive system is the pivotal place of the origin and evolution of the AIS. Our studies support the general statement that AIS appears after the jawless/jawed vertebrate split. However our study further reveals the fact that AIS is in its twilight in amphioxus and the evolution of the molecules in amphioxus are waiting for recruitment by the emergence of AIS.

Amphioxus molecular biology: insights into vertebrate evolution and developmental mechanisms

The cephalochordate amphioxus is the best available proxy for the last common invertebrate ancestor of the vertebrates. During the last decade, the developmental genetics of amphioxus have been extensively examined for insights into the evolutionary origin and early evolution of the vertebrates. Comparisons between expression domains of homologous genes in amphioxus and vertebrates have strengthened proposed homologies between specific body parts. Molecular genetic studies have also highlighted parallels in the developmental mechanisms of amphioxus and vertebrates. In both groups, a similar nested pattern of Hox gene expression is involved in rostrocaudal patterning of the neural tube, and homologous genes also appear to be involved in dorsoventral neural patterning. Studies of amphioxus molecular biology have also hinted that the protochordate ancestor of the vertebrates included cell populations that modified their developmental genetic pathways during early vertebrate evolution to yield definitive neural crest and neurogenic placodes. We also discuss how the application of expressed sequence tag and gene-mapping approaches to amphioxus have combined with developmental studies to advance our understanding of chordate genome evolution. We conclude by considering the potential offered by the sequencing of the amphioxus genome, which was completed in late 2004.

Macrophage migration inhibitory factor (MIF) in chinese amphioxus as a molecular marker of immune evolution during the transition of invertebrate/vertebrate

Macrophage migration inhibitory factor (MIF) is an important cytokine related to host defenses and autoimmune diseases. Here, we reported two full-length cDNA clones isolated from Chinese amphioxus (Branchiostoma belcheri tsingtaunese). Amino acid sequences analysis and structure prediction of these two molecules, called Bbt-MIF-I and Bbt-MIF-II, respectively, indicated that several conservative domains existed in the two amphioxus MIFs and their sequences were highly homologous to their counterparts of other species. Intriguingly, the Bbt-MIFs gene is present in multi-copy per haploid genome, which is very unusual compared with vertebrate's MIF gene given the known genome duplication theory. The genomic copy number, expression pattern of MIF gene and phylogenetic analysis of MIF proteins all suggested that a leap forward happened for MIF gene during the evolution from invertebrate to vertebrate. Considering the crucial role of MIF in innate immunity, MIF might serve as one of key molecular markers of evolution of immune system.