Ka Hou Chu

Cloning, expression, and primary structure of Metapenaeus ensis tropomyosin, the major heat-stable shrimp allergen

Shrimp is a common cause of seafood hypersensitivity. To study the mechanism of seafood hypersensitivity at the molecular level, we have determined the primary structure of the major heat-stable allergen of shrimp by cloning, expression, nucleotide sequencing, and amino acid sequence determination of an IgE-reactive cDNA clone, Met e I, isolated from a Metapenaeus ensis expression library in lambda gt 11. We first constructed a cDNA library from the shrimp M. ensis in lambda gt 11. We then screened the library with sera from patients with hypersensitivity reactions to shrimp and identified a positive IgE-reactive clone, designated as Met e I. This cDNA was purified to homogeneity and subsequently expressed in the plasmid pGEX. Serum antibodies from patients with shrimp allergy demonstrated positive IgE reactivity by immunoblotting to a protein encoded by the clone Met e I; sera from nonallergic control subjects were not reactive. The nucleotide sequence of this cDNA clone revealed an open reading frame of 281 amino acid residues, coding for a protein of 34 kd. Comparison of the Met e I amino acid sequence with the Genbank database showed that Met e I is highly homologous to multiple isoforms of tropomyosin.

Phylogeny of Decapoda using two nuclear protein-coding genes: Origin and evolution of the Reptantia

The phylogeny of Decapoda is contentious and many hypotheses have been proposed based on morphological cladistic analyses. Recent molecular studies, however, yielded contrasting results despite their use of similar data (nuclear and mitochondrial rDNA). Here we present the first application of two nuclear protein-coding genes, phosphoenolpyruvate carboxykinase and sodium-potassium ATPase alpha-subunit, to reconstruct the phylogeny of major infraorders within Decapoda. A total of 64 species representing all infraorders of Pleocyemata were analyzed with five species from Dendrobranchiata as outgroups. Maximum likelihood and Bayesian inference reveal that the Reptantia and all but one infraorder are monophyletic. Thalassinidea, however, is polyphyletic. The nodal support for most of the infraordinal and inter-familial relationships is high. Stenopodidea and Caridea form a clade sister to Reptantia, which comprises two major clades. The first clade, consisting of Astacidea, Achelata, Polychelida and three thalassinidean families (Axiidae, Calocarididae and Eiconaxiidae), corresponds essentially to the old taxon suborder Macrura Reptantia. Polychelida nests within Macrura Reptantia instead of being the most basal reptant as suggested in previous studies. The high level of morphological and genetic divergence of Polychelida from Achelata and Astacidea justifies its infraorder status. The second major reptant clade consists of Anomura, Brachyura and two thalassindean families (Thalassinidae and Upogebiidae). Anomura and Brachyura form Meiura, with moderate support. Notably thalassinidean families are sister to both major reptant clades, suggesting that the stem lineage reptants were thalassinidean-like. Moreover, some families (e.g. Nephropidae, Diogenidae, Paguridae) are paraphyletic, warranting further studies to evaluate their status. The present study ably demonstrates the utility of nuclear protein-coding genes in phylogenetic inference in decapods. The topologies obtained are robust and the two molecular markers are informative across a wide range of taxonomic levels. We propose that nuclear protein-coding genes should constitute core markers for future phylogenetic studies of decapods, especially for higher systematics.

Identification and molecular characterization of Charybdis feriatus tropomyosin, the major crab allergen

BACKGROUND Crab sensitivity is one of the most common seafood allergies. However, to date, there has been no report on the molecular characterization of crab allergens and no comparative analysis with other seafood allergens. OBJECTIVE This study was undertaken to clone, identify, and determine the primary structure of a major IgE-reactive molecule in crab. METHODS We constructed an expression cDNA library from a common crab, Charybdis feriatus. This library was then screened with the use of sera from subjects with a well-documented history of type I hypersensitivity reactions upon ingestion of crab. An IgE-reactive clone was chosen and subcloned into plasmids for nucleotide sequence determination and expression in Escherichia coli. RESULTS We identified a 1-kb cDNA designated as Cha f 1. Expression of Cha f 1 produces a 34-kd recombinant protein reactive to the IgE antibodies from patients with crab allergies but not from control subjects. Cha f 1 has an opening reading frame of 264 amino acids and demonstrates marked homology to the shrimp tropomyosin Met e 1. Absorption of allergic sera with Cha f I removes IgE reactivity to crab extract. Moreover, absorption of allergic sera with recombinant shrimp Met e 1 tropomyosin removes IgE reactivity to Cha f 1. CONCLUSIONS This 34-kd protein, designated as Cha f 1, is the first identified major allergen of crab. Nucleotide and amino acid comparison shows that this protein is the crab tropomyosin. The molecular basis of shrimp and crab allergy is readily demonstrated at the nucleotide and amino acid level.

Crustacean neuropeptide genes of the CHH/MIH/GIH family: implications from molecular studies.

The crustacean eyestalk CHH/MIH/GIH gene family represents a unique group of neuropeptide originally identified in crustaceans. These neuropeptides shared a high degree of amino acid identity, and the conservation of cysteine residues at the same relative positions. Based on their biological, biochemical, and molecular properties, they can be divided into the CHH and MIH subtypes with two major members in each subtype. In the shrimp, the CHH-subtypes can be divided into two forms (CHH-A and CHH-B). The CHH-A gene also comprises several isoforms which shared a high overall sequence identity. Although the MIH subtypes are postulated to have evolved from the CHH subtypes, the number of major MIH subtypes in each species has yet to be confirmed. While most of the genes consist of the basic plan of three exons and two introns, other alternative spliced variants have recently been described. Moreover, these alternative forms are usually expressed in non-eyestalk tissues. These findings suggest that these neuropeptides may have a broader spectrum of functions in crustaceans. The results from phylogenetic analysis suggest that the evolution of this group of neuropeptides occurs in a manner similar is to the gene duplication and mutation events hypothesized for the origin of the prolactin and growth hormone gene family of the vertebrate pituitary system.

Composition and genetic diversity of picoeukaryotes in subtropical coastal waters as revealed by 454 pyrosequencing

Information on genetic diversity of picoeukaryotes (<2–3 μm) comes mainly from traditional gene cloning and sequencing, but this method suffers from cloning biases and limited throughput. In this study, we explored the feasibility of using the cloning-independent and massively parallel 454 pyrosequencing technology to study the composition and genetic diversity of picoeukaryotes in the coastal waters of the subtropical western Pacific using the hypervariable V4 region of the 18S rRNA gene. Picoeukaryote assemblages between two sites with different hydrography and trophic status were also compared. The approach gave a high coverage of the community at genetic difference ⩾5% but still underestimated the total diversity at a genetic difference ⩽2%. Diversity of picoeukaryotes was higher in an oligomesotrophic bay than in a eutrophic bay. Stramenopiles, dinoflagellates, ciliates and prasinophytes were the dominant groups comprising approximately 27, 19, 11 and 11%, respectively, of the picoeukaryotes. Water samples collected from the two bays contained different high-level taxonomic groups and phylotype operational taxonomic units of picoeukaryotes. Our study represents one of the first and most comprehensive examinations of marine picoeukaryotic diversity using the 454 sequencing-by-synthesis technology.

The complete mitochondrial genome of the large yellow croaker, Larimichthys crocea (Perciformes, Sciaenidae): Unusual features of its control region and the phylogenetic position of the Sciaenidae

To understand the systematic status of Larimichthys crocea in the Percoidei, we determined the complete mitochondrial (mt) genome sequence using 454 sequencing-by-synthesis technology. The complete mt genome is 16,466 bp in length including the typical structure of 22 tRNAs, 2 rRNAs, 13 protein-coding genes and the noncoding control region (CR). Further sequencing for the complete CR was performed using the primers Cyt b-F and 12S-R on six L. crocea individuals and two L. polyactis individuals. Interestingly, all seven CR sequences from L. crocea were identical while the three sequences from L. polyactis were distinct (including one from GenBank). Although the conserved blocks such as TAS and CSB-1, -2, and -3 are readily identifiable in the control regions of the two species, the typical central conserved blocks CSB-D, -E, and -F could not be detected, while they are found in Cynoscion acoupa of Sciaenidae and other Percoidei species. Phylogenetic analysis shows that L. crocea is a relatively recently emerged species in Sciaenidae and this family is closely related to family Pomacanthidae within the Percoidei. L. crocea, as the first species of Sciaenidae with complete mitochondrial genome available, will provide important information on the molecular evolution of the group. Moreover, the genus-specific pair of primers designed in this study for amplifying the complete mt control region will be very useful in studies on the population genetics and conservation biology of Larimichthys.

A biological survey of ballast water in container ships entering Hong Kong

The role of ballast water in the introduction of exotic species has recently received extensive attention. The aim of this study is to assess the importance of ballast water discharge as a vector for the introduction of exotic species into Hong Kong waters. Twelve ballast water samples were collected from 5 container ships entering Hong Kong between June1994 and October 1995. The ballast water originated from ports on both sides of the Pacific Ocean. At least 81 species from 8 animal phyla and 5 protist phyla were found. Most of the major marine taxonomic groups were represented and many planktonic larval stages were included. Species richness in the ballast tanks decreased with the age of ballast water. Copepoda was the most diverse and abundant taxonomic group. The density of calanoid and cyclopoid copepods decreased with the age of ballast water, but that of harpacticoid copepods did not change significantly with time. Bivalve, crustacean, polychaete and ascidian larvae from ballast water samples were observed to settle in laboratory culture tanks. The mussel Mytilopsis sallei which was introduced to Hong Kong in 1980, was one of the bivalves that settled readily. Results of this study indicate that ballast water can be a major source for the introduction of exotic species to Hong Kong waters. Regulatory guidelines on the discharge of ballast water should be established.

The First Internal Transcribed Spacer (ITS-1) of Ribosomal DNA as a Molecular Marker for Phylogenetic and Population Analyses in Crustacea

Abstract: The objective of the present study is to explore the feasibility of using the first internal transcribed spacer (ITS-1) of ribosomal DNA as a molecular marker for studying the interspecific and intraspecific genetic variations among crustaceans. We designed primers that could amplify ITS-1 from a majority of taxonomic groups of crustaceans. The gene was found to exhibit a high degree of length polymorphism among different groups, ranging from 182 bp in the barnacle Balanus amphitrite to approximately 820 bp in the spiny lobster Panulirus japonicus. With respect to differences between congeneric species, it was found that the ITS-1 sequences of 3 mitten crabs, Eriocheir sinensis, Eriocheir leptognathus, and Eriocheir formosa, exhibit 5.4% to 16.3% nucleotide divergence, suggesting that ITS-1 is informative for phylogenetic analysis at the species level. Yet there are extensive (0.9%–2.3%) variations within individual E. formosa, so that phylogenetic analyses could be obscured. ITS-1 was found to vary between 2 geographical populations of the shrimp Penaeus japonicus. The variations involved substitutions as well as insertions/deletions between shrimp from Australia and South China Sea. These results show that ITS-1 is highly divergent among different crustaceans and could be an appropriate marker for molecular systematic studies at the species and population levels, although the presence of intragenomic variation needs to be taken into consideration.

Phylogeography of the mitten crab Eriocheir sensu stricto in East Asia: Pleistocene isolation, population expansion and secondary contact.

We examined the impact of Pleistocene glacial cycles on geographical distribution and genetic structure of the mitten crab Eriocheir sensu stricto in East Asia using sequence variation of mitochondrial cytochrome c oxidase I and cytochrome b gene segments. Phylogenies revealed four distinct but shallow structured lineages in Eriocheir s. s. Three lineages dominated the East China Sea-Yellow Sea, the Sea of Japan and the South China Sea on the margins of the region, and one lineage occurred on Okinawa Island. This geographical distribution represents a general phylogeographic pattern in East Asia, which is closely associated with the fluctuations of marginal seas and islands during the Pleistocene. The four lineages are estimated to have diverged during the mid-Pleistocene. Demographic expansions were observed in each lineage, starting within the second-to-latest interglacial period in the marginal sea lineages ( approximately 70-130ka) and within the last glacial period in the Okinawa lineage ( approximately 25-80ka). Expansions have probably taken place northward along the coast of the East China Sea-Yellow Sea, following the rise of sea levels. Centered on the southern Korean Peninsula, expansions have likely occurred northward along the west coast and eastward along the south coast of the Sea of Japan. Each marginal sea has served as a single refugium during glacial periods. Two secondary contact regions were identified, one of the East China Sea-Yellow Sea and South China Sea lineages, and another of the East China Sea-Yellow Sea and Sea of Japan lineages. Phylogeography of Eriocheir s. s. provides insights into the evolutionary history and mechanism for generating biodiversity in East Asia.

Characterization of an additional molt inhibiting hormone-like neuropeptide from the shrimp Metapenaeus ensis

We have identified a second form of the type-II neuropeptide encoding a molt inhibiting hormone-like (MeeMIH-B) neuropeptide. MeeMIH-B showed only a 70% amino acid identity to the MIH-A (formerly MIH) isolated from the same species, suggesting a possible different function of the deduced neuropeptide. Like other neuropeptide members of the CHH family, the MIH-B gene consists of three exons separated by two introns. The levels of MIH-B mRNA transcript in the eyestalk decrease in the initial phase of gonad maturation and increase towards the end of maturation. The drop in MIH-B level suggests an inhibitory role for this neuropeptide in the initiation of vitellogenesis. MIH-B transcripts can also be detected in the brain, thoracic ganglion and ventral nerve cord. Together with the CHH-B peptide that we have previously described, this is the second peptide of the CHH family that can also be identified in the ventral nerve cord and in the XOSG complex. A recombinant MIH-B was produced and a polyclonal antibody against rMIH-B was subsequently generated. Specific anti-rMIH-B antiserum recognized the presence of MIH-B in the sinus gland, X-organs, as well as a giant neuron of the ventral nerve cord. Injection of rMIH-B delayed the molting cycle of the maturing female. Taken together, the results of this study suggest that a drop in MIH-B level may be required for the delay in the molting of the maturing females.