Penaeus monodon gene discovery project: the generation of an EST collection and establishment of a database

Shrimp single WAP domain (SWD)-containing protein exhibits proteinase inhibitory and antimicrobial activities

Single WAP domain (SWD)-containing proteins are small proteins with a C-terminal region containing a single whey acidic protein (WAP) domain. In the present study, the cDNAs representing three isoforms of SWD proteins (SWDPm1, SWDPm2 and SWDPm3) were identified from hemocytes of the black tiger shrimp, Penaeus monodon. The deduced peptides revealed that they contain a putative signal peptide of 24 amino acids and encode for a mature peptide of 69, 68 and 56 amino acids, respectively, which contain typical characters similar to those of the shrimp SWD proteins (type III crustin) with a Pro-Arg region and a WAP domain towards the C-terminus. Tissue distribution analysis by RT-PCR showed that all three SWDPm transcripts were primarily found in hemocytes. Transcript expression of SWDPm1 was down-regulated upon injection with Staphylococcus aureus whilst there was no change of SWDPm2 and SWDPm3 expression. In contrast, white spot syndrome virus (WSSV) injection resulted in a biphasic response with up-regulation of SWDPm1 and SWDPm2 transcripts at 6h followed by significant down-regulation by 24h after infection. Genomic organization of the SWDPm2 gene revealed the presence of three exons interrupted by two introns. To characterize the biological functions of the SWD protein, the mature SWDPm2 protein encoding cDNA was cloned and expressed in Escherichia coli. Purified recombinant (r)SWDPm2 exhibits antibacterial activity against several Gram-positive, but not Gram-negative, bacteria and is a competitive inhibitor of subtilisin A with an inhibition constant (Ki) of 1.98nM. Thus, rSWDPm2 may contribute to the inhibitory regulation of subtilisin A from bacterial infection and P. monodon SWD protein likely function as immune effectors in defense against invasion of shrimp pathogens.

Up-regulation of ribophorin I after yellow head virus (YHV) challenge in black tiger shrimp Penaeus monodon

This work constitutes the second report from a continuing investigation of shrimp genes that may be involved in apoptosis associated death resulting from yellow head virus (YHV) infection. Here, we describe from the black tiger shrimp Penaeus monodon, a ribophorin I-like gene that is probably a subunit of the oligosaccharyltransferase complex (OST), a key enzyme in N-linked glycosylation that occurs in the endoplasmic reticulum. The OST complex also contains DAD1 (defender against apoptotic death 1) that has been reported to control apoptosis and that we have previously reported from P. monodon. The full length ribophorin I of P. monodon comprised 2157 bp with the ORF of 1806 bp corresponding to 601 deduced amino acids and three putative N-linked glycosylation sites. Analysis revealed hydrophobic properties implying that it could be a membrane protein. Tissue distribution analysis using real-time RT-PCR with SYBR Green revealed that ribophorin I was endogenously expressed in all examined tissues of normal shrimp. However, unlike DAD1 that was down-regulated after YHV challenge, ribophorin I expression was up-regulated and remained high until the moribund stage.

The ribophorin I from Penaeus monodon shrimp: cDNA cloning, expression and phylogenetic analysis

Ribophorin I, a 67 kDa subunit of the oligosaccharyl transferase complex, is involved in facilitating N-linked glycosylation of polypeptides. We have isolated a full length Penaeus monodon cDNA encoding an insect/mammalian ribophorin I homologue by screening a lymphoid cDNA library and by performing rapid amplification of cDNA ends polymerase chain reaction of lymphoid RNA. The cDNA clone of shrimp ribophorin I (PmRibI) consists of 2263 nucleotides encoding 601 amino acid residues. Primary structure analysis of PmRibI indicated that it is a type I transmembrane protein, comprising a cleavable signal sequence of 23 residues at the amino terminus, preceding 434 residues of the luminal domain, 17 residues of the transmembrane domain, and 150 residues of the cytoplasmic domain at the carboxy terminus. The protein has a calculated molecular mass of 67.98 kDa with a pI of 6.05. This putative PmRibI cDNA clone was also expressed as PmRibI-6His in Sf9 cells. The recombinant PmRibI has an apparent molecular weight of 70 kDa, similar to the MW calculated from the deduced cDNA sequence. The inferred protein sequence of PmRibI has 52% identity with that of Strongylocentrotus purpuratus, 49% identity with that of Danio rerio, and 47% identity with mammalian ribophorin I. Phylogenetic analysis showed that PmRibI is most closely related to the echinoderm ribophorin I. The expression of the ribophorin I gene is tissue specific, with its mRNA highly abundant in hemocytes, gill, lymphoid organ and hepatopancreas.

Down-regulation of defender against apoptotic death (DAD1) after yellow head virus (YHV) challenge in black tiger shrimp Penaeus monodon

Here we describe the highly conserved gene, defender against apoptotic death (DAD1) identified from an EST library of the black tiger shrimp Penaeus monodon. The full-length cDNA of DAD1 of P. monodon comprised 638bp with an ORF of 345bp corresponding to 114 deduced amino acids. The deduced amino acid sequence was compared to known DAD1 sequences in the GenBank and in other databases. Phylogenetic analysis revealed that P. monodon DAD1 clustered with DAD1 from other invertebrates. Real-time RT-PCR with RNA extracts from normal P. monodon revealed DAD1 expression in several tissues including those of digestive and defense organs such as the hepatopancreas and hemocytes, respectively. If death from YHV infection was related to increased levels of apoptosis, we reasoned that the level of DAD1 should decrease as YHV infections progressed, especially in hemocytes (HC), one of its main targets. Real-time RT-PCR with RNA extracts from HC of P. monodon challenged with YHV revealed that the transcriptional level of DAD1 declined dramatically (approximately 50%) after YHV challenge. Although this suggests that DAD1 plays a role in mortality caused by YHV, control of apoptosis is complex and involves the interaction of many proteins, few of which have been characterized for shrimp. Thus, firm conclusions regarding the role of DAD1 must await the description and characterization of other proteins.

Systematic sequencing of mRNA from the Antarctic krill (Euphausia superba) and first tissue specific transcriptional signature

Background

Little is known about the genome sequences of Euphausiacea (krill) although these crustaceans are abundant components of the pelagic ecosystems in all oceans and used for aquaculture and pharmaceutical industry. This study reports the results of an expressed sequence tag (EST) sequencing project from different tissues of Euphausia superba (the Antarctic krill).

Results

We have constructed and sequenced five cDNA libraries from different Antarctic krill tissues: head, abdomen, thoracopods and photophores. We have identified 1.770 high-quality ESTs which were assembled into 216 overlapping clusters and 801 singletons resulting in a total of 1.017 non-redundant sequences. Quantitative RT-PCR analysis was performed to quantify and validate the expression levels of ten genes presenting different EST countings in krill tissues. In addition, bioinformatic screening of the non-redundant E. superba sequences identified 69 microsatellite containing ESTs. Clusters, consensuses and related similarity and gene ontology searches were organized in a dedicated E. superba database .

Conclusion

We defined the first tissue transcriptional signatures of E. superba based on functional categorization among the examined tissues. The analyses of annotated transcripts showed a higher similarity with genes from insects with respect to Malacostraca possibly as an effect of the limited number of Malacostraca sequences in the public databases. Our catalogue provides for the first time a genomic tool to investigate the biology of the Antarctic krill.

Anti-lipopolysaccharide factors from the black tiger shrimp, Penaeus monodon, are encoded by two genomic loci

Different isoforms of the ALF homologues (ALFPm1-5) have been previously identified from Penaeus monodon expressed sequence tag (EST) database (http://pmonodon.biotec.or.th). The nucleotide and amino acid sequences of the P. monodon ALF homologues were analyzed and categorized into two groups, ALFPm1 and 2 in group A and ALFPm3-5 in group B. The genomic sequences of the two ALF gene groups were obtained by using the PCR and genome walking techniques. The ALF group A gene consisted of three exons interrupted by two introns whereas the ALF group B gene contained four exons interrupted by three introns. The alignment of genomic sequences with the ALF cDNA sequences revealed that different transcripts in both groups were generated by alternative RNA splicing of the pre-mRNA transcripts. The 5' upstream sequences of the two ALF groups contained the putative cis-regulatory elements, including the activator protein 1, the Octamer, the GATA, the nuclear factor-kappaB, and the GAAA motifs, which possibly promoted transcription in response to infection as in other antimicrobial peptide genes. The RT-PCR analysis revealed that although all ALF isoforms were expressed in individual shrimp, the ALFPm2 and 3 were the major or authentic ALFs in the hemocytes. The expression of both ALFPm2 and 3 were increased in response to Vibrio harveyi infection indicating the important function of the ALFs against bacterial invasion.

Cloning, expression and antimicrobial activity of crustinPm1, a major isoform of crustin, from the black tiger shrimp Penaeus monodon

Crustin antibacterial homologues, containing a whey acidic protein (WAP) domain, have been identified from the haemocyte library of the black tiger shrimp, Penaeus monodon. Sequence analysis of these cDNAs indicates the presence of several isoforms of crustin in P. monodon. CrustinPm1, the most abundant isoform, contains an open reading frame of 435bp encoding a precursor of 145 amino acids that comprises 17 amino acid signal peptides and 128 amino acid mature peptides. The peptides contain a Gly-Pro rich region at the amino-terminus and a single whey acidic protein (WAP) domain at the carboxyl-terminus. In order to characterize the properties and biological activities of this peptide, crustinPm1 was overexpressed in Escherichia coli. The recombinant crustinPm1 has a molecular mass of 14.7kDa with a predicted pI of 8.3. Antimicrobial assays demonstrated that recombinant crustinPm1 exhibited antimicrobial activity against only Gram-positive bacteria with strong inhibition against Staphylococcus aureus and Streptococcus iniae. In addition, the study of inhibition mechanism revealed that the antimicrobial activity of crustinPm1 was a result of bactericidal effect. In situ hybridization with crustinPm1 antisense probes showed strong hybridization signals in a certain haemocyte population of unchallenged shrimp, indicating that crustinPm1 transcript is differentially expressed in different subsets of haemocyte cells.

Comparative analysis of differentially expressed genes in normal and white spot syndrome virus infected Penaeus monodon

Background

White spot syndrome (WSS) is a viral disease that affects most of the commercially important shrimps and causes serious economic losses to the shrimp farming industry worldwide. However, little information is available in terms of the molecular mechanisms of the host-virus interaction. In this study, we used an expressed sequence tag (EST) approach to observe global gene expression changes in white spot syndrome virus (WSSV)-infected postlarvae of Penaeus monodon.

Results

Sequencing of the complementary DNA clones of two libraries constructed from normal and WSSV-infected postlarvae produced a total of 15,981 high-quality ESTs. Of these ESTs, 46% were successfully matched against annotated genes in National Center of Biotechnology Information (NCBI) non-redundant (nr) database and 44% were functionally classified using the Gene Ontology (GO) scheme. Comparative EST analyses suggested that, in postlarval shrimp, WSSV infection strongly modulates the gene expression patterns in several organs or tissues, including the hepatopancreas, muscle, eyestalk and cuticle. Our data suggest that several basic cellular metabolic processes are likely to be affected, including oxidative phosphorylation, protein synthesis, the glycolytic pathway, and calcium ion balance. A group of immune-related chitin-binding protein genes is also likely to be strongly up regulated after WSSV infection. A database containing all the sequence data and analysis results is accessible at .

Conclusion

This study suggests that WSSV infection modulates expression of various kinds of genes. The predicted gene expression pattern changes not only reflect the possible responses of shrimp to the virus infection but also suggest how WSSV subverts cellular functions for virus multiplication. In addition, the ESTs reported in this study provide a rich source for identification of novel genes in shrimp.