Similarity/dissimilarity studies of protein sequences based on a new 2D graphical representation.

A (two-dimensional) 2D graphical representation of protein sequences based on six physicochemical properties of amino acids is outlined. The numerical characterization of protein graphs is given as descriptors of protein sequences. It is not only useful for comparative study of proteins but also for encoding innate information about the structure of proteins. The coefficient of determination is proposed as a new similarity/dissimilarity measure. Finally, a simple example is taken to highlight the behavior of the new similarity/dissimilarity measure on protein sequences taken from the ND6 (NADH dehydrogenase subunit 6) proteins for eight different species. The results demonstrate the approach is convenient, fast, and efficient.

Analysis of similarity/dissimilarity of protein sequences.

On the basis of a selected pair of physicochemical properties of amino acids, we introduce a dynamic 2D graphical representation of protein sequences. Then, we introduce and compare two numerical characterizations of protein graphs as descriptors to analyze the nine ND5 proteins. The approach is simple, convenient, and fast.

Analysis of similarity/dissimilarity of DNA sequences based on a class of 2D graphical representation.

On the basis of a class of 2D graphical representations of DNA sequences, sensitivity analysis has been performed, showing the high-capability of the proposed representations to take into account small modifications of the DNA sequences. And sensitivity analysis also indicates that the absolute differences of the leading eigenvalues of the L/L matrices associated with DNA increase with the increase of the number of the base mutations. Besides, we conclude that the similarity analysis method based on the correlation angles can better eliminate the effects of the lengths of DNA sequences if compared with the method using the Euclidean distances. As application, the examination of similarities/dissimilarities among the coding sequences of the first exon of beta-globin gene of different species has been performed by our method, and the reasonable results verify the validity of our method.

Complete sequence and organization of Antheraea pernyi nucleopolyhedrovirus, a dr-rich baculovirus.

BACKGROUND: The completion and reporting of baculovirus genomes is extremely important as it advances our understanding of gene function and evolution. Due to the large number of viral genomes now sequenced it is very important that authors present significantly detailed analyses to advance the understanding of the viral genomes. However, there is no report of the Antheraea pernyi nucleopolyhedrovirus (AnpeNPV) genome. RESULTS: The genome of AnpeNPV, which infects Chinese tussah silkworm (Antheraea pernyi), was sequenced and analyzed. The genome was 126,629 bp in size. The G+C content of the genome, 53.4%, was higher than that of most of the sequenced baculoviruses. 147 open reading frames (ORFs) that putatively encode proteins of 50 or more amino acid residues with minimal overlap were determined. Of the 147 ORFs, 143 appeared to be homologous to other baculovirus genes, and 4 were unique to AnpeNPV. Furthermore, there are still 29 and 33 conserved genes present in all baculoviruses and all lepidopteran baculoviruses respectively. In addition, the total number of genes common to all lepidopteran NPVs is sill 74, however the 74 genes are somewhat different from the 74 genes identified before because of some new sequenced NPVs. Only 6 genes were found exclusively in all lepidopteran NPVs and 12 genes were found exclusively in all Group I NPVs. AnpeNPV encodes v-trex(Anpe115, a 3' to 5' repair exonuclease), which was observed only in CfMNPV and CfDEFNPV in Group I NPVs. This gene potentially originated by horizontal gene transfer from an ancestral host. In addition, AnpeNPV encodes two conotoxin-like gene homologues (ctls), ctl1 and ctl2, which were observed only in HycuNPV, OpMNPV and LdMNPV. Unlike other baculoviruses, only 3 typical homologous regions (hrs) were identified containing 2~9 repeats of a 30 bp-long palindromic core. However, 24 perfect or imperfect direct repeats (drs) with a high degree of AT content were found within the intergenic spacer regions that may function as non-hr, ori-like regions found in GrleGV, CpGV and AdorGV. 9 drs were also found in intragenic spacer regions of AnpeNPV. CONCLUSION: AnpeNPV belongs to Group I NPVs and is most similar to HycuNPV, EppoNPV, OpMNPV and CfMNPV based on gene content, genome arrangement, and amino acid identity. In addition, analysis of genes that flank hrs supported the argument that these regions are involved in the transfer of sequences between the virus and host.

Oral administration activity determination of recombinant osteoprotegerin from silkworm larvae.

Osteoprotegerin (OPG) regulates the formation of osteoclasts and is involved in the regulation of bone resorption and remodeling. To investigate the feasibility of using silkworm (Bombyx mori) larvae to produce recombinant osteoprotegerin as a oral administration drug, the rh-OPG was expressed in the larvae of silkworm through the silkworm baculovirus expression system, and was orally administered to mice. Compared with the control, oral administration of rh-OPG was effective to decrease serum calcium concentration in normal mice, and block the bone loss induced by the loss of estrogen in ovariectomized mice. These results indicated that oral administration of rh-OPG expressed in silkworm larvae had the proper bioactivity.

Expression, purification and characterization of a three-domain Kazal-type inhibitor from silkworm pupae (Bombyx mori).

Serine protease inhibitors are essential for host physiological and immunological activities in insects. Analyzing the amino-acid sequence of a cDNA coding for a serine protease inhibitor in Bombyx mori (BmSPI), we found that BmSPI contained three homologous domains with a conserved sequence of C-X(3)-C-X(9)-C-X(6)-Y-X(7)-C-X(3)-C-X(11)-C similar to that of Kazal-type serine protease inhibitors, suggesting BmSPI as a new member of the Kazal-type serine protease inhibitor family. To characterize the three-domain Kazal-type inhibitor from silkworm pupae, the recombinant protein was expressed in Escherichia coli BL21 (DE3) Star. After purification with affinity and reversed-phase chromatographies, the recombinant BmSPI with a molecular mass of 33.642 Da was shown to be a specific subtilisin A inhibitor. Further studies indicated that the K(i) value of the recombinant BmSPI was 3.35 nM and the inhibitor seemed to form a 1:1 complex with subtilisin A. This is a first description of the structure and characterization of Kazal-type inhibitor with three domains cloned from silkworm pupae, B. mori.

Expression of open reading frames in silkworm pupal cDNA library.

A cDNA library containing 2409 singletons was constructed from whole silkworm pupae (Bombyx mori) In addition, the types of genes overexpressed in pupa were analyzed. These genes contained 79 types of proteins with the exception of enzyme, mitochondrial DNA, andribosomal protein. Also analyzed were the expression and nonexpression of open reading frame (ORF) sequences in Escherichia coli. cDNA sequences were compared to the silkworm (B. mori) genome in the GenBank database and the silkworm cDNA database including the SilkBase and KAIKOBLAST databases and 498 novel expressed sequence tags (ESTs) and 217 unknown ESTs were found. After comparison with all available ORF-complete mRNA sequences from the same organism (fruitfly, mosquito, and apis) in the RefSeq collection, 1659 full-length cDNA were identified. In addition, the structure of silkworm mRNA was analyzed, and it was found that 66.8% of silkworm mRNA tailed with poly(A) contained the highly conserved AAUAAA signal and the signal located 10-17 nucleotides upstream of the putative poly(A). Finally, the composition of nucleotides in promoter region for all ESTs was surveyed. The results imply that the TTTTA box may possess some functions in regulating transcription and expression of some genes.

Identification and analysis of YELLOW protein family genes in the silkworm, Bombyx mori.

BACKGROUND: The major royal jelly proteins/yellow (MRJP/YELLOW) family possesses several physiological and chemical functions in the development of Apis mellifera and Drosophila melanogaster. Each protein of the family has a conserved domain named MRJP. However, there is no report of MRJP/YELLOW family proteins in the Lepidoptera. RESULTS: Using the YELLOW protein sequence in Drosophila melanogaster to BLAST silkworm EST database, we found a gene family composed of seven members with a conserved MRJP domain each and named it YELLOW protein family of Bombyx mori. We completed the cDNA sequences with RACE method. The protein of each member possesses a MRJP domain and a putative cleavable signal peptide consisting of a hydrophobic sequence. In view of genetic evolution, the whole Bm YELLOW protein family composes a monophyletic group, which is distinctly separate from Drosophila melanogaster and Apis mellifera. We then showed the tissue expression profiles of Bm YELLOW protein family genes by RT-PCR. CONCLUSION: A Bombyx mori YELLOW protein family is found to be composed of at least seven members. The low homogeneity and unique pattern of gene expression by each member among the family ensure us to prophesy that the members of Bm YELLOW protein family would play some important physiological functions in silkworm development.

Expression, purification and characterization of human GM-CSF using silkworm pupae (Bombyx mori) as a bioreactor.

To date, many recombinant proteins have been expressed in Bombyx mori cells or silkworm larvae, apart from in pupae. Silkworm pupae may be more suitable for the expression of heterologous proteins as a bioreactor. If maintained at an appropriate temperature, silkworm pupae could be inoculated with recombinant baculovirus for the expression of a protein of interest. In this study, human granulocyte-macrophage colony-stimulating factor was successfully expressed in silkworm pupae using B. mori nucleopolyhedrovirus, purified and characterized with respect to its physico-chemical properties. The target protein expressed had an apparent molecular mass of 29 kDa and an isoelectric point of 5.1. The protein was purified using three chromatographic steps with a final recovery of 10.3%. Finally, approximately 3.5mg of the protein was obtained with a biological activity of up to 8.4 x 10(6) cfu mg(-1). The results of this study suggest that silkworm pupae represent a convenient and low-cost bioreactor for the expression of heterologous proteins.

Computational prediction of microRNA genes in silkworm genome.

MicroRNAs (miRNAs) constitute a novel, extensive class of small RNAs (approximately 21 nucleotides), and play important gene-regulation roles during growth and development in various organisms. Here we conducted a homology search to identify homologs of previously validated miRNAs from silkworm genome. We identified 24 potential miRNA genes, and gave each of them a name according to the common criteria. Interestingly, we found that a great number of newly identified miRNAs were conserved in silkworm and Drosophila, and family alignment revealed that miRNA families might possess single nucleotide polymorphisms. miRNA gene clusters and possible functions of complement miRNA pairs are discussed.

High level expression of functionally active human lactoferrin in silkworm larvae.

In this paper, recombinant human lactoferrin (rhLf) was expressed very well using Bombyx mori nuclear polyhedrosis baculovirus expression system. Infection of silkworm larvae with recombinant virus, vBm-hLf, the rhLf was efficiently secreted into larvae hemolymph and the concentration of product purified was about 65 microg/ml. The isolated rhLf molecular mass was approximately 78 kDa, lower than that of the human lactoferrin (hLf) standards, which may be due to incomplete glycosylation or protein degradation. Furthermore, the rhLf was characterized and its biological activities were evaluated by in vivo bioassay using dextran sodium sulfate (DSS)-induced colitis mouse model that mimics some characteristics of colitis disease in human. We conclude that silkworm expression system can be used successfully to express functional human lactoferrin.

Expression of cholera toxin B subunit and assembly as functional oligomers in silkworm.

The nontoxic B subunit of cholera toxin (CTB) can significantly increase the ability of proteins to induce immunological tolerance after oral administration, when it was conjugated to various proteins. Recombinant CTB offers great potential for treatment of autoimmune disease. Here we firstly investigated the feasibility of silkworm baculovirus expression vector system for the cost-effective production of CTB under the control of a strong polyhedrin promoter. Higher expression was achieved via introducing the partial non-coding and coding sequences (ATAAAT and ATGCCGAAT) of polyhedrin to the 5' end of the native CTB gene, with the maximal accumulation being approximately 54.4 mg/L of hemolymph. The silkworm bioreactor produced this protein vaccine as the glycoslated pentameric form, which retained the GM1-ganglioside binding affinity and the native antigenicity of CTB. Further studies revealed that mixing with silkworm-derived CTB increases the tolerogenic potential of insulin. In the nonconjugated form, an insulin : CTB ratio of 100 : 1 was optimal for the prominent reduction in pancreatic islet inflammation. The data presented here demonstrate that the silkworm bioreactor is an ideal production and delivery system for an oral protein vaccine designed to develop immunological tolerance against autoimmune diabetes and CTB functions as an effective mucosal adjuvant for oral tolerance induction.

[Expression and activity determination of TNFR domain of osteoprotegerin in E.coli and corresponding antibody preparation].

Osteoprotegerin (OPG) plays an important role in the regulation of bone resorption and remodeling. The TNFR domain of OPG, which is involved in the inhibition of formation and activity of osteoclasts, was amplified by PCR and inserted into multiple cloning site of PET-28a. The recombinant plasmid was transferred into E.coli BL21 to express recombinant protein. It was found that expressed product existed in the form of inclusion body. The inclusion body was solubilized, renatured and purified by affinity chromatography. Polyclonal antibodies with high specificity were obtained from the serum of rabbit immunized with purified recombinant protein. Mice were used to determine the hypocalcemic effect of the recombinant protein. Results showed that the recombinant protein expressed in E.coli had the proper bioactivity.

Expression and activity determination of human angiostatin (k1-3) in culture cells and larvae of silkworm.

Angiostatin (k1-3) gene was inserted into Bombyx mori baculovirus transfer vector pBacPAK8 and cotransfected with lineared DNA of Bm-BacPAK6 virus into BmN cells. The homologous recombination occurred inside the cells, and the recombinant virus BacPAK-angiostatin was expressed, as identified by DNA dot blotting. The BmN cells and fifth instars were infected by the recombinant virus BacPAK-angiostatin; expression product was run in the SDS-PAGE, and its immunoreactivity was determined by using ELISA and Western blotting. The bio-activity of the protein product was determined by using human umbilical vein endothelial cells ( ECV304 ) proliferation test in vitro and by using CAM vascular inhibition test in vivo. The expression activity achieved the highest point at the 72nd hour in BmN cells (22 u / 2x10(6) cells) and at 144th hour in larvae (159 u/ml). At the concentration of 2.5 u/ml, angiostatin induced apoptosis of endothelial cells in 24 h and also inhibited angiogenesis in CAM.

Infectious Bursal Disease Virus Structural Protein VP2 Expressed by a Baculovirus Recombinant in Bombyx mori.

VP2 cDNA gene of the infectious bursal disease virus HZ96 strain, encoding a major host-protective antigen, was cloned into baculovirus transfer vector pBacPAK8, resulting in a recombinant transfer vector pBacPAK-VP2. The vector pBacPAK-VP2 and linearized DNA of modified baculovirus Bm-BacPAK6 were co-transfected into the cultured Bombyx mori (Bm) N cells, in which homologous recombination occurred. Then, baculovirus recombinants were screened out. The Bm cells and Bm larvae were infected with the baculovirus recombinant that can expresse VP2, and Bm N cells and haemolymph of Bm larvae were collected for assays. The results of ELISA and Western immunoblotting assays demonstrated that VP2 was expressed in the cultured Bm cells and the Bm larvae.

[An in vitro nuclear run-on assay for nuclear function of angiogenin].

A sensitive and quantitative in vitro analysis method was established to detect the nascent RNAs stimulated by angiogenin using the nuclei isolated from human umbilical vein endothelial cells (HUVE). Angiogenin was mixed with nuclei in the reaction buffer, then transcription was initiated by adding the NTPs mixture. The RNA products were measured quantitatively by [alpha-(32)P]CTP incorporation with a liquid scintillation counter, either after removing free isotope by using spin column, or cutting the electrophoresis lane and counting after autoradiography. It was found that the optimum reacting temperature was 30 degrees, the most suitable reaction time was 30 min for this system, and the transcription enhancement activity of angiogenin was dose-dependent with the feasible concentration being 1 mg/L. Higher concentration of angiogenin degraded the RNA products in the system, suggesting that there is a mechanism to control the entry and accumulation of angiogenin in the target cells, which ensured angiogenin to play its role properly in the cells. Based on the evidence that angiogenin bound to DNA in nucleolus and enhanced RNA transcription, it was proposed that angiogenin might act as a trans-acting factor in nucleus to regulate RNA transcription, and inhibition of angiogenin-stimulated RNA transcription might be a promising target for screening anti-angiogenesis inhibitor.

[Effects of bm47 deletion on viral replication and transcription of Bombyx mori nucleopolyhedrovirus].

Bombyx mori nucleopolyhedrovirus (BmNPV) bm47 gene is found in all sequenced lepidopteran nucleopolyhedroviruses (NPVs). It is one of the core genes of NPVs. However, the role of bm47 in the biological cycle of NPV remains unknown. In this study, the Red recombination system was used to knock out bm47 from BmNPV to construct bm47-ko-Bacmid in E. coli BW25113 system. Then bm47 gene was introduced back to the viral genome using the Bac-to-Bac system to create the repair virus bm47-re-Bacmid. TCID50 assay and real-time PCR (qPCR) were used to evaluate the effects of bm47 deletion on viral DNA replication, gene transcription, and protein expression. qPCR results showed that bm47 knock-out had no significant effect on viral DNA replication. However, the qPCR results showed that bm47-ko-Bacmid significantly decreased the transcription levels of early gene lef-3, late gene vp39, and very late gene p10 at 48 h and 72 h after viral transfection of BmN cells (P < 0.05). This work will provide a foundation for further studies on the biological function of BmNPV bm47 in viral replication and transcription.

Characterization of late gene expression factor LEF-10 from Bombyx mori nucleopolyhedrovirus.

The LEF-10 expression factor from the Bombyx mori nuclear polyhedrosis virus (BmNPV) does not have significant homology with other late expression factors and is thought to be a transcriptional cofactor. To investigate the function of LEF-10, a Red recombination system was used to knock out the lef-10 gene from the BmNPV genome and a lef-10 gene knockout virus (ko-Bacmid) was constructed. The lef-10 gene was repaired back to the viral genome using a Bac-to-Bac system to create the repaired virus (re-Bacmid). When ko-Bacmid was transfected into BmN cells, the detected titer of progeny virus in the medium was zero, whereas the titer of the progeny re-Bacmid remained at a level similar to that of the wild type virus (wt-Bacmid). The viral DNA replication, transcription and expression of viral early, late and very late genes after ko-Bacmid transfection into BmN cells were evaluated. The quantitative polymerase chain reaction showed that the ko-Bacmid viral genome replication level remained low and that the ko-Bacmid viral gene transcription level was significantly lower than those of wt-Bacmid and re-Bacmid. No expression of the early gene lef-3 was detected. These results suggest that the lef-10 gene has significant effects on DNA replication of the viral genome and BmNPV gene transcription at each phase and deletion of the lef-10 gene affects the level of expression of the viral early gene directly.

Identification and characterization of the DNA replication origin recognition complex gene family in the silkworm Bombyx mori.

The ORC (origin recognition complex) binds to the DNA replication origin and recruits other replication factors to form the pre-replication complex. The cDNA and genomic sequences of all six subunits of ORC in Bombyx mori (BmORC1-6) were determined by RACE (rapid amplification of cDNA ends) and bioinformatic analysis. The conserved domains were identified in BmOrc1p-6p and the C-terminal of BmOrc6p features a short sequence that may be specific for Lepidoptera. As in other organisms, each of the six BmORC subunits had evolved individually from ancestral genes in early eukaryotes. During embryo development, the six genes were co-regulated, but different ratios of the abundance of mRNAs were observed in 13 tissues of the fifth instar day-6 larvae. Infection by BmNPV (B. mori nucleopolyhedrovirus) initially decreased and then increased the abundance of BmORC. We suggest that some of the BmOrc proteins may have additional functions and that BmOrc proteins participate in the replication of BmNPV.

Comparative proteomic analysis between the domesticated silkworm (Bombyx mori) reared on fresh mulberry leaves and on artificial diet.

To gain an insight into the effects of different diets on growth and development of the domesticated silkworm at protein level, we employed comparative proteomic approach to investigate the proteomic differences of midgut, hemolymph, fat body and posterior silk gland of the silkworms reared on fresh mulberry leaves and on artificial diet. Seventy-six differentially expressed proteins were identified by MALDI TOF/TOF MS, and among them, 41 proteins were up-regulated, and 35 proteins were downregulated. Database searches, combined with GO analysis and KEGG pathway analysis revealed that some hemolymph proteins such as Nuecin, Gloverin-like proteins, PGRP, P50 and beta/-N-acetylglucosamidase were related to innate immunity of the silkworm, and some proteins identified in silkworm midgut including Myosin 1 light chain, Tropomyosin 1, Profilin, Serpin-2 and GSH-Px were involved in digestion and nutrition absorption. Moreover, two up-regulated enzymes in fat body of larvae reared on artificial diet were identified as V-ATPase subunit B and Arginine kinase which participate in energy metabolism. Furthermore, 6 down-regulated proteins identified in posterior silk gland of silkworm larvae reared on artificial diet including Ribosomal protein SA, EF-2, EF-1gamma, AspAT, ERp57 and PHB were related to silk synthesis. Our results suggested that the different diets could alter the expression of proteins related to immune system, digestion and absorption of nutrient, energy metabolism and silk synthesis poor nutrition and absorption of nutrition in silkworm. The results also confirmed that the poor nutrient absorption, weakened innate immunity, decreased energy metabolism and reduced silk synthesis are the main reasons for low cocoons yield, inferior filament quality, low survival rate of young larvae and insufficient resistance against specific pathogens in the silkworms fed on artificial diet.