Molecular characterization of a Bombyx mori protein disulfide isomerase (bPDI)

Protein and phytohormone profiles of Mahanarva spectabilis salivary glands infesting different forages

Given the importance of pastures for feeding cattle, the study of factors that affect their productivity is essential to get plant material of higher nutritional quality. Thus, the study of insect-plant interaction is important for the development of control strategies. Pasture spittlebugs affect forage grasses causing severe damage. We tested hormone and protein profiles differentially expressed in the salivary glands of Mahanarva spectabilis when fed with different pasture genotypes. The LC/MS approaches combined with bioinformatics tools were used to identify the mains biological processes in the salivary glands. The grouping revealed a greater number of proteins involved in biological processes of metabolic synthesis, biotic/abiotic stress, and ion transport across the membrane. The proteomic profiles were altered when insects were fed with different grasses. We also detected phytohormones in the salivary glands involved in the modulation of defense responses in host plants. These results allowed the analysis of important biological processes such as cell homeostasis, stress proteins, nucleic acid metabolism, regulation of muscle contraction, and transport and export of biomolecules. This represents an important advance in the understanding of the plant-pest interaction and can contribute to the choice of target elicitors, which allow effective strategies in the control of pasture spittlebugs.

Proteomic analysis of differentially expressed proteins in the lipopolysaccharide-stimulated hepatopancreas of the freshwater crayfish Procambarus clarkii

Procambarus clarkii is one of the most important aquatic invertebrates in China and has high commercial value. However, aquaculture has suffered great economic loss due to outbreaks of infectious diseases in P. clarkii. To identify red swamp crayfish related proteins involved in the response to bacterial infection, we analysed immune-related proteins following lipopolysaccharide (LPS) stimulation by quantitative proteomics. The proteome of the hepatopancreas of P. clarkii challenged with LPS and phosphate-buffered saline was analysed to evaluate the immune response. Based on liquid chromatography coupled with tandem mass spectrometry, 16 upregulated and 29 downregulated proteins were identified. A Gene Ontology analysis demonstrated 5 biological process, 11 cellular component, and 6 molecular function subcategories. The Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis indicated that the identified proteins were mainly involved in metabolism, phagosome, and ribosome. Real-time quantitative reverse transcription-PCR revealed that eight immune-related genes were upregulated after LPS stimulation compared to the control. Taken together, the data enhance our understanding of the immune response of crayfish to LPS.

Improving Silkworm Genome Annotation Using a Proteogenomics Approach

The silkworm genome has been deeply sequenced and assembled, but accurate genome annotation, which is important for modern biological research, remains far from complete. To improve silkworm genome annotation, we carried out a proteogenomics analysis using 9.8 million mass spectra collected from different tissues and developmental stages of the silkworm. The results confirmed the translational products of 4307 existing gene models and identified 1701 novel genome search-specific peptides (GSSPs). Using these GSSPs, 74 novel gene-coding sequences were identified, and 121 existing gene models were corrected. We also identified 1182 novel junction peptides based on an exon-skipping database that resulted in the identification of 973 alternative splicing sites. Furthermore, we performed RNA-seq analysis to improve silkworm genome annotation at the transcriptional level. A total of 1704 new transcripts and 1136 new exons were identified, 2581 untranslated regions (UTRs) were revised, and 1301 alternative splicing (AS) genes were identified. The transcriptomics results were integrated with the proteomics data to further complement and verify the new annotations. In addition, 14 incorrect genes and 10 skipped exons were verified using the two analysis methods. Altogether, we identified 1838 new transcripts and 1593 AS genes and revised 5074 existing genes using proteogenomics and transcriptome analyses. Data are available via ProteomeXchange with identifier PXD009672. The large-scale proteogenomics and transcriptome analyses in this study will greatly improve silkworm genome annotation and contribute to future studies.

Molecular Characterization of Endoplasmic Reticulum Oxidoreductin 1 from Bombyx mori

We isolated a complementary DNA (cDNA) clone encoding endoplasmic reticulum oxidoreductin 1 (bERO1, a specific oxidant of protein disulfide isomerase (PDI)) from Bombyx mori. This protein has a putative open reading frame (ORF) of 489 amino acids and a predicted size of 57.4 kDa. Although bERO1 protein shares less than 57% amino acid sequence homology with other reported ERO1s, it contains two conserved redox active motifs, a Cys-X-X-X-X-Cys motif of N-terminal and Cys-X-X-Cys-X-X-Cys motif of C-terminal. Both motifs are typically present in ERO1 protein family members. The bEro1 mRNA expression was highest in posterior silk gland on the sixth day of the 5th instar larvae. Expression of bEro1 mRNA also markedly increased during endoplasmic reticulum (ER) stress induced by stimulation with antimycin, calcium ionophore A23187, dithiothreitol, H₂O₂, monencin, and tunicamycin. In addition, expression levels of bEro1 exactly coincided with that of bPdi. This is the first result suggesting that bERO1 plays an essential role in ER quality control through the combined activities of bERO1 and bPDI as a catalyst of protein folding in the ER and sustaining cellular redox homeostasis.

Molecular characterization of two novel molecular chaperones in bacterial-challenged Apostichopus japonicus

Molecular chaperones of 78 kDa glucose-regulated protein (GRP78) and protein disulfide isomerase (PDI) are involved in protein folding and assembly in the endoplasmic reticulum (ER). Increasing evidences also suggest that these two molecules play an important role in immune response. In the present study, we cloned and characterized GRP78 and PDI genes from Apostichopus japonicus by RNA-seq and RACE approaches (designated as AjGRP78 and AjPDI, respectively). The AjGRP78 cDNA was of 2355bp including an open reading frame (ORF) of 2013 bp encoding a protein of 670 amino acids with three heat shock protein 70 (HSP70) family signatures. AjGRP78 contained a 23-amino acid signal peptide at the N-terminus and a HDEL motif at the C-terminus, which supported the location of the protein in the ER. The full length cDNA of AjPDI was of 1893 bp with a 5' untranslated region (UTR) of 153 bp, a 3' UTR of 228 bp and an ORF of 1512 bp encoding a protein of 503 amino acids. A 17-amino acid signal peptide, two thioredoxin domains with two active sites of CGHC, and KDEL retention signal were totally conserved in the deduced amino acid of AjPDI. Phylogenic analysis and multiple alignments have shown that both genes shared remarkably higher degree of structural conservation and sequence identities with other counterparts from invertebrates and vertebrates, further supporting that the two proteins were novel members of molecular chaperone family. Spatial expression analysis revealed that AjGRP78 mRNA transcripts were dominantly expressed in the tentacle, while AjPDI mRNA levels were abundant in the muscle, intestine and respiratory trees. For Vibrio splendidus challenged sea cucumber, the peak expression of AjGRP78 and AjPDI mRNAs in coelomocytes were detected at 24h with 1.73-fold increase and at 6h with 1.83-fold increase compared with the control group, respectively. Similarly, a significant increase in the relative mRNA levels of AjGRP78 and AjPDI was also identified in 1 μg mL(-1) LPS exposed primary cultured coelomocytes. These results collectively suggested that AjGRP78 and AjPDI were ER chaperones of A. japonicus, of which expression is induced upon bacterial infection.

Comparative proteomic analysis reveals the suppressive effects of dietary high glucose on the midgut growth of silkworm

The silkworm, Bombyx mori, is an important model of lepidoptera insect, and it has been used for several models of human diseases. In human being, long-term high-sugar diet can induce the occurrence of diabetes and other related diseases. Interestingly, our experiments revealed the high glucose diet also has a suppressive effect on the development of silkworms. To investigate the molecular mechanism by which high-glucose diet inhibited the midgut growth in silkworms, we employed comparative proteomic analysis to globally identify proteins differentially expressed in normal and high-glucose diet group silkworms. In all, 28 differently proteins were suppressed and 5 proteins induced in high-glucose diet group. Gene ontology analysis showed that most of these differently proteins are mainly involved in metabolic process, catalytic and cellular process. A development related protein, imaginal disk growth factor (IDGF), was further confirmed by western blot exclusively expressing in the normal diet group silkworms. Taken together, our data suggests that IDGF plays a critical role in impairing the development of silkworms by a high-glucose diet.

BIOLOGICAL SIGNIFICANCE

Glucose has been thought to play essential roles in growth and development of silkworm. In this paper, we certified firstly that high-glucose diet can suppress the growth of silkworm, and comparative proteomic was employed to reveal the inhibition mechanism. Moreover, an important regulation related protein (IDGF) was found to involve in this inhibition process. These results will help us get a deeper understanding of the relationship between diet and healthy. Furthermore, IDGF may be the critical protein for reducing the blood sugar in silkworm, and it may be used for screening human hypoglycemic drug. The work has not been submitted elsewhere for publication, in whole or in part, and all the authors have approved the manuscript.

Channel catfish (Ictalurus punctatus) protein disulphide isomerase, PDIA6: molecular characterization and expression regulated by bacteria and virus inoculation

Protein disulfide isomerases (PDIs) are thought to aid protein folding and assembly by catalyzing formation and shuffling of cysteine disulfide bonds in the endoplasmic reticulum (ER). Currently, increasing evidence suggests PDIs play an important role in host cell invasion and they are relevant targets for the host immune response. However the roles of specific PDIs in teleosts are little known. Here, we characterized the Protein disulfide isomerase family A, member 6 (PDIA6) from channel catfish, Ictalurus punctatus (named as ccPDIA6). The catfish ccPDIA6 gene was homologous to those of other vertebrate species with 13 exons and 12 introns. The consensus full-length ccPDIA6 cDNA contained an ORF of 1320 bp encoding a putative protein of 439 amino acids. It had a 19 amino acid signal peptide and two active thioredoxin-like domains. Sequence of phylogenic analysis and multiple alignments showed that ccPDIA6 was conserved throughout vertebrate evolution. Southern blot analysis suggested the presence of one copy of the ccPDIA6 gene in the catfish genome. Tissue distribution shows that ccPDIA6 was expressed in all examined tissues at the mRNA level. When using the aquatic zoonotic pathogens such as Edwardsiella tara, Streptococcus iniae, and channel catfish reovirus （CCRV） to challenge channel catfish, ccPDIA6 expression was significant changed in immune-related tissues such as head kidney, intestine, liver and spleen. The results suggested that ccPDIA6 might play an important role in the immunity of channel catfish. This is the first report that the PDI gene may be involved in fish host defense against pathogen infection.

Proteomics of cryoprotective dehydration in Megaphorura arctica Tullberg 1876 (Onychiuridae: Collembola)

The Arctic springtail, Megaphorura arctica Tullberg 1876 (Onychiuridae: Collembola), is one of the few organisms known to survive the extreme stresses of its environment by using cryoprotective dehydration. We have undertaken a proteomics study comparing M. arctica, acclimated at -2°C, the temperature known to induce the production of the anhydroprotectant trehalose in this species, and -6°C, the temperature at which trehalose expression plateaus, against control animals acclimated at +5°C. Using difference gel electrophoresis, and liquid chromatography tandem mass spectrometry, we identified three categories of differentially expressed proteins with specific functions, up-regulated in both the -2°C and -6°C animals, that were involved in metabolism, membrane transport and protein folding. Proteins involved in cytoskeleton organisation were only up-regulated in the -6°C animals.

Molecular cloning and expression pattern analysis of two novel disulfide isomerases in shrimp

Protein disulfide isomerase (PDI) catalyzes formation and isomerization of disulfide bridges and has chaperone activity. Currently, increasing evidence suggests the significance of PDI in immune and stress responses. To clarify the role of PDIs in the innate immunity of shrimp, two PDI genes were isolated and identified from Fenneropenaeus chinensis (fleshy prawn). FcPDI1 is 1878bp in length and encodes a protein of 383 amino acids. It has 18-amino acid signal peptide, 3 thioredoxin domains with 3 active sites of CGHC, and KEDL retention signal at its C-end. FcPDI1 is an atypical PDI. The open reading frame of FcPDI2 encodes a 497-amino acid protein and shows the classical domain organization a-b-b'-a'. Phylogenic analysis and multiple alignments show that FcPDI1 is similar to PDI that contains 3 thioredoxin domains from other species including invertebrates and vertebrates. FcPDI2, LvPDI, and insect PDIs are grouped into one cluster and are similar to PDIs having a-b-b'-a' domain organization. Tissue distribution shows that FcPDI1 and FcPDI2 were expressed in all detected tissues at the mRNA level. Changes in FcPDI1 and FcPDI2 expression at the mRNA level in hemocytes, hepatopancreas, gills, and ovaries upon Vibrio or white spot syndrome virus challenge were also analyzed. The results suggest that FcPDI1 and FcPDI2 might have roles in the innate immunity of shrimp. FcPDI1 was also successfully expressed in Escherichia coli and the recombinant FcPDI1 showed insulin reductase activity. Results show that FcPDI might play an important role in the innate immunity of shrimp.

Bombyx mori transferrin: genomic structure, expression and antimicrobial activity of recombinant protein

Transferrin (Tf) is a multifunctional, iron binding protein found in both vertebrates and invertebrates. Although transferrin has been suggested to play a role in innate immunity, its immunological function during infection has not been characterized. In this study, we identified and characterized Bombyx mori transferrin (BmTf). The promoter region of BmTf has numerous putative NF-kappaB binding sites, suggesting its possible function in innate immunity. Analysis of BmTf gene expression shows that it is highly inducible in response to a wide variety of pathogens including bacteria, fungus, and viruses. Recombinant BmTf protein produced in a baculovirus system exhibits iron binding capacity and antibacterial activity against various Gram-positive and -negative bacteria. Taken together, our results indicate that BmTf is an inducible immune effector molecule that may play an important role in pathogen clearance of insect innate immunity.

Comparative proteomic analysis of bacterial wilt susceptible and resistant tomato cultivars

To investigate the molecular mechanisms of bacterial resistance in susceptible and resistant cultivars of tomato, a proteomic approach was adopted. Four cultivars of tomato were selected on the basis of their response to bacterial (Pseudomonas solanacearum) inoculation wherein cultivar Roma and Riogarande, and cultivar Pusa Ruby and Pant Bahr were considered as resistant and susceptible cultivars, respectively. Proteins were extracted from leaves of 3-week-old seedlings of the four cultivars and separated by 2-DE. A total of nine proteins were found to be differentially expressed between the susceptible and resistant cultivars. Amino acid sequences of these proteins were determined with a protein sequencer. The identified proteins belongs to the categories of energy, protein destination and storage, and defense. Of these proteins, a 60kDa chaperonin and an apical membrane antigen were significantly upregulated in resistant cultivars compared with susceptible cultivars. Application of jasmonic acid and salicylic acid resulted in significant changes in levels of apical membrane antigen and protein disulfide-isomerase. Taken together, these results suggest that apical membrane antigen might be involved in bacterial resistance process through salicylic acid induced defense mechanism signaling in tomato plants.

Differential expression of immune-related genes and transposable elements in black tiger shrimp (Penaeus monodon) exposed to a range of environmental stressors

The health of aquatic species is dependent on interactions between the environment, pathogens and the host. Under intensive shrimp aquaculture, environmental conditions can degrade, causing significant stress to the cultured organisms. To investigate the effect of environmental stress on shrimp hemocyte gene expression profiles, we applied suppression subtractive hybridization (SSH) in juvenile Penaeus monodon exposed to hyperthermal, hypoxic or hyposmotic conditions. Random sequencing of 258 clones from the SSH revealed 176 distinct sequences of which 58 shared high similarity to sequences in the public databases. The three most common groups of identifiable unique sequences in the SSH libraries were the POL region of non-LTR retrotransposons (31%), genes with immune or potential immune functions (30%), and genes involved in protein synthesis and processing (18%). Stress-regulated differential expression was further verified by quantitative qRT-PCR, with seven out of eight randomly selected genes showing qRT-PCR profiles that conformed to the patterns predicted by SSH. Hence this work provides a list of genes which appear to be up- or down-regulated in response to stress, providing a basis for studying the genetic response of shrimp to environmental stress.

Changes in cellular secretory processing during baculovirus infection

In the baculovirus expression vector system (BEVS), secretory green fluorescent protein (sGFP) transcripts were expressed from day 2 to day 5 post-infection (p.i.), while transcripts of the endoplasmic reticulum (ER) molecular chaperone Bombyx mori protein disulfide isomerase (bPDI) were measurable in mock cells and in cells at day 1 p.i. The GFP was expressed from day 3 to day 5 p.i. whereas the levels of two ER chaperone proteins, bPDI and calnexin, decreased from day 3 p.i. and were not detected from day 4 p.i. These findings suggest that the rate-limited expression of ER molecular chaperones is strongly associated with the maximal expression of exogenous proteins in BEVS.

ATFC is a novel transducer for the unfolded protein response in Bombyx mori BM5 cells

We report the isolation of activating transcription factor of chaperone (ATFC), a novel cDNA from Bombyx mori BM5 cells that encodes a putative transducer of endoplasmic reticulum (ER) stress. The 236 amino acids of ATFC include both a basic region and a leucine zipper at the C-terminus, in contrast to Hac1p of yeast which features these structures at its N-terminus. ATFC expression was strongly up-regulated by ER stress. ATFC could specifically bind to the unfolded protein response element. BM5 cells transfected with ATFC cDNA displayed enhanced ER chaperone expression in response to ER stress. These results indicate that ATFC encodes a putative transducer of ER stress.