Genhong Wang

Genome-wide identification and expression analysis of serine proteases and homologs in the silkworm Bombyx mori

BackgroundSerine proteases (SPs) and serine proteases homologs (SPHs) are a large group of proteolytic enzymes, with important roles in a variety of physiological processes, such as cell signalling, defense and development. Genome-wide identification and expression analysis of serine proteases and their homologs in the silkworm might provide valuable information about their biological functions.ResultsIn this study, 51 SP genes and 92 SPH genes were systematically identified in the genome of the silkworm Bombyx mori. Phylogenetic analysis indicated that six gene families have been amplified species-specifically in the silkworm, and the members of them showed chromosomal distribution of tandem repeats. Microarray analysis suggests that many silkworm-specific genes, such as members of SP_fam12, 13, 14 and 15, show expression patterns that are specific to tissues or developmental stages. The roles of SPs and SPHs in resisting pathogens were investigated in silkworms when they were infected by Escherichia coli, Bacillus bombysepticus, Batrytis bassiana and B. morinucleopolyhedrovirus, respectively. Microarray experiment and real-time quantitative RT-PCR showed that 18 SP or SPH genes were significantly up-regulated after pathogen induction, suggesting that SP and SPH genes might participate in pathogenic microorganism resistance in B. mori.ConclusionSilkworm SP and SPH genes were identified. Comparative genomics showed that SP and SPH genes belong to a large family, whose members are generated mainly by tandem repeat evolution. We found that silkworm has species-specific SP and SPH genes. Phylogenetic and microarray analyses provide an overview of the silkworm SP and SPHs, and facilitate future functional studies on these enzymes.

Genome-Wide Identification and Immune Response Analysis of Serine Protease Inhibitor Genes in the Silkworm, Bombyx mori

In most insect species, a variety of serine protease inhibitors (SPIs) have been found in multiple tissues, including integument, gonad, salivary gland, and hemolymph, and are required for preventing unwanted proteolysis. These SPIs belong to different families and have distinct inhibitory mechanisms. Herein, we predicted and characterized potential SPI genes based on the genome sequences of silkworm, Bombyx mori. As a result, a total of eighty SPI genes were identified in B. mori. These SPI genes contain 10 kinds of SPI domains, including serpin, Kunitz_BPTI, Kazal, TIL, amfpi, Bowman-Birk, Antistasin, WAP, Pacifastin, and alpha-macroglobulin. Sixty-three SPIs contain single SPI domain while the others have at least two inhibitor units. Some SPIs also contain non-inhibitor domains for protein-protein interactions, including EGF, ADAM_spacer, spondin_N, reeler, TSP_1 and other modules. Microarray analysis showed that fourteen SPI genes from lineage-specific TIL family and Group F of serpin family had enriched expression in the silk gland. The roles of SPIs in resisting pathogens were investigated in silkworms when they were infected by four pathogens. Microarray and qRT-PCR experiments revealed obvious up-regulation of 8, 4, 3 and 3 SPI genes after infection with Escherichia coli, Bacillus bombysepticus, Beauveria bassiana or B. mori nuclear polyhedrosis virus (BmNPV), respectively. On the contrary, 4, 11, 7 and 9 SPI genes were down-regulated after infection with E. coli, B. bombysepticus, B. bassiana or BmNPV, respectively. These results suggested that these SPI genes may be involved in resistance to pathogenic microorganisms. These findings may provide valuable information for further clarifying the roles of SPIs in the development, immune defence, and efficient synthesis of silk gland protein.

Reference genes identified in the silkworm Bombyx mori during metamorphism based on oligonucleotide microarray and confirmed by qRT‐PCR

Gene expression quantification at mRNA level is very important for post‐genomic studies, as gene expression level is the reflection of the special biological function of the target gene. Methods used for gene expression quantification, such as microarray or quantitative real‐time polymerase chain reaction (qRT‐PCR), require stable expressed reference genes. Thus, finding suitable control genes is essential for gene quantification. In this study, a genome‐wide survey of reference genes during metamorphism was performed on silkworm Bombyx mori. Twelve genes were chosen as putative reference genes based on a whole genome oligonucleotide microarray normalized by external controls. Then, qRT‐PCR was employed for further validation and selection of potential reference gene candidates. The results were analyzed, and stable genes were selected using geNorm 3.4 and NormFinder software. Finally, considering factors from every aspect, translation initiation factor 4A, translation initiation factor 3 subunit 4, and translation initiation factor 3 subunit 5 (represented by sw22934, swl4876, and swl3956) were selected as reliable internal controls across the examined developmental stages, while cytoplasmic actin (sw22671), the commonly used reference gene in a previous study was shown to vary drastically throughout the examined developmental stages. For future research, we recommend the use of the geometric mean of those three stable reference genes as an accurate normalization factor for data normalization of different developmental stages during metamorphism.

Resistance to BmNPV via overexpression of an exogenous gene controlled by an inducible promoter and enhancer in transgenic silkworm, Bombyx mori.

The hycu-ep32 gene of Hyphantria cunea NPV can inhibit Bombyx mori nucleopolyhedrovirus (BmNPV) multiplication in co-infected cells, but it is not known whether the overexpression of the hycu-ep32 gene has an antiviral effect in the silkworm, Bombyx mori. Thus, we constructed four transgenic vectors, which were under the control of the 39 K promoter of BmNPV (39 KP), Bombyx mori A4 promoter (A4P), hr3 enhancer of BmNPV combined with 39 KP, and hr3 combined with A4P. Transgenic lines were created via embryo microinjection using practical diapause silkworm. qPCR revealed that the expression level of hycu-ep32 could be induced effectively after BmNPV infection in transgenic lines where hycu-ep32 was controlled by hr3 combined with 39 KP (i.e., HEKG). After oral inoculation of BmNPV with 3 × 105 occlusion bodies per third instar, the mortality with HEKG-B was approximately 30% lower compared with the non-transgenic line. The economic characteristics of the transgenic lines remained unchanged. These results suggest that overexpression of an exogenous antiviral gene controlled by an inducible promoter and enhancer is a feasible method for breeding silkworms with a high antiviral capacity.

Nuclear receptors in Bombyx mori: insights into genomic structure and developmental expression.

Nuclear receptors (NRs) function as ligand-dependent transcription factors and are involved in diverse biological processes in different animals. The updated assembly of complete genome sequence of the Bombyx mori enabled a systematic analysis of the NRs in the five holometabolous insects including B. mori, Drosophila melanogaster, Anopheles gambiae, Apis mellifera, and Tribolium castaneum. As a result, nineteen NRs were identified in the B. mori genome, each of eighteen NRs has 1:1:1:1 ortholog in the other four insects. Interestingly, the average intron number of ligand-binding domain (LBD) of each NR gene in B. mori was 2.4, much higher than that in the other four insects; the genomic position of introns in LBDs of all orthologs for each NR presents more diversity. Phylogenetic trees of all NRs from the five insects were consistent or aberrant with classical phylogeny of these insect species. The characteristics in number, genomic structure and phylogeny of all NRs revealed their evolutionary conservation and divergence during insect evolution. The expression patterns of several NR genes displayed temporal specificity similar to that in D. melanogaster and may be associated with the key biological processes during silkworm metamorphosis. The RNAi of BmbetaFTZ-F1 resulted in abnormality in larva-pupa transition, further suggesting it is also crucial for silkworm metamorphosis. In conclusion, the present study provided new insights into the structure, evolution, expression, and functions of silkworm NRs.

A transgenic animal with antiviral properties that might inhibit multiple stages of infection

Bombyx mori nucleopolyhedrovirus (BmNPV) is the primary pathogen of silkworms, causing severe economic losses in sericulture. To create antiviral silkworm strains, we constructed a transgenic vector in which the dsRNA for five tandem BmNPV genes was controlled by the BmNPV hr3 enhancer and IE1 promoter. The antivirus gene Bmlipase-1 was driven by B. mori midgut-specific promoter P2. Transgenic strains (SW-H) were generated via embryo microinjection using the practical silkworm strain SW. After infection with a high dose of BmNPV, the survival rates of SW-H and non-transgenic SW were 64% and 13%, respectively. SW-H could be the first transgenic animal that is highly antiviral and that might inhibit the virus at multiple stages of infection.

Cloning and evolutionary analysis of tobacco MAPK gene family

The mitogen-activated protein (MAP) kinase cascade is an important signaling module which is involved in biotic and abiotic stress responses as well as plant growth and development. In this study, we identified 17 tobacco MAPKs including 11 novel tobacco MAPK genes that have not been identified before. Comparative analysis with MAPK gene families from other plants, such as Athaliana thaliana, rice and poplar, suggested that tobacco MAPKs (such as NtMPK1, NtMPK3 and NtMPK8) might play similar functions in response to abiotic and biotic stresses. QRT-PCR analysis revealed that a total of 14 NtMPKs were regulated by SA and/or MeJA, suggesting their potential roles involved in plant defense response. In addition, 6 NtMPKs were induced by drought treatment, implying their roles in response to drought stress. Our results indicated that most of tobacco MAPK might be involved in plant defense response, which provides the basis for further analysis on physiological functions of tobacco MAPKs.

Cloning and characterization of a novel Nicotiana tabacum ABC transporter involved in shoot branching

The ATP-binding cassette (ABC) superfamily is a large protein family with diverse physiological functions in all kingdoms of life. One distinguished subfamily, the pleiotropic drug resistance (PDR) transporters, has only been identified in plants and fungi. Here, we identified a Nicotiana tabacum PDR gene, NtPDR6, which is a homolog of Petunia hybrida PDR1. The full-length cDNA of NtPDR6 had a 4482-bp open reading frame encoding a full-size ABC transporter with 1493 amino acids. Sequence comparison showed that NtPDR6 had high homology with plant PDR proteins. NtPDR6 was strongly induced by phosphate starvation as well as by 1-naphthalene acetic acid. Tissue expression pattern analysis showed that NtPDR6 was detected in all surveyed tissues but preferentially in roots. We cloned the 1.3-kb NtPDR6 promoter and found that there was one phosphate starvation response-related element Pho-like and several root-specific expression-related elements rootmotiftapox1 in the NtPDR6 promoter. A tissue-specific pattern of NtPDR6 promoter-β-glucuronidase expression was dominantly observed in subepidermal cells and the elongation zone of lateral roots. RNA interference technology was used to knock down NtPDR6 expression, and there was a significantly increased branching phenotype in the NtPDR6 knockdown plants. These data suggest that NtPDR6 plays a key role in regulation of shoot branching processes.

Characterization of Argonaute family members in the silkworm, Bombyx mori

Abstract  The Argonaute protein family is a highly conserved group of proteins, which have been implicated in RNA silencing in both plants and animals. Here, four members of the Argonaute family were systemically identified based on the genome sequence of Bombyx mori. Based on their sequence similarity, BmAgo1 and BmAgo2 belong to the Ago subfamily, while BmAgo3 and BmPiwi are in the Piwi subfamily. Phylogenetic analysis reveals that silkworm Argonaute family members are conserved in insects. Conserved amino acid residues involved in recognition of the 5′ end of the small RNA guide strand and of the conserved (aspartate, aspartate and histidine [DDH]) motif present in their PIWI domains suggest that these four Argonaute family members may have conserved slicer activities. The results of microarray expression analysis show that there is a low expression level for B. mori Argonaute family members in different tissues and different developmental stages, except for BmPiwi. All four B. mori Argonaute family members are upregulated upon infection with B. mori nucleopolyhedrovirus. The complete coding sequence of BmPiwi, the homolog of Drosophila piwi, was cloned and its expression occurred mainly in the area where spermatogonia and spermatocytes appear. Our results provide an overview of the B. mori Argonaute family members and suggest that they may have multiple roles. In addition, this is also the first report, to our knowledge, of the response of RNA silencing machinery to DNA virus infection in insects.

Cathepsin B protease is required for metamorphism in silkworm, Bombyx mori

Cathepsin B belongs to lysosomal cysteine protease of the papain family. Temporal and spatial expression analysis of cathepsin B of Bombyx mori (BmCtB) was carried out based on Expression Sequence Tags (ESTs) data, oligonucleotide microarray, reverse transcription polymerase chain reaction (RT‐PCR) and quantitative real‐time PCR. Expression of BmCtB was observed in all of the tissues and stages. Among the 10 tested tissues, the fat body and posterior silk gland are the two most enriched tissues with BmCtB. During Bombyx development, there was an expression fastigium of BmCtB during metamorphosis. RNA interference was used to suppress the expression of cathepsin B during metamorphosis. Significant developmental defective phenotypes were obtained in the RNAi treated group. The dramatically reduced expression of BmCtB was confirmed by Northern blot and quantitative real‐time PCR. These evidences strongly suggest cathepsin B protein‐ase was predominantly involved in the metabolism process of fat body and the posterior silk gland and was critical for metamorphism and development of silkworm, Bombyx mori.