The fat body cell-free system for tissue-specific transcription of plasma protein gene of Bombyx mori

Suppressive activity of a viral histone H4 against two host chromatin remodelling factors: lysine demethylase and SWI/SNF

Histone H4, a nucleosome subunit in eukaryotes, plays crucial roles in DNA package and regulation of gene expression through covalent modification. A viral histone H4 encoded in Cotesia plutellae bracovirus (CpBV), a polydnavirus, is called CpBV-H4. It is highly homologous to other histone H4 proteins excepting 38 extra amino acid residues in the N terminus. CpBV-H4 can form octamer with other histone subunits and alter host gene expression. In this study, CpBV-H4 was transiently expressed in a natural host (Plutella xylostella) and its suppressive activity on host gene expression was evaluated by the suppressive subtractive hybridization (SSH) technique. The SSH targets down-regulated by CpBV-H4 were read with the 454 pyrosequencing platform and annotated using the genome of P. xylostella. The down-regulated genes (610 contigs) were annotated in most functional categories based on gene ontology. Among these SSH targets, 115 genes were functionally distinct, including two chromatin remodelling factors: a lysine-specific demethylase (Px-KDM) and a chromatin remodelling complex [Px-SWI/SNF (SWItch/Sucrose Non-Fermentable)]. Px-KDM was highly expressed in all tested tissues during the entire larval period. Suppression of Px-KDM expression by specific RNA interference (RNAi) significantly (P<0.05) reduced haemocyte nodule formation in response to immune challenge and impaired both larval and pupal development. Px-SWI/SNF was expressed in all developmental stages. Suppression of Px-SWI/SNF expression by RNAi reduced cellular immune response and interfered with adult metamorphosis. These results suggest that CpBV-H4 can alter host gene expression by interfering with chromatin modification and remodelling factors in addition to its direct epigenetic control activity.

Shotgun proteomic analysis of the fat body during metamorphosis of domesticated silkworm (Bombyx mori)

Protein expression profiles in the fat bodies of larval, pupal, and moth stages of silkworm were determined using shotgun proteomics and MS sequencing. We identified 138, 217, and 86 proteins from the larval, pupal and moth stages, respectively, of which 12 were shared by the 3 stages. There were 92, 150, and 45 specific proteins identified in the larval, pupal and moth stages, respectively, of which 17, 68, and 9 had functional annotations. Among the specific proteins identified in moth fat body, sex-specific storage-protein 1 precursor and chorion protein B8 were unique to the moth stage, indicating that the moth stage fat body is more important for adult sexual characteristics. Many ribosomal proteins (L23, L4, L5, P2, S10, S11, S15A and S3) were found in pupal fat bodies, whereas only three (L14, S20, and S7) and none were identified in larval and moth fat bodies, respectively. Twenty-three metabolic enzymes were identified in the pupal stage, while only four and two were identified in the larval and moth stages, respectively. In addition, an important protein, gloverin2, was only identified in larval fat bodies. Gene ontology (GO) analysis of the proteins specific to the three stages linked them to the cellular component, molecular function, and biological process categories. The most diverse GO functional classes were involved by the relatively less specific proteins identified in larva. GO analysis of the proteins shared among the three stages showed that the pupa and moth stages shared the most similar protein functions in the fat body.

BmHrp28 is a RNA-binding protein that binds to the female-specific exon 4 of Bombyx mori dsx pre-mRNA

The Bombyx mori sex determination gene Bmdsx is alternatively spliced in the male and female to produce the male- and female-specific proteins. In an effort to better understand the mechanism of the alternative splicing regulation of Bmdsx, we conducted a gel-shift assay followed by LC-MS/MS analysis to identify the putative proteins bound to the cis-element CE1+6 in the exon 4 of Bmdsx. A protein named as BmHrp28 which is homologous to the Drosophila Hrp48, a member of the hnRNPA/B family, was identified and expressed in Escherichia coli for testing RNA-protein binding in vitro. All of the results showed that BmHrp28 specifically bound to the CE1+6 RNA probe. BmHrp28 has two RNA recognition motifs at the N-terminal and a glycine-rich motif at the C-terminal. It might be one of the factors involved in the male-specific splicing of Bmdsx.

Establishment of a novel in vivo sex-specific splicing assay system to identify a trans-acting factor that negatively regulates splicing of Bombyx mori dsx female exons

The Bombyx mori homolog of doublesex, Bmdsx, plays an essential role in silkworm sexual development. Exons 3 and 4 of Bmdsx pre-mRNA are specifically excluded in males. To explore how this occurs, we developed a novel in vivo sex-specific splicing assay system using sexually differentiated cultured cells. A series of mutation analyses using a Bmdsx minigene with this in vivo splicing assay system identified three distinct sequences (CE1, CE2, and CE3) positioned in exon 4 as exonic splicing silencers responsible for male-specific splicing. Gel shift analysis showed that CE1 binds to a nuclear protein from male cells but not that from female cells. Mutation of UAA repeats within CE1 inhibited the binding of the nuclear protein to the RNA and caused female-specific splicing in male cells. We have identified BmPSI, a Bombyx homolog of P-element somatic inhibitor (PSI), as the nuclear factor that specifically binds CE1. Down-regulation of endogenous BmPSI by RNA interference significantly increased female-specific splicing in male cells. This is the first report of a PSI homolog implicated in the regulated sex-specific splicing of dsx pre-mRNA.

Analysis of tissue-specific region in sericin 1 gene promoter of Bombyx mori

The gene encoding sericin 1 (Ser1) of silkworm (Bombyx mori) is specifically expressed in the middle silk gland cells. To identify element involved in this transcription-dependent spatial restriction, truncation of the 5' terminal from the sericin 1 (Ser1) promoter is studied in vivo. A 209bp DNA sequence upstream of the transcriptional start site (-586 to -378) is found to be responsible for promoting tissue-specific transcription. Analysis of this 209bp region by overlapping deletion studies showed that a 25bp region (-500 to -476) suppresses the ectopic expression of the Ser1 promoter. An unknown factor abundant in fat body nuclear extracts is shown to bind to this 25bp fragment. These results suggest that this 25bp region and the unknown factor are necessary for determining the tissue-specificity of the Ser1 promoter.

Accurate pre-mRNA splicing using a nuclear extract from Bombyx mori fat body

A cell-free pre-mRNA splicing system was developed from the nuclear extract of Bombyx mori fat bodies. The synthetic pre-mRNA from the cytoplasmic actin gene of B. mori (BmA3 ) was used as a substrate for in vitro splicing. The pre-mRNA was accurately spliced in the nuclear extract prepared from the fat body. Sequencing of the amplicon by RT-PCR revealed that the spliced site in vitro was identical to the site in vivo. We found that a part of the input capped pre-mRNA was accurately spliced after 2h of incubation. In addition, the RT-PCR analysis precisely mapped the branch point to an adenine located at 30 nucleotides before the 3' end of the first intron in BmA3. This system was a first example that differentiated tissue in insects yielded active extracts for in vitro splicing.

Inducible gene expression of moricin, a unique antibacterial peptide from the silkworm (Bombyx mori)

Molecular cloning of cDNAs encoding moricin, a novel antibacterial peptide from the silkworm (Bombyx mori), was performed using a fat-body cDNA library. A reverse-transcription PCR product encoding a partial nucleotide sequence of moricin was used as a probe. Nucleotide sequencing of four positive clones revealed two types of moricin cDNAs designated moricin 1 and 2. cDNAs for moricin 1 and 2 shared 97.2% identity in their nucleotide sequences. Although one amino acid residue (Phe6) of moricin 1 in the putative signal peptide was replaced with Lys6 in moricin 2, amino acid sequences of their mature portions were identical. Moricin gene expression in B. mori larvae injected with Escherichia coli was observed in fat-bodies, haemocytes and the Malpighian tubule, but not in other tissues like the midgut and silk glands. Accumulation of moricin gene transcripts induced by E. coli reached a maximum level 8 h after injection and persisted up to 48 h. It was confirmed that lipopolysaccharide (LPS) and lipid A, which are cell-wall components of E. coli, triggered moricin gene expression. Comparison of gene expression between moricin 1 and 2 by PCR using specific primers indicated that moricin 2 gene was more strongly expressed than moricin 1 gene. A genomic clone encoding moricin 2 was screened from a B. mori genomic library using a moricin cDNA as a probe. Regulatory motifs for gene expression such as nuclear-factor-kappaB-binding-site-like sequence (kappaB site) and nuclear-factor-interleukin-6-binding-site-like sequence (NF-IL-6 site) were found in the 5'-upstream regulatory region. An electrophoretic-mobility-shift assay revealed that there are bacterial LPS-inducible nuclear proteins that can bind to the kappaB site and other sites in the regulatory region.

In vitro transcription systems from cultured cells and fat-body tissue of the silkworm, Bombyx mori

This article describes the development of cell-free transcription systems from the cultured cells and fat body tissues of a Lepidpteran insect, the silkworm, Bombyx mori. Detailed protocols are provided for the culture of a B. mori cell line, rearing larvae, preparation of whole cell as well as nuclear extract and conditions for in vitro transcription of cloned plasma protein gene templates.

Core promoter elements are essential as selective determinants for function of the yeast transcription factor GAL11

The GAL11 gene product, which copurifies with RNA polymerase II holoenzyme, is necessary for full expression of many, but not all, genes in yeast. Here we shows that the GAL11 dependence of a gene for expression is determined by the core promoter structure. In the GAL80 gene, a gal11 null mutation caused reduction of TATA-dependent transcription, but exerted no effect on initiator-mediated transcription. GAL11 stimulated TATA-dependent transcription, but did not affect the TATA-independent transcription in HIS4. GAL11 was also required for transcription mediated by a canonical TATA sequence but not by a nonconsensus TATA sequence of HIS3. These results suggest that GAL11 is specifically involved in the transcription machinery formed on the TATA element.

Identification of regulatory sequences of juvenile hormone-sensitive and -insensitive serum protein-encoding genes

The promoters of three juvenile hormone (JH)-sensitive, and one JH-insensitive hexamerin-encoding genes (Hex) were isolated from Trichoplusia ni, and sequences necessary for, or affecting, transcriptional activity were identified by biochemical and functional methods. The transcription start points (tsp) for each of the four Hex were determined biochemically, by both primer extension and the sequencing of multiple, independent full-length cDNA clones. The function of each inferred tsp, as an actual tsp, was confirmed by in vitro transcription assay. The transcription initiator sequence, GNACAGT, was identical for three of the Hex, while the fourth used a divergent motif. Using the in vitro transcription system, a minimal core promoter of 60 bp (bp -34 to +24) of the BJHSP1 (basic JH suppressible protein 1) gene, containing a single TATA box motif approximately 30 bp upstream of the tsp, was functionally sufficient to support alpha-amanitin-sensitive transcription. The same construct was also transcriptionally functional in a homologous cell line transfection assay. The corresponding region of the other Hex also contains a similarly positioned TATA box motif, and promoter constructs for each, that included that included the tsp, initiator and inferred basal transcription apparatus binding site, were all transcriptionally functional in a cell line transfection assay. The action of sequences 5' to the minimal promoter region in modulating the rate of transcription was shown by a cell line transfection assay of a nested deletion series of the promoter for the BJHSP1 gene, in which the results identified a strongly suppressive element between positions -160 and -109. This system of Hex genes, including those sensitive to JH and one not sensitive, should be useful in a comparative approach toward identifying those regulatory motifs that are functionally necessary to transduce the regulatory action of JH.