Construction and characterization of bacterial artificial chromosome libraries from the silkworm, Bombyx mori.

Two bacterial artificial chromosome (BAC) libraries were constructed using nuclear DNA from posterior silkglands of the silkworm (Bombyx mori) strains p50 and C108. The libraries contain a total of 36,864 clones, or approximately 9 genome equivalents. The average insert sizes in the libraries were 134.5 kb and 120.8 kb, respectively. PCR-based screening was performed on the p50 library using probes for 34 sequence-tagged sites (STSs). Between 3 and 11 (6.1 hits on average) clones were isolated with each STS, in good agreement with the library size, 5.8 genome equivalents. The previously reported close linkage between the Bombyx homologs of the invected (Bm in) and engrailed (Bm en) genes was confirmed by construction of a BAC contig that contained both. Moreover, screening revealed novel information about the chromosomal organization of the sericin-1 and DH-PBAN genes, which were localized within a 22-kb interval and are divergently oriented. These results show that it is possible to construct contigs and analyze chromosome organization using these libraries. Received: 12 October 1998 / Accepted: 10 February 1999     

Construction of a single nucleotide polymorphism linkage map for the silkworm, Bombyx mori, based on bacterial artificial chromosome end sequences

We have developed a linkage map for the silkworm Bombyx mori based on single nucleotide polymorphisms (SNPs) between strains p50T and C108T initially found on regions corresponding to the end sequences of bacterial artificial chromosome (BAC) clones. Using 190 segregants from a backcross of a p50T female x an F1 (p50T x C108T) male, we analyzed segregation patterns of 534 SNPs between p50T and C108T, detected among 3840 PCR amplicons, each associated with a p50T BAC end sequence. This enabled us to construct a linkage map composed of 534 SNP markers spanning 1305 cM in total length distributed over the expected 28 linkage groups. Of the 534 BACs whose ends harbored the SNPs used to construct the linkage map, 89 were associated with 107 different ESTs. Since each of the SNP markers is directly linked to a specific genomic BAC clone and to whole-genome sequence data, and some of them are also linked to EST data, the SNP linkage map will be a powerful tool for investigating silkworm genome properties, mutation mapping, and map-based cloning of genes of industrial and agricultural interest.     

Purification and characterization of cocoonase from the silkworm Bombyx mori

Cocoonase (CCN) which facilitates the degradation of a cocoon is recognized as a trypsin-like serine protease. In this study, CCN from the silkworm Bombyx mori was purified and comprehensively characterized. Its activity was maximal at about pH 9.8. It was stable above pH 3.4 at 4?°C and below 50?°C at pH 7.5. CuSO₄, FeSO₄, and ZnSO₄ showed inhibitory effects on CCN, but other salts improved activity. Typical trypsin inhibitors inhibited CCN, but the relative inhibitory activities were much lower than those against bovine trypsin. An extract of cocoon shells inhibited trypsin, but it was only slightly inhibitory against CCN. There were significant differences in catalytic efficiencies and substrate specificities as between CCN and bovine trypsin.     

家蚕BmBrat基因的克隆与鉴定

NHL家族蛋白具有调控细胞增殖与分化的功能,在哺育动物中被广泛研究。本文克隆得到家蚕NHL蛋白家族成员BmBrat基因,通过RACE技术获得该基因cDNA全长序列为3 614 bp,其ORF为2 580 bp,编码859个氨基酸,预测其蛋白分子量为94.3 kDa,等电点为6.65。利用RT-PCR技术检测其在五龄3 d家蚕各组织表达情况,结果表明其在幼虫各组织均有表达,包括丝腺、中肠、脂肪体、马氏管等,且卵巢和头部表达量最高;胚胎时期表达谱分析显示其在胚胎发育第4天和第5天有高量表达。经原核表达、蛋白纯化及免疫小鼠后获得家蚕BmBrat多克隆抗体,且Western blotting及免疫荧光检测显示该抗体可以特异检测家蚕BmBrat蛋白;免疫荧光结果表明BmBrat蛋白定位于家蚕血细胞胞质中,为进一步研究BmBrat基因的生物学功能奠定了基础。     

Retrotransposable elements on the W chromosome of the silkworm, Bombyx mori

The sex chromosomes of the silkworm, Bombyxmori, are designated ZW(XY) for females and ZZ(XX) for males. The W chromosome of B. mori does not recombine with the Z chromosome and autosomes and no genes for morphological characters have been mapped to the W chromosome as yet. Furthermore, femaleness is determined by the presence of a single W chromosome, regardless of the number of autosomes or Z chromosomes. To understand these interesting features of the W chromosome, it is necessary to analyze the W chromosome at the molecular biology level. Initially to isolate DNA sequences specific for the W chromosome as randomly amplified polymorphic DNA (RAPD) markers, we compared the genomic DNAs between males and females by PCR with arbitrary 10-mer primers. To the present, we have identified 12 W-specific RAPD markers, and with the exception of one RAPD marker, all of the deduced amino acid sequences of these W-specific RAPD markers show similarity to previously reported amino acid sequences of retrotransposable elements from various organisms. After constructing a genomic DNA lambda phage library of B. mori we obtained two lambda phage clones, one containing the W-Kabuki RAPD sequence and one containing the W-Samurai RAPD sequence and found that these DNA sequences comprised nested structures of many retrotransposable elements. To further analyze the W chromosome, we obtained 14 W-specific bacterial artificial chromosome (BAC) clones from three BAC libraries and subjected these clones to shotgun sequencing. The resulting assembly of sequences did not produce a single contiguous sequence due to the presence of many retrotransposable elements. Therefore, we coupled PCR with shotgun sequencing. Through these analyses, we found that many long terminal repeat (LTR) and non-LTR retrotransposons, retroposons, DNA transposons and their derivatives, have accumulated on the W chromosome as strata. These results strongly indicate that retrotransposable elements are the main structural component of the W chromosome.     

Molecular characterization of a peritrophic membrane protein from the silkworm, Bombyx mori

The peritrophic membrane lines the gut of most insects at one or more stages of their life cycles. It facilitates the digestive processes in the guts and protects from invasion by pathogens or food particles. In the current study, a novel PM protein, designated as BmMtch, was identified from the silkworm, Bombyx mori. The open reading frame of BmMtch is 888 bp in length, encoding 295 amino acid residues consisting of two domains (Mito_carr domains) and three transmembrane regions. They are localized on the 11th chromosome as single copy with one exon only. Quantitative real time PCR analysis (qRT-PCR) revealed that BmMtch was mainly expressed in larval fat bodies, Malpighian tubules, testis and ovaries, and could be detected through all stages of the life cycle of silkworm. Immuno-fluorescence analysis indicated that BmMtch was localized within the goblet cell of larval midgut. Western blotting analysis showed that BmMtch were detected in total proteins of PM and larval midgut. The characteristics of BmMtch indicated that BmMtch represents a novel member of insect PM proteins, without chitin-binding domains.     

Serine hydroxymethyltransferase from the silkworm Bombyx mori: Identification,distribution, and biochemical characterization

Serine hydroxymethyltransferase (SHMT) catalyzes the interconversion of serine and tetrahydrofolate (THF) to glycine and methylenetetrahydrofolate. cDNA encoding Bombyx mori SHMT (bmSHMT) was cloned and sequenced. The deduced amino acid sequence consisted of 465 amino acids and was found to share homology with other SHMTs. Recombinant bmSHMT was overexpressed in Escherichia coli and purified to homogeneity. The enzyme showed optimum activity at pH 3.0 and 30°C and was stable under acidic conditions. The K_m and k_cat/K_m values for THF in the presence of Nicotinamide adenine dinucleotide phosphate (NADP⁺) were 0.055 mM and 0.081 mM^?1 s^?1, respectively, whereas those toward NADP⁺ were 0.16 mM and 0.018 mM^?1 s^?1 and toward l ‐serine were 1.8 mM and 0.0022 mM^?1 s^?1, respectively. Mutagenesis experiments revealed that His119, His132, and His135 are important for enzymatic activity. Our results provide insight into the roles and regulation mechanism of one‐carbon metabolism in the silkworm B. mori.     

Biochemical characterization of maintenance DNA methyltransferase DNMT-1 from silkworm,Bombyx mori

DNA methylation is an important epigenetic mechanism involved in gene expression of vertebrates and invertebrates. In general, DNA methylation profile is established by de novo DNA methyltransferases (DNMT-3A, -3B) and maintainance DNA methyltransferase (DNMT-1). DNMT-1 has a strong substrate preference for hemimethylated DNA over the unmethylated one. Because the silkworm genome lacks an apparent homologue of de novo DNMT, it is still unclear that how silkworm chromosome establishes and maintains its DNA methylation profile. As the first step to unravel this enigma, we purified recombinant BmDNMT-1 using baculovirus expression system and characterized its DNA-binding and DNA methylation activity. We found that the BmDNMT-1 preferentially methylates hemimethylated DNA despite binding to both unmethylated and hemimethylated DNA. Interestingly, BmDNMT-1 formed a complex with DNA in the presence or absence of methyl group donor, S-Adenosylmethionine (AdoMet) and the AdoMet-dependent complex formation was facilitated by Zn²⁺ and Mn²⁺. Our results provide clear evidence that BmDNMT-1 retained the function as maintenance DNMT but its sensitivity to metal ions is different from mammalian DNMT-1.     

Cloning and characterization of a ribonuclease L inhibitor from the silkworm, Bombyx mori.

The ribonuclease L (RNase L) pathway plays an important role in the response of cells to double-stranded RNA (dsRNA) during the events such as virus infection. Ribonuclease L inhibitor (RLI) belonging to the ABC transporter family is known as a regulator of the RNase L pathway. The homologs of RLI were reported in many organisms including the fruit fly and mosquito, but their functions in insects and arthropods have not been elucidated to date. In the present study, we cloned a cDNA of a silkworm RLI homolog, termed BmRLI, and its nucleotide sequence was determined. RT-PCR analysis revealed that the expression of BmRLI mRNA was marked in the testis, ovary and fat body. From the cDNA, recombinant protein with an apparent molecular mass of 69 kDa was expressed in Escherichia coli and cultured insect cells. Although no obvious effect of up-regulation of the BmRLI expression on RNAi was observed, its down-regulation slightly reduced RNAi efficiency.     

Molecular and biochemical characterization of juvenile hormone epoxide hydrolase from the silkworm, Bombyx mori

One major route of insect juvenile hormone (JH) degradation is epoxide hydration by JH epoxide hydrolase (JHEH). A full-length cDNA (1536 bp) encoding a microsomal JHEH was isolated from the silkworm, Bombyx mori. Bommo-JHEH cDNA contains an open reading frame encoding a 461-amino acid protein (52 kDa), which reveals a high degree of similarity to the previously reported insect JHEHs. The residues Tyr298, Tyr373, and the HGWP motif corresponding to the oxyanion hole of JHEHs and the residues Asp227, His430, and Glu403 in the catalytic triad are well conserved in Bommo-JHEH. Bommo-JHEH was highly expressed in the fat body, where its mRNA expression pattern was in contrast to the pattern of hemolymph levels of JH during the larval development, suggesting that Bommo-JHEH plays an important role in JH degradation. Recombinant Bommo-JHEH (52 kDa) expressed in Sf9 insect cells was membrane-bound and had a high level of enzyme activity (300-fold over the control activity). This Bommo-JHEH study provides a better understanding of how JH levels are regulated in the domesticated silkworm.     

Proteome profile of spinneret from the silkworm,Bombyx mori

The silkworm spinneret is an important tissue for silk fibrillogenesis and spinning. All biochemical processes during silk fibrillogenesis are correlated with silk properties. Understanding the role of spinneret in silk fibrillogenesis may help to reveal the mechanism of silk fibrillogenesis as well as improve silk quality for commercial purposes. Thus, we profiled the proteome of silkworm spinneret. A total of 1572 proteins and 232 differential abundance proteins were identified. Silk fibrillogenesis‐related proteins, such as cuticle proteins, ion‐transporting proteins, muscular proteins, and energy metabolic proteins, were abundant in spinneret. Metabolic pathway and GO enrichment analyses revealed that the identified proteins were involved in energy metabolism, chitin binding, and cuticle construction. Active energy metabolism may provide abundant energy for the muscle contraction as well as ion and water exchange. The chitin binding and cuticle construction process may provide sufficient shear forces for silk formation. Our data suggest that silkworm spinneret provides a suitable physiological and biochemical environment for silk fibrillogenesis. These proteins are potential targets for improving silk quality in the silk industry. Data are available via ProteomeXchange with identifier PXD004455.     

Construction and analysis of bacterial artificial chromosome libraries from a marine microbial assemblage

Cultivation-independent surveys of ribosomal RNA genes have revealed the existence of novel microbial lineages, many with no known cultivated representatives. Ribosomal RNA-based analyses, however, often do not provide significant information beyond phylogenetic affiliation. Analysis of large genome fragments recovered directly from microbial communities represents one promising approach for characterizing uncultivated microbial species better. To assess further the utility of this approach, we constructed large-insert bacterial artificial chromosome (BAC) libraries from the genomic DNA of planktonic marine microbial assemblages. The BAC libraries we prepared had average insert sizes of 80 kb, with maximal insert sizes > 150 kb. A rapid screening method assessing the phylogenetic diversity and representation in the library was developed and applied. In general, representation in the libraries agreed well with previous culture-independent surveys based on polymerase chain reaction (PCR)amplified rRNA fragments. A significant fraction of the genome fragments in the BAC libraries originated from as yet uncultivated microbial species, thought to be abundant and widely distributed in the marine environment. One entire BAC insert, derived from an uncultivated, surface-dwelling euryarchaeote, was sequenced completely. The planktonic euryarchaeal genome fragment contained some typical archaeal genes, as well as unique open reading frames (ORFs) suggesting novel function. In total, our results verify the utility of BAC libraries for providing access to the genomes of as yet uncultivated microbial species. Further analysis of these BAC libraries has the potential to provide significant insight into the genomic potential and ecological roles of many indigenous microbial species, cultivated or not.