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Genomics & Proteomics

posted Mar 4, 2011, 7:19 AM by rajesh gk

Title

Nucleotide sequence and transcriptional analysis of the DNA polymerase gene of Bombyx mori nuclear polyhedrosis virus.

Authors

Chaeychomsri S, Ikeda M, Kobayashi M.

Laboratory of Sericulture and Entomoresources, School of Agriculture, Nagoya University, Japan.

Journal

Virology. 1995 Jan 10;206(1):435-47.

Abstract

A gene encoding a putative DNA polymerase (pol) of Bombyx mori nuclear polyhedrosis virus (BmSNPV) was cloned and sequenced. The gene included an open reading frame (ORF) encoding a polypeptide of 988 amino acids with a predicted molecular mass of 114.65 kDa. The deduced amino acid sequence of the BmSNPV pol ORF showed an overall identity of 96 and 45% to those of the Autographa californica NPV (AcMNPV) pol ORF and the Lymantria dispar NPV pol ORF, respectively, and contained sequences conserved in a variety of eukaryotic and viral replicative DNA polymerases. The BmSNPV pol lacked a canonical TATAA element but contained a G+C-rich sequence in the transcriptional initiation region. Analyses by Northern blot hybridization, RNase protection assay, primer extension, and 3' and 5' RACE (rapid amplification of cDNA ends) showed that at least seven different transcripts of approximately 3.1 kb that shared a common 3' end were expressed from the BmSNPV pol. The expression of these transcripts from BmSNPV pol was regulated differentially during virus infection. Transcription of five of the seven species initiated in the close vicinity of and within the motif 5'-GCGTGCT-3'. One transcript placed its initiation site within the motif 5'-AGAGCGT-3' and the remaining one within the motif 5'-GGCGGTGG-3'. The motifs 5'-GCGTGCT-3' and 5'-AGAGCGT-3' have been identified in pol and other genes of AcMNPV as conserved sequences containing transcriptional initiation sites, whereas the motif 5'-GGCGGTGG-3', which is arranged as a direct repeat in BmSNPV pol but not in AcMNPV pol, has not been defined as the sequence responsible for transcriptional initiation sites. The BmSNPV pol transcripts were detectable at 2 hr postinfection (p.i.), peaked at 10 hr p.i., and declined to a low level by 18 hr p.i. The expression of BmSNPV pol was not inhibited but delayed dramatically by the protein synthesis inhibitor cycloheximide upon treatment of infected cells, whereas aphidicolin, an inhibitor of DNA polymerase, inhibited BmSNPV pol transcription. These results suggest a complicated and unique mechanism for the regulation of BmSNPV pol expression.

Citation

http://www.ncbi.nlm.nih.gov/pubmed/7831799 PMID: 7831799 [PubMed - indexed for MEDLINE]

 

Title

Exogenous prostaglandin F2alpha as a mediator in the regulation of silkworm growth and silk gland genome.

Authors

Miao YG, Nair KS.

Department of Sericulture, College of Animal Sciences, Zhejiang University, Hangzhou-310029, PR China. miaoyg@zju.edu.cn

Journal

Prostaglandins Other Lipid Mediat. 2003 Nov;72(3-4):147-54.

Abstract

Prostaglandins are locally acting hormones that have remarkable variety of physiological functions. They are rapidly synthesized in several types of vertebrate cells as oxygenated metabolites of arachidonic acid in response to various stimuli. In many insect species they are biosynthesized in fat body and hemocytes mainly in response to bacterial infections. In the present study, we administered synthetic analog of prostaglandin F2alpha, the most prominent of the prostaglandins to the 48 h old fifth instar silkworm, Bombyx mori L. at a single dose of 4 microg per larva to study its effects on the larval growth pattern and silk synthesis. The possible role of PGF2alpha at altering the quantum of silk synthesis by controlling the silk gene expression was also studied. The genomic DNA was isolated from the posterior silk gland on Days 5 and 7 of the fifth instar from the prostaglandin treated and the control larvae and were random amplified with arbitrary primers. The result presented notable variation in the amplified product suggesting the participation of PGF2alpha in the silk biosynthesis controlling the silk gene expression. The feeding period of treated larvae was unaffected while the cocoon characters exhibited considerable improvement. The filament traits also were improved notably in the treated larvae. The participation of PGF2alpha analog in the silk biosynthetic process with its physiological and molecular implications are discussed.

Citation

http://www.ncbi.nlm.nih.gov/pubmed/14674626 PMID: 14674626 [PubMed - indexed for MEDLINE]

 

Title

A new chitinase-related gene, BmChiR1, is induced in the Bombyx mori anterior silk gland at molt and metamorphosis by ecdysteroid.

Authors

Takahashi M, Kiuchi M, Kamimura M.

Department of Sericulture, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8634, Japan.

Journal

Insect Biochem Mol Biol. 2002 Feb;32(2):147-51.

Abstract

A novel ecdysteroid-inducible gene was isolated from the anterior silk gland of the silkworm by mRNA differential display and named Bombyx mori chitinase-related gene 1 (BmChiR1). cDNA for BmChiR1 is 3.7 kbp encoding 1080 amino acids. Its predicted protein sequence consists of two tandem-repeated sequences, both showing high similarities to arthropod chitinases but lacking the active site glutamate essential for catalytic activity, suggesting that BmChiR1 protein has no chitinolytic activity. BmChiR1 mRNA was expressed simultaneously with chitinase mRNA in the anterior silk gland at the ends of the penultimate and last larval instar. Injection of 20-hydroxyecdysone (20E) into feeding last instar larvae induced accumulation of BmChiR1 mRNA. Topical application of a juvenile hormone analog, fenoxycarb, just after the 20E injection, suppressed this induction. BmChiR1 expression is therefore upregulated by ecdysteroid and downregulated by juvenile hormone.

Citation

http://www.ncbi.nlm.nih.gov/pubmed/11755056 PMID: 11755056 [PubMed - indexed for MEDLINE]

 

Title

MicroRNA expression profiling during the life cycle of the silkworm (Bombyx mori). Free PMC Article

Authors

Liu S, Zhang L, Li Q, Zhao P, Duan J, Cheng D, Xiang Z, Xia Q.

The Key Sericultural Laboratory of Agricultural Ministry, College of Biotechnology, Southwest University, Chongqing 400715, PR China. lsp98668@163.com

Journal

BMC Genomics. 2009 Sep 28;10:455.

Abstract

BACKGROUND: MicroRNAs (miRNAs) are expressed by a wide range of eukaryotic organisms, and function in diverse biological processes. Numerous miRNAs have been identified in Bombyx mori, but the temporal expression profiles of miRNAs corresponding to each stage transition over the entire life cycle of the silkworm remain to be established. To obtain a comprehensive overview of the correlation between miRNA expression and stage transitions, we performed a whole-life test and subsequent stage-by-stage examinations on nearly one hundred miRNAs in the silkworm. RESULTS: Our results show that miRNAs display a wide variety of expression profiles over the whole life of the silkworm, including continuous expression from embryo to adult (miR-184), up-regulation over the entire life cycle (let-7 and miR-100), down-regulation over the entire life cycle (miR-124), expression associated with embryogenesis (miR-29 and miR-92), up-regulation from early 3rd instar to pupa (miR-275), and complementary pulses in expression between miR-34b and miR-275. Stage-by-stage examinations revealed further expression patterns, such as emergence at specific time-points during embryogenesis and up-regulation of miRNA groups in late embryos (miR-1 and bantam), expression associated with stage transition between instar and molt larval stages (miR-34b), expression associated with silk gland growth and spinning activity (miR-274), continuous high expression from the spinning larval to pupal and adult stages (miR-252 and miR-31a), a coordinate expression trough in day 3 pupae of both sexes (miR-10b and miR-281), up-regulation in pupal metamorphosis of both sexes (miR-29b), and down-regulation in pupal metamorphosis of both sexes (miR-275). CONCLUSION: We present the full-scale expression profiles of miRNAs throughout the life cycle of Bombyx mori. The whole-life expression profile was further investigated via stage-by-stage analysis. Our data provide an important resource for more detailed functional analysis of miRNAs in this animal.

Citation

PMID: 19843344 [PubMed - indexed for MEDLINE]PMCID: PMC2770533

 

Title

Annotation and expression of carboxylesterases in the silkworm, Bombyx mori.

Authors

Yu QY, Lu C, Li WL, Xiang ZH, Zhang Z.

The Institute of Agricultural and Life Sciences, Chongqing University, Chongqing 400044, China. quanyouyu@126.com

Journal

BMC Genomics. 2009 Nov 24;10:553.

Abstract

BACKGROUND: Carboxylesterase is a multifunctional superfamily and ubiquitous in all living organisms, including animals, plants, insects, and microbes. It plays important roles in xenobiotic detoxification, and pheromone degradation, neurogenesis and regulating development. Previous studies mainly used Dipteran Drosophila and mosquitoes as model organisms to investigate the roles of the insect COEs in insecticide resistance. However, genome-wide characterization of COEs in phytophagous insects and comparative analysis remain to be performed. RESULTS: Based on the newly assembled genome sequence, 76 putative COEs were identified in Bombyx mori. Relative to other Dipteran and Hymenopteran insects, alpha-esterases were significantly expanded in the silkworm. Genomics analysis suggested that BmCOEs showed chromosome preferable distribution and 55% of which were tandem arranged. Sixty-one BmCOEs were transcribed based on cDNA/ESTs and microarray data. Generally, most of the COEs showed tissue specific expressions and expression level between male and female did not display obvious differences. Three main patterns could be classified, i.e. midgut-, head and integument-, and silk gland-specific expressions. Midgut is the first barrier of xenobiotics peroral toxicity, in which COEs may be involved in eliminating secondary metabolites of mulberry leaves and contaminants of insecticides in diet. For head and integument-class, most of the members were homologous to odorant-degrading enzyme (ODE) and antennal esterase. RT-PCR verified that the ODE-like esterases were also highly expressed in larvae antenna and maxilla, and thus they may play important roles in degradation of plant volatiles or other xenobiotics. CONCLUSION: B. mori has the largest number of insect COE genes characterized to date. Comparative genomic analysis suggested that the gene expansion mainly occurred in silkworm alpha-esterases. Expression evidence indicated that the expanded genes were specifically expressed in midgut, integument and head, implying that these genes may have important roles in detoxifying secondary metabolites of mulberry leaves, contaminants in diet, and odorants. Our results provide some new insights into functions and evolutionary characteristics of COEs in phytophagous insects.

Citation

PMID: 19930670 [PubMed - indexed for MEDLINE]PMCID: PMC2784812 Free PMC Article

 

Title

Identification and expression analysis of ras gene in silkworm, Bombyx mori.

Authors

Ogura T, Tan A, Tsubota T, Nakakura T, Shiotsuki T.

Department of Applied Life Sciences, Kyoto University, Kyoto, Japan.

Journal

PLoS One. 2009 Nov 25;4(11):e8030.

Abstract

Ras proteins play important roles in development especially for cell proliferation and differentiation in various organisms. However, their functions in the most insect species are still not clear. We identified three ras cDNAs from the silk worm, Bombyx mori. These sequences corresponded to three Ras of Drosophila melanogaster, but not to three mammalian Ras (H-Ras, K-Ras, N-Ras). Subsequently, the expression profiles of ras were investigated by quantitative real-time PCR using whole body of individuals from the embryonic to adult stages, and various tissues of 4th and 5th instar larvae. Each of three Bombyx ras showed different expression patterns. We also showed membrane localization of their products. These results indicate that the three Bombyx Ras are functional and have different roles.

Citation

PMID: 19946625 [PubMed - indexed for MEDLINE]PMCID: PMC2777509 Free PMC Article

 

Title

MicroRNAs show diverse and dynamic expression patterns in multiple tissues of Bombyx mori.

Authors

Liu S, Gao S, Zhang D, Yin J, Xiang Z, Xia Q.

The Key Sericultural Laboratory of Agricultural Ministry, College of Biotechnology, Southwest University, Chongqing 400715, PR China.

Journal

BMC Genomics. 2010 Feb 2;11:85.

Abstract

BACKGROUND: MicroRNAs (miRNAs) repress target genes at the post-transcriptional level, and function in the development and cell-lineage pathways of host species. Tissue-specific expression of miRNAs is highly relevant to their physiological roles in the corresponding tissues. However, to date, few miRNAs have been spatially identified in the silkworm. RESULTS: We establish for the first time the spatial expression patterns of nearly 100 miRNAs in multiple normal tissues (organs) of Bombyx mori females and males using microarray and Northern-blotting analyses. In all, only 10 miRNAs were universally distributed (including bmo-let-7 and bmo-bantam), while the majority were expressed exclusively or preferentially in specific tissue types (e.g., bmo-miR-275 and bmo-miR-1). Additionally, we examined the developmental patterns of miRNA expression during metamorphosis of the body wall, silk glands, midgut and fat body. In total, 63 miRNAs displayed significant alterations in abundance in at least 1 tissue during the developmental transition from larvae to pupae (e.g., bmo-miR-263b and bmo-miR-124). Expression patterns of five miRNAs were significantly increased during metamorphosis in all four tissues (e.g., bmo-miR-275 and bmo-miR-305), and two miRNA pairs, bmo-miR-10b-3p/5p and bmo-miR-281-3p/5p, showed coordinate expression. CONCLUSIONS: In this study, we conducted preliminary spatial measurements of several miRNAs in the silkworm. Periods of rapid morphological change were associated with alterations in miRNA expression patterns in the body wall, silk glands, midgut and fat body during metamorphosis. Accordingly, we propose that corresponding ubiquitous or tissue-specific expression of miRNAs supports their critical roles in tissue specification. These results should facilitate future functional analyses.

Citation

PMID: 20122259 [PubMed - indexed for MEDLINE]PMCID: PMC2835664 Free PMC Article

 

Title

MicroRNAs of Bombyx mori identified by Solexa sequencing.

Authors

Liu S, Li D, Li Q, Zhao P, Xiang Z, Xia Q.

The Key Sericultural Laboratory of Agricultural Ministry, College of Biotechnology, Southwest University, Tiansheng Road, Beibei, Chongqing 400715, PR China.

Journal

BMC Genomics. 2010 Mar 3;11:148.

Abstract

BACKGROUND: MicroRNA (miRNA) and other small regulatory RNAs contribute to the modulation of a large number of cellular processes. We sequenced three small RNA libraries prepared from the whole body, and the anterior-middle and posterior silk glands of Bombyx mori, with a view to expanding the repertoire of silkworm miRNAs and exploring transcriptional differences in miRNAs between segments of the silk gland. RESULTS: With the aid of large-scale Solexa sequencing technology, we validated 257 unique miRNA genes, including 202 novel and 55 previously reported genes, corresponding to 324 loci in the silkworm genome. Over 30 known silkworm miRNAs were further corrected in their sequence constitutes and length. A number of reads originated from the loop regions of the precursors of two previously reported miRNAs (bmo-miR-1920 and miR-1921). Interestingly, the majority of the newly identified miRNAs were silkworm-specific, 23 unique miRNAs were widely conserved from invertebrates to vertebrates, 13 unique miRNAs were limited to invertebrates, and 32 were confined to insects. We identified 24 closely positioned clusters and 45 paralogs of miRNAs in the silkworm genome. However, sequence tags showed that paralogs or clusters were not prerequisites for coordinated transcription and accumulation. The majority of silkworm-specific miRNAs were located in transposable elements, and displayed significant differences in abundance between the anterior-middle and posterior silk gland. CONCLUSIONS: Conservative analysis revealed that miRNAs can serve as phylogenetic markers and function in evolutionary signaling. The newly identified miRNAs greatly enrich the repertoire of insect miRNAs, and provide insights into miRNA evolution, biogenesis, and expression in insects. The differential expression of miRNAs in the anterior-middle and posterior silk glands supports their involvement as new levels in the regulation of the silkworm silk gland.

Citation

PMID: 20199675 [PubMed - indexed for MEDLINE]PMCID: PMC2838851

 Free PMC Article

 

Title

Analysis of Transcripts Expressed in One-Day-Old Larvae and Fifth Instar Silk Glands of Tasar Silkworm, Antheraea mylitta.

Authors

Maity S, Goel SI, Roy S, Ghorai S, Bhattacharyya S, Venugopalan A, Ghosh AK.

Department of Biotechnology, Indian Institute of Technology, Kharagpur 721302, India.

Journal

Comp Funct Genomics. 2010:246738. Epub 2010 May 4

Abstract

Antheraea mylitta is one of the wild nonmulberry silkworms, which produces tasar silk. An EST project has been undertaken to understand the gene expression profile of A. mylitta silk gland. Two cDNA libraries, one from the whole bodies of one-day-old larvae and the other from the silkglands of fifth instar larvae, were constructed and sequenced. A total of 2476 good-quality ESTs (1239 clones) were obtained and grouped into 648 clusters containing 390 contigs and 258 singletons to represent 467 potential unigenes. Forty-five sequences contained putative coding region, and represented potentially novel genes. Among the 648 clusters, 241 were categorized according to Gene Ontology hierarchy and showed presence of several silk and immune-related genes. The A. mylitta ESTs have been organized into a freely available online database "AmyBASE". These data provide an initial insight into the A. mylitta transcriptome and help to understand the molecular mechanism of silk protein production in a Lepidopteran species.

Citation

PMID: 20454581 [PubMed - in process]PMCID: PMC2864506 Free PMC Article

 

 

Title

Population-level transcriptome sequencing of nonmodel organisms Erynnis propertius and Papilio zelicaon

Authors

O'Neil Shawn ; Dzurisin Jason ; Carmichael Rory ; Lobo Neil ; Emrich Scott ; Hellmann Jessica

Journal

BMC Genomics

Abstract

Background: Several recent studies have demonstrated the use of Roche 454 sequencing technology for de novo transcriptome analysis. Low error rates and high coverage also allow for effective SNP discovery and genetic diversity estimates. However, genetically diverse datasets, such as those sourced from natural populations, pose challenges for assembly programs and subsequent analysis. Further, estimating the effectiveness of transcript discovery using Roche 454 transcriptome data is still a difficult task.

Results: Using the Roche 454 FLX Titanium platform, we sequenced and assembled larval transcriptomes for two butterfly species: the Propertius duskywing, Erynnis propertius (Lepidoptera: Hesperiidae) and the Anise swallowtail, Papilio zelicaon (Lepidoptera: Papilionidae). The Expressed Sequence Tags (ESTs) generated represent a diverse sample drawn from multiple populations, developmental stages, and stress treatments.

Despite this diversity, > 95% of the ESTs assembled into long (> 714 bp on average) and highly covered (> 9.6× on average) contigs. To estimate the effectiveness of transcript discovery, we compared the number of bases in the hit region of unigenes (contigs and singletons) to the length of the best match silkworm (Bombyx mori) protein--this "ortholog hit ratio" gives a close estimate on the amount of the transcript discovered relative to a model lepidopteran genome. For each species, we tested two assembly programs and two parameter sets; although CAP3 is commonly used for such data, the assemblies produced by Celera Assembler with modified parameters were chosen over those produced by CAP3 based on contig and singleton counts as well as ortholog hit ratio analysis. In the final assemblies, 1,413 E. propertius and 1,940 P. zelicaon unigenes had a ratio > 0.8; 2,866 E. propertius and 4,015 P. zelicaon unigenes had a ratio > 0.5.

Conclusions Ultimately, these assemblies and SNP data will be used to generate microarrays for ecoinformatics examining climate change tolerance of different natural populations. These studies will benefit from high quality assemblies with few singletons (less than 26% of bases for each assembled transcriptome are present in unassembled singleton ESTs) and effective transcript discovery (over 6,500 of our putative orthologs cover at least 50% of the corresponding model silkworm gene).

Citation

FULL TEXT

 

Title

Genetic diversity, molecular phylogeny and selection evidence of the silkworm mitochondria implicated by complete resequencing of 41 genomes

Authors

Li Dong ; Guo Yiran ; Shao Haojing ; Tellier Laurent ; Wang Jun ; Xiang Zhonghuai ; Xia Qingyou

Journal

BMC Evolutionary Biology, 2010

Abstract

Background: Mitochondria are a valuable resource for studying the evolutionary process and deducing phylogeny. A few mitochondria genomes have been sequenced, but a comprehensive picture of the domestication event for silkworm mitochondria remains to be established. In this study, we integrate the extant data, and perform a whole genome resequencing of Japanese wild silkworm to obtain breakthrough results in silkworm mitochondrial (mt) population, and finally use these to deduce a more comprehensive phylogeny of the Bombycidae.

Results: We identified 347 single nucleotide polymorphisms (SNPs) in the mt genome, but found no past recombination event to have occurred in the silkworm progenitor. A phylogeny inferred from these whole genome SNPs resulted in a well-classified tree, confirming that the domesticated silkworm, Bombyx mori, most recently diverged from the Chinese wild silkworm, rather than from the Japanese wild silkworm. We showed that the population sizes of the domesticated and Chinese wild silkworms both experience neither expansion nor contraction. We also discovered that one mt gene, named cytochrome b, shows a strong signal of positive selection in the domesticated clade. This gene is related to energy metabolism, and may have played an important role during silkworm domestication.

Conclusions: We present a comparative analysis on 41 mt genomes of B. mori and B. mandarina from China and Japan. With these, we obtain a much clearer picture of the evolution history of the silkworm. The data and analyses presented here aid our understanding of the silkworm in general, and provide a crucial insight into silkworm phylogeny.

Citation

FULL TEXT

 

Title

Deep sequencing of small RNA libraries reveals dynamic regulation of conserved and novel microRNAs and microRNA-stars during silkworm development

Authors

Jagadeeswaran Guru ; Zheng Yun ; Sumathipala Niranji ; Jiang Haobo ; Arrese Estela ; Soulages Jose ; Zhang Weixiong ; Sunkar Ramanjulu

Journal

BMC Genomics, 2010; 11(1) p. 52

Abstract

Background: In eukaryotes, microRNAs (miRNAs) have emerged as critical regulators of gene expression. The Silkworm (Bombyx mori L.) is one of the most suitable lepidopteran insects for studying the molecular aspects of metamorphosis because of its large size, availability of mutants and genome sequence. Besides, this insect also has been amply studied from a physiological and biochemical perspective. Deep sequencing of small RNAs isolated from different stages of silkworm is a powerful tool not only for measuring the changes in miRNA profile but also for discovering novel miRNAs.

Results: We generated small RNA libraries from feeding larvae, spinning larvae, pupae and adults of B. mori and obtained ~2.5 million reads of 18-30 nt. Sequence analysis identified 14 novel and 101 conserved miRNAs. Most novel miRNAs are preferentially expressed in pupae, whereas more than 95% of the conserved miRNAs are dynamically regulated during different developmental stages. Remarkably, the miRNA-star (miR*) of four miRNAs are expressed at much higher levels than their corresponding miRNAs, and their expression profiles are distinct from their corresponding miRNA profiles during different developmental stages. Additionally, we detected two antisense miRNA loci (miR-263-S and miR-263-AS; miR-306-S and miR-306-AS) that are expressed in sense and antisense directions. Interestingly, miR-263 and miR-306 are preferentially and abundantly expressed in pupae and adults, respectively.

Conclusions: We identified 101 homologs of conserved miRNAs, 14 species-specific and two antisense miRNAs in the silkworm. Our results provided deeper insights into changes in conserved and novel miRNA and miRNA* accumulation during development.

Citation

FULL TEXT

 

Title

MicroRNAs of Bombyx mori identified by Solexa sequencing

Authors

Liu Shiping ; Li Dong ; Li Qibin ; Zhao Ping ; Xiang Zhonghuai ; Xia Qingyou

Journal

BMC Genomics, 2010; 11(1), p. 148

Abstract

Background: MicroRNA (miRNA) and other small regulatory RNAs contribute to the modulation of a large number of cellular processes. We sequenced three small RNA libraries prepared from the whole body, and the anterior-middle and posterior silk glands of Bombyx mori, with a view to expanding the repertoire of silkworm miRNAs and exploring transcriptional differences in miRNAs between segments of the silk gland.

Results: With the aid of large-scale Solexa sequencing technology, we validated 257 unique miRNA genes, including 202 novel and 55 previously reported genes, corresponding to 324 loci in the silkworm genome. Over 30 known silkworm miRNAs were further corrected in their sequence constitutes and length. A number of reads originated from the loop regions of the precursors of two previously reported miRNAs (bmo-miR-1920 and miR-1921). Interestingly, the majority of the newly identified miRNAs were silkworm-specific, 23 unique miRNAs were widely conserved from invertebrates to vertebrates, 13 unique miRNAs were limited to invertebrates, and 32 were confined to insects. We identified 24 closely positioned clusters and 45 paralogs of miRNAs in the silkworm genome. However, sequence tags showed that paralogs or clusters were not prerequisites for coordinated transcription and accumulation. The majority of silkworm-specific miRNAs were located in transposable elements, and displayed significant differences in abundance between the anterior-middle and posterior silk gland.

Conclusions: Conservative analysis revealed that miRNAs can serve as phylogenetic markers and function in evolutionary signaling. The newly identified miRNAs greatly enrich the repertoire of insect miRNAs, and provide insights into miRNA evolution, biogenesis, and expression in insects. The differential expression of miRNAs in the anterior-middle and posterior silk glands supports their involvement as new levels in the regulation of the silkworm silk gland.

Citation

FULL TEXT

 

Title

MicroRNAs show diverse and dynamic expression patterns in multiple tissues of Bombyx mori

Authors

Liu Shiping ; Gao Song ; Zhang Danyu ; Yin Jiyun ; Xiang Zhonghuai ; Xia Qingyou

Journal

BMC Genomics, 2010; 11 (1) p.85

Abstract

Background: MicroRNAs (miRNAs) repress target genes at the post-transcriptional level, and function in the development and cell-lineage pathways of host species. Tissue-specific expression of miRNAs is highly relevant to their physiological roles in the corresponding tissues. However, to date, few miRNAs have been spatially identified in the silkworm.

Results: We establish for the first time the spatial expression patterns of nearly 100 miRNAs in multiple normal tissues (organs) of Bombyx mori females and males using microarray and Northern-blotting analyses. In all, only 10 miRNAs were universally distributed (including bmo-let-7 and bmo-bantam), while the majority were expressed exclusively or preferentially in specific tissue types (e.g., bmo-miR-275 and bmo-miR-1). Additionally, we examined the developmental patterns of miRNA expression during metamorphosis of the body wall, silk glands, midgut and fat body. In total, 63 miRNAs displayed significant alterations in abundance in at least 1 tissue during the developmental transition from larvae to pupae (e.g., bmo-miR-263b and bmo-miR-124). Expression patterns of five miRNAs were significantly increased during metamorphosis in all four tissues (e.g., bmo-miR-275 and bmo-miR-305), and two miRNA pairs, bmo-miR-10b-3p/5p and bmo-miR-281-3p/5p, showed coordinate expression.

Conclusions: In this study, we conducted preliminary spatial measurements of several miRNAs in the silkworm. Periods of rapid morphological change were associated with alterations in miRNA expression patterns in the body wall, silk glands, midgut and fat body during metamorphosis. Accordingly, we propose that corresponding ubiquitous or tissue-specific expression of miRNAs supports their critical roles in tissue specification. These results should facilitate future functional analyses.

Citation

FULL TEXT

 

Title

The QTLs, Determination of Cocoon Shell Weight Trait in Mulberry Silkworm (Bombyx mori L.)

Authors

M. Taeb ; B. Rabiee ; S.Z. Mirhosseini ; A.R. Bizhannia

Journal

Biotechnology, 2010; 9 (1); p. 41-47

Abstract

The silkworm is an important economical insect in sericultural field. Its major production-economic characteristics are polygenic. In this study, three F2 populations (second generation) derived from three cross between three pairs, parents of Lemon Khorasan (as maternal) and 107 (as paternal) lines. we contacted AFLP (amplified fragment length polymorphism) technique for mapping genetic factors or QTLs that effect on Cocoon Shell Weight (CSW) trait. Following it we used 20 selected primer combinations of PstI/TaqI and DNAs were individually extracted to phenol-chloroform method. They digested by two restriction enzymes (TaqI and PstI) and also produced DNA fragments amplified by appropriate adaptors separately. After transferring of DNAs samples on annealed 6% polyacrylamide gels and genotyping of individuals, the linkage maps of each population were drawed. The QTLs for cocoon shell weight trait in LRS = LRT>12.5 (LOD>2.71) threshold level based on permutation test (n = 1000) and using compound interval mapping methods were analyzed and detected 5, 1 and 1 QTLs that were localized on linkage groups 9, 11; 12 and 24 in each studied F2 populations, respectively. The QTLs had different gene effects from over dominance, dominance to partial dominance.

Citation

FULL TEXT

 

Title

Isolation and Characterization of a Silkworm cDNA Encoding a Protein Homologous to the 14kDa Protein of Bovine Ubiquinol-cytochrome C Reductase

Authors

Guangwei Xing ; Jinghong Xing ; Suhua Wang

Journal

International Journal of Biology, 2009; 1(2)

Abstract

In this study, we characterized the small subunit of ubiquinol-cytochrome C reductase (Bmuccr) of the silkworm<br />Bombyx mori, a model insect of Lepidopteron species. The Bmuccr gene covers a 1.4 kb genome region and contains 3<br />exons. The ORF contained 354bp and encoded 117 amino acid residues, which shares 69% overall amino acid sequence<br />identities with the subunit VII of ubiquinol-cytochrome C reductase from bovine. Phylogenetic tree showed Bmuccr had<br />high homology with T. castaneum homologous. The multiple sequence alignment of 16 subunit VII homologues shows<br />that Bmuccr is very hydrophilic, has a characteristic charge distribution, and has a high helical content. Expression<br />analysis indicated that Bmuccr was highly expressed in larva stage and was down-regulated in embryos stage and adult<br />stage of silkworm. The tissue-specific expression indicated Bmuccr had high-expression level in tissues that consume<br />oxygen. The analysis of domain structure of this protein suggested that it might be involved in correct assembly of the<br />cytochrome bcl complex. Definition of the homologous of bovine subunit VII of ubiquinol-cytochrome C reductase<br />should facilitate further analysis of structure/function relationships of silkworm cytochrome bcl complex.

Citation

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Title

Characterization of the Gene BmEm4, a Homologue of Drosophila E(spl)m4, from the Silkworm, Bombyx mori

Authors

Fenghui Zeng ; Hongxia Xie ; Zuoming Nie ; Jian Chen ; Zhengbing Lv ; Jianqing Chen ; Dan Wang ; Lili Liu ; Wei Yu ; Qing Sheng ; Xiangfu Wu ; Yaozhou Zhang

Journal

Comparative and Functional Genomics, 2009

Abstract

The Drosophila E(spl)m4 gene contains some highly conserved motifs (such as the Brd box, GY box, K box, and CAAC motif) in its 3′ untranslated region (3′UTR). It was shown to be a microRNA target gene in Drosophila and to play an important role in the regulation of neurogenesis. We identified a homologue of the E(spl)m4 gene from Bombyx mori called BmEm4 and examined the expression patterns of BmEm4 mRNA and protein. There was a lack of correlation in the expression of the mRNA and protein between the different developmental stages, which raises the possibility of posttranscriptional regulation of the BmEm4 mRNA. Consistent with this idea is the finding that the 3′ UTR contains two putative binding sites for microRNAs. Moreover, given that the expression is the highest in the larval head, as confirmed by immunohistochemistry, we propose that BmEm4 may also be involved in the regulation of neurogenesis. Immunostaining indicated that BmEm4 is located primarily in the cytoplasm.

Citation

FULL TEXT

 

Title

Annotation and expression of carboxylesterases in the silkworm, Bombyx mori

Authors

Yu Quan-You ; Lu Cheng ; Li Wen-Le ; Xiang Zhong-Huai ; Zhang Ze

Journal

BMC Genomics, 2009; 10(1)

Abstract

Background: Carboxylesterase is a multifunctional superfamily and ubiquitous in all living organisms, including animals, plants, insects, and microbes. It plays important roles in xenobiotic detoxification, and pheromone degradation, neurogenesis and regulating development. Previous studies mainly used Dipteran Drosophila and mosquitoes as model organisms to investigate the roles of the insect COEs in insecticide resistance. However, genome-wide characterization of COEs in phytophagous insects and comparative analysis remain to be performed.

Results: Based on the newly assembled genome sequence, 76 putative COEs were identified in Bombyx mori. Relative to other Dipteran and Hymenopteran insects, alpha-esterases were significantly expanded in the silkworm. Genomics analysis suggested that BmCOEs showed chromosome preferable distribution and 55% of which were tandem arranged. Sixty-one BmCOEs were transcribed based on cDNA/ESTs and microarray data. Generally, most of the COEs showed tissue specific expressions and expression level between male and female did not display obvious differences. Three main patterns could be classified, i.e. midgut-, head and integument-, and silk gland-specific expressions. Midgut is the first barrier of xenobiotics peroral toxicity, in which COEs may be involved in eliminating secondary metabolites of mulberry leaves and contaminants of insecticides in diet. For head and integument-class, most of the members were homologous to odorant-degrading enzyme (ODE) and antennal esterase. RT-PCR verified that the ODE-like esterases were also highly expressed in larvae antenna and maxilla, and thus they may play important roles in degradation of plant volatiles or other xenobiotics. Conclusion: B. mori has the largest number of insect COE genes characterized to date. Comparative genomic analysis suggested that the gene expansion mainly occurred in silkworm alpha-esterases. Expression evidence indicated that the expanded genes were specifically expressed in midgut, integument and head, implying that these genes may have important roles in detoxifying secondary metabolites of mulberry leaves, contaminants in diet, and odorants. Our results provide some new insights into functions and evolutionary characteristics of COEs in phytophagous insects.

Citation

FULL TEXT

 

Title

An integrated genetic linkage map for silkworms with three parental combinations and its application to the mapping of single genes and QTL

Authors

Zhan Shuai ; Huang Jianhua ; Guo Qiuhong ; Zhao Yunpo ; Li Weihua ; Miao Xuexia ; Goldsmith Marian ; Li Muwang ; Huang Yongping

Journal

BMC Genomics (2009), 10 (1) 389

Abstract

Bombyx mori, the domesticated silkworm, is a well-studied model insect with great economic and scientific significance. Although more than 400 mutations have been described in silkworms, most have not been identified, especially those affecting economically-important traits. Simple sequence repeats (SSRs) are effective and economical tools for mapping traits and genetic improvement. The current SSR linkage map is of low density and contains few polymorphisms. The purpose of this work was to develop a dense and informative linkage map that would assist in the preliminary mapping and dissection of quantitative trait loci (QTL) in a variety of silkworm strains.

Through an analysis of > 50,000 genotypes across new mapping populations, we constructed two new linkage maps covering 27 assigned chromosomes and merged the data with previously reported data sets. The integrated consensus map contains 692 unique SSR sites, improving the density from 6.3 cM in the previous map to 4.8 cM. We also developed 497 confirmed neighboring markers for corresponding low-polymorphism sites, with 244 having polymorphisms. Large-scale statistics on the SSR type were suggestive of highly efficient markers, based upon which we searched 16,462 available genomic scaffolds for SSR loci. With the newly constructed map, we mapped single-gene traits, the QTL of filaments, and a number of ribosomal protein genes.

The integrated map produced in this study is a highly efficient genetic tool for the high-throughput mapping of single genes and QTL. Compared to previous maps, the current map offers a greater number of markers and polymorphisms; thus, it may be used as a resource for marker-assisted breeding.

Citation

FULL TEXT

 

Title

The small heat shock protein (sHSP) genes in the silkworm, Bombyx mori, and comparative analysis with other insect sHSP genes

Authors

Li Zi-Wen ; Li Xue ; Yu Quan-You ; Xiang Zhong-Huai ; Kishino Hirohisa ; Zhang Ze

Journal

BMC Evolutionary Biology (2009), 9 (1) 215

Abstract

Background: Small heat shock proteins (sHSPs) are products of heat shock response and of other stress responses, and ubiquitous in all three domains of life, archaea, bacteria, and eukarya. They mainly function as molecular chaperones to protect proteins from being denatured in extreme conditions. Study on insect sHSPs could provide some insights into evolution of insects that have adapted to diverse niches in the world.

Results: Taking advantage of the newly assembled genome sequence, we performed a genome-wide analysis of the candidate sHSP genes in the silkworm, Bombyx mori. Based on known silkworm sHSP sequences, we identified 16 silkworm sHSP genes. Most of them are distributed on two silkworm chromosomes 5 and 27, respectively. 15 of 16 silkworm sHSPs have expression evidence. The comparative analysis of insect sHSPs from B. mori, Drosophila melanogaster, Apis mellifera, Tribolium castaneum, and Anopheles gambiae revealed that there is only one orthologous cluster whereas remaining clusters are species-specific on the phylogenetic tree. This suggested that most of sHSPs might have diverged in function across insects investigated. In addition, the data presented in this study also revealed that sHSPs in the insect orthologous cluster are highly conserved in both sequence and expression pattern. In sum, insect sHSPs show a completely different evolutionary pattern from that found in vertebrate sHSPs.

Conclusion:B. mori has the largest number of insect sHSP genes characterized to date, including 16 genes. The inference that most species-specific sHSPs might have diverged in function across insects investigated will help us understand the adaptability of these insects to diverse environments.

Citation

FULL TEXT

 

Title

MicroRNA expression profiling during the life cycle of the silkworm (Bombyx mori)

Authors

Liu Shiping ; Zhang Liang ; Li Qibin ; Zhao Ping ; Duan Jun ; Cheng Daojun ; Xiang Zhonghuai ; Xia Qingyou

Journal

BMC Genomics (2009), 10 (1) 455

Abstract

Background: MicroRNAs (miRNAs) are expressed by a wide range of eukaryotic organisms, and function in diverse biological processes. Numerous miRNAs have been identified in Bombyx mori, but the temporal expression profiles of miRNAs corresponding to each stage transition over the entire life cycle of the silkworm remain to be established. To obtain a comprehensive overview of the correlation between miRNA expression and stage transitions, we performed a whole-life test and subsequent stage-by-stage examinations on nearly one hundred miRNAs in the silkworm.

Results: Our results show that miRNAs display a wide variety of expression profiles over the whole life of the silkworm, including continuous expression from embryo to adult (miR-184), up-regulation over the entire life cycle (let-7 and miR-100), down-regulation over the entire life cycle (miR-124), expression associated with embryogenesis (miR-29 and miR-92), up-regulation from early 3rd instar to pupa (miR-275), and complementary pulses in expression between miR-34b and miR-275. Stage-by-stage examinations revealed further expression patterns, such as emergence at specific time-points during embryogenesis and up-regulation of miRNA groups in late embryos (miR-1 and bantam), expression associated with stage transition between instar and molt larval stages (miR-34b), expression associated with silk gland growth and spinning activity (miR-274), continuous high expression from the spinning larval to pupal and adult stages (miR-252 and miR-31a), a coordinate expression trough in day 3 pupae of both sexes (miR-10b and miR-281), up-regulation in pupal metamorphosis of both sexes (miR-29b), and down-regulation in pupal metamorphosis of both sexes (miR-275).

Conclusion: We present the full-scale expression profiles of miRNAs throughout the life cycle of Bombyx mori. The whole-life expression profile was further investigated via stage-by-stage analysis. Our data provide an important resource for more detailed functional analysis of miRNAs in this animal.

Citation

FULL TEXT

 

Title

Analysis of genetic diversity of muga silkworm (Antheraea assamensis, Helfer; Lepidoptera : Saturniidae) using RAPD-based molecular markers

Authors

Kartik Neog1, H. Ranjit Singh2, Balagopalan Unni2* and A. K. Sahu3

1Central Muga Eri Research and Training Institute (CMER&TI), Central Silk Board, Lahdoigarh, Jorhat 785 700, Assam, India. 2Biotechnology Division, North East Institute of Science and Technology (NEIST), Jorhat 785 006, India. 3Regional Muga Research Station (RMRS), Central Silk Board, Boko, Kamrup, Assam, India.

Journal

African Journal of Biotechnology Vol. 9(12), pp. 1746-1752, 22 March, 2010

Abstract

Eleven populations of muga silkworm, Antheraea assamensis Helfer, the golden silk yarn producer of northeast India, was subjected to RAPD marker analysis in order to assess its genetic diversity. The genomic DNA extracted from muga silkworms were analysed using 50 random primers among which 36 polymorphic primers generated 309 bands. RAPD profile of the isolated DNA revealed a high level of genetic polymorphism. The average amplicons per primer was found to be 8.58, and 94.82% amplicons were polymorphic. Cluster analysis based on Jaccard’s similarity coefficients resulted in the formation of two main clusters with one population on one cluster and the remaining on the other cluster. Jaccard’s similarity coefficients ranged from 0.122 to 0.863 indicating a high level of genetic diversity within muga silkworm collection. The study concluded that, although there lays little morphological differences among the collected muga silkworm populations, the populations are highly polymorphic which might have enabled the silkworm to survive under a restricted geographical location, that is north east region of India only but under diverse climatic conditions for a long period. This study may be useful in identifying diverse genetic stocks of A. assamensis, which may be conserved on a priority basis. Key words: Muga silkworm, Antheraea assamensis, RAPD markers, genetic diversity.

Citation

ISSN 1684–5315 © 2010 Academic Journals Accepted 16 February, 2010 Available online at http://www.academicjournals.org/AJB

 

Title

Tissue-/stage-dependent expression of a cloned Bombyx mandarina QM homologue.

Authors

Hwang JS, Goo TW, Yun EY, Lee JH, Kang SW, Kim KY, Kwon OY.

National Sericulture and Entomology Research Institute, Rural Development Administration, Suwon, South Korea.

Journal

Biomol Eng. 2000 Jun;16(6):211-5.

Abstract

QM, a novel gene that was firstly isolated as a putative tumor suppressor gene from Wilms' tumor cell line. Although it is well known that the QM gene product plays an important role within the tumor cells, the precise role of QM in the non-tumor cells has remained elusive. With in this mind we isolated a cDNA encoding QM homologue from Bombyx mandarina to understand the function of QM. The 596 bp cDNA has an open reading frame of 219 amino acids and a predicted mol. wt. of 25 kDa. The protein has more than 88% amino acid sequence identity to the QM protein from Drosophila melanogaster. mRNA expression gradually increased from 1-2 days after egg laying to 2 days of finial instar, while very low expressions were detected for either the pupae and the moth stages. The organs, posterior/middle division of silkgland, midgut, fat body and malpighian tubes, also show relatively high mRNA expression levels, respectively. The high degree of conservation and expression of the B. mandarina QM homologous suggest that it has a selectively conserved amino acid sequence due, presumably, to an important biological role which is associated with pupae formation.

Citation

http://www.ncbi.nlm.nih.gov/pubmed/10894116 PMID: 10894116 [PubMed - indexed for MEDLINE]

 

Title

[Mutagenic analysis on the polyhedrin gene (polh) of Bombyx mori nuclear polyhedrosis virus (BmNPV)]

[Article in Chinese]

Authors

Cao Y, Xiao QX, Huang YD, Ge CB, Huang ZR, Liu LS.

Department of Sericulture and Fashion Design, South China Agricultural University, Guanzhou 510642, China.

Journal

Yi Chuan Xue Bao. 2000;27(11):972-81.

Abstract

In our early studies, the abnormal shape of the polyhedra of Bombyx mori nuclear polyhedrosis virus (BmNPV) induced by chemical mutagens of MMC. 9-AA and EMS occurred, and the genome of the mutated BmNPV obtained from the successive test had some change in the restriction endonuclease partners of EcoRI, BglII and BamHI. The present studies showed that the arrangement of the crystal lattice of the polyhedrin was disorderly, and the SDS-PAGE electropherogram of the polyhedrin depicted distinct change in comparison with control group. The results of sequencing analysis showed that many point mutations with characteristics of the base substitution had occurred at some sites of the BmNPV polh gene in three mutated groups, and these results funther revealed molecular mutagenesis of the mutagens effective to BmNPV. It was not confirmable that the point mutations of polh gene in the mutated BmNPV have relationship to abnormal shape of the polyhedra.

Citation

http://www.ncbi.nlm.nih.gov/pubmed/11209691 PMID: 11209691 [PubMed - indexed for MEDLINE]

 

Title

[Protein databank for several tissues derived from five instar of silkworm]

[Article in Chinese]

Authors

Zhong BX.

Department of Sericulture and Apiculture Science, College of Animal Sciences, Zhejiang University, Hangzhou 310029, China.

Journal

Yi Chuan Xue Bao. 2001;28(3):217-24.

Abstract

We attempted to construct protein databank of silkworm (Bombyx mori L.) for clarifying the gene expression and post-translational modification. Proteins from silkworm body wall, fat body and middle intestines were separated by two-dimensional electrophoresis. The N-terminal amino acid sequences of 40 proteins and their homology to proteins from other organisms were determined. 58.5% proteins were high homologous to the already reported proteins in D. melanogaster and 36.5% to those in other organisms. Only 5% of the proteins were homologous to the known protein in silkworm. The N-terminal sequences of 27 proteins were first found in silkworm, and all these data were registered in SWISS-PROT through the Internet. The results suggested that the information of gene expression and post-translational modification could be obtained by the information of protein databank.

Citation

http://www.ncbi.nlm.nih.gov/pubmed/11280994 PMID: 11280994 [PubMed - indexed for MEDLINE]

 

posted Jul 16, 2010, 1:29 AM by rajesh gk

Title

Analysis of genetic diversity of muga silkworm (Antheraea assamensis, Helfer; Lepidoptera : Saturniidae) using RAPD-based molecular markers

Authors

Kartik Neog1, H. Ranjit Singh2, Balagopalan Unni2* and A. K. Sahu3

1Central Muga Eri Research and Training Institute (CMER&TI), Central Silk Board, Lahdoigarh, Jorhat 785 700, Assam, India. 2Biotechnology Division, North East Institute of Science and Technology (NEIST), Jorhat 785 006, India. 3Regional Muga Research Station (RMRS), Central Silk Board, Boko, Kamrup, Assam, India.

Journal

African Journal of Biotechnology Vol. 9(12), pp. 1746-1752, 22 March, 2010

Abstract

Eleven populations of muga silkworm, Antheraea assamensis Helfer, the golden silk yarn producer of northeast India, was subjected to RAPD marker analysis in order to assess its genetic diversity. The genomic DNA extracted from muga silkworms were analysed using 50 random primers among which 36 polymorphic primers generated 309 bands. RAPD profile of the isolated DNA revealed a high level of genetic polymorphism. The average amplicons per primer was found to be 8.58, and 94.82% amplicons were polymorphic. Cluster analysis based on Jaccard’s similarity coefficients resulted in the formation of two main clusters with one population on one cluster and the remaining on the other cluster. Jaccard’s similarity coefficients ranged from 0.122 to 0.863 indicating a high level of genetic diversity within muga silkworm collection. The study concluded that, although there lays little morphological differences among the collected muga silkworm populations, the populations are highly polymorphic which might have enabled the silkworm to survive under a restricted geographical location, that is north east region of India only but under diverse climatic conditions for a long period. This study may be useful in identifying diverse genetic stocks of A. assamensis, which may be conserved on a priority basis. Key words: Muga silkworm, Antheraea assamensis, RAPD markers, genetic diversity.

Citation

ISSN 1684–5315 © 2010 Academic Journals Accepted 16 February, 2010 Available online at http://www.academicjournals.org/AJB

 

Title

Tissue-/stage-dependent expression of a cloned Bombyx mandarina QM homologue.

Authors

Hwang JS, Goo TW, Yun EY, Lee JH, Kang SW, Kim KY, Kwon OY.

National Sericulture and Entomology Research Institute, Rural Development Administration, Suwon, South Korea.

Journal

Biomol Eng. 2000 Jun;16(6):211-5.

Abstract

QM, a novel gene that was firstly isolated as a putative tumor suppressor gene from Wilms' tumor cell line. Although it is well known that the QM gene product plays an important role within the tumor cells, the precise role of QM in the non-tumor cells has remained elusive. With in this mind we isolated a cDNA encoding QM homologue from Bombyx mandarina to understand the function of QM. The 596 bp cDNA has an open reading frame of 219 amino acids and a predicted mol. wt. of 25 kDa. The protein has more than 88% amino acid sequence identity to the QM protein from Drosophila melanogaster. mRNA expression gradually increased from 1-2 days after egg laying to 2 days of finial instar, while very low expressions were detected for either the pupae and the moth stages. The organs, posterior/middle division of silkgland, midgut, fat body and malpighian tubes, also show relatively high mRNA expression levels, respectively. The high degree of conservation and expression of the B. mandarina QM homologous suggest that it has a selectively conserved amino acid sequence due, presumably, to an important biological role which is associated with pupae formation.

Citation

http://www.ncbi.nlm.nih.gov/pubmed/10894116 PMID: 10894116 [PubMed - indexed for MEDLINE]

 

Title

[Mutagenic analysis on the polyhedrin gene (polh) of Bombyx mori nuclear polyhedrosis virus (BmNPV)]

[Article in Chinese]

Authors

Cao Y, Xiao QX, Huang YD, Ge CB, Huang ZR, Liu LS.

Department of Sericulture and Fashion Design, South China Agricultural University, Guanzhou 510642, China.

Journal

Yi Chuan Xue Bao. 2000;27(11):972-81.

Abstract

In our early studies, the abnormal shape of the polyhedra of Bombyx mori nuclear polyhedrosis virus (BmNPV) induced by chemical mutagens of MMC. 9-AA and EMS occurred, and the genome of the mutated BmNPV obtained from the successive test had some change in the restriction endonuclease partners of EcoRI, BglII and BamHI. The present studies showed that the arrangement of the crystal lattice of the polyhedrin was disorderly, and the SDS-PAGE electropherogram of the polyhedrin depicted distinct change in comparison with control group. The results of sequencing analysis showed that many point mutations with characteristics of the base substitution had occurred at some sites of the BmNPV polh gene in three mutated groups, and these results funther revealed molecular mutagenesis of the mutagens effective to BmNPV. It was not confirmable that the point mutations of polh gene in the mutated BmNPV have relationship to abnormal shape of the polyhedra.

Citation

http://www.ncbi.nlm.nih.gov/pubmed/11209691 PMID: 11209691 [PubMed - indexed for MEDLINE]

 

Title

[Protein databank for several tissues derived from five instar of silkworm]

[Article in Chinese]

Authors

Zhong BX.

Department of Sericulture and Apiculture Science, College of Animal Sciences, Zhejiang University, Hangzhou 310029, China.

Journal

Yi Chuan Xue Bao. 2001;28(3):217-24.

Abstract

We attempted to construct protein databank of silkworm (Bombyx mori L.) for clarifying the gene expression and post-translational modification. Proteins from silkworm body wall, fat body and middle intestines were separated by two-dimensional electrophoresis. The N-terminal amino acid sequences of 40 proteins and their homology to proteins from other organisms were determined. 58.5% proteins were high homologous to the already reported proteins in D. melanogaster and 36.5% to those in other organisms. Only 5% of the proteins were homologous to the known protein in silkworm. The N-terminal sequences of 27 proteins were first found in silkworm, and all these data were registered in SWISS-PROT through the Internet. The results suggested that the information of gene expression and post-translational modification could be obtained by the information of protein databank.

Citation

http://www.ncbi.nlm.nih.gov/pubmed/11280994 PMID: 11280994 [PubMed - indexed for MEDLINE]

posted Jul 9, 2010, 8:58 AM by rajesh gk

Title

Molecular characterization of a Bombyx mori protein disulfide isomerase (bPDI).  Free PMC Article

Authors

Goo TW, Yun EY, Hwang JS, Kang SW, Park S, You KH, Kwon OY.

Department of Sericulture and Entomology, National Institute of Agricultural Science and Technology, RDA, Suwon, Korea.

Journal

Cell Stress Chaperones. 2002 Jan;7(1):118-25.

Abstract

We have isolated a complementary deoxyribonucleic acid clone that encodes the protein disulfide isomerase of Bombyx mori (bPDI). This protein has a putative open reading frame of 494 amino acids and a predicted size of 55.6 kDa. In addition, 2 thioredoxin active sites, each with a CGHC sequence, and an endoplasmic reticulum (ER) retention signal site with a KDEL motif were found at the C-terminal. Both sites are typically found in members of the PDI family of proteins. The expression of bPDI messenger ribonucleic acid (mRNA) was markedly increased during ER stress induced by stimulation with calcium ionophore A23187, tunicamycin, and dithiothreitol, all of which are known to cause an accumulation of unfolded proteins in the ER. We also examined the tissue distribution of bPDI mRNA and found pronounced expression in the fat body of insects. Hormonal regulation studies showed that juvenile hormone, insulin, and a combination of juvenile hormone and transferrin (although not transferrin alone) affected bPDI mRNA expression. A challenge with exogenous bacteria also affected expression, and the effect peaked 16 hours after infection. These results suggest that bPDI is a member of the ER-stress protein group, that it may play an important role in exogenous bacterial infection of the fat body, and that its expression is hormone regulated.

Citation

http://www.ncbi.nlm.nih.gov/pubmed/11892983 PMID: 11892983 [PubMed - indexed for MEDLINE]PMCID: PMC514797

 

Title

Phylogenetic relationship of Bombyx mori protein disulfide isomerase.

Authors

Goo TW, Yun EY, Hwang JS, Kang SW, You KH, Kwon OY.

Department of Sericulture and Entomology, National Institute of Agricultural Science and Technology, RDA, Suwon, Korea.

Journal

Z Naturforsch C. 2002 Jan-Feb;57(1-2):189-96.

Abstract

A cDNA that encodes protein disulfide isomerase was isolated from Bombyx mori (bPDI), in which an open reading frame of 494 amino acids contained two PDI-typical thioredoxin active sites of WCGHCK and an ER retention signal of the KDEL motif at its C-terminal. The bPDI protein shared less than 55% of the amino acid sequence homology with other reported PDIs. bPDI is most genetically similar to the D. melanogaster PDI. The most serious evolutional diversity was observed between the metazoa and nematoda through PDI evolutional processing. Although bPDI shows a relatively low amino acid homology with other PDIs, in which both sites of the two thioredoxin active sites and the endoplasmic reticulum (ER) retention signal are completely conserved, it was successfully recognized by anti-rat PDI antibodies. This suggests that bPDI may have the activity of a protein isomerase and a chaperone.

Citation

http://www.ncbi.nlm.nih.gov/pubmed/11926534 PMID: 11926534 [PubMed - indexed for MEDLINE]

 

Title

The genetics and genomics of the silkworm, Bombyx mori.

Authors

Goldsmith MR, Shimada T, Abe H.

Biological Sciences Department, University of Rhode Island, Kingston, Rhode Island 02881, USA. mki101@uri.edu

Journal

Annu Rev Entomol. 2005;50:71-100.

Abstract

We review progress in applying molecular genetic and genomic technologies to studies in the domesticated silkworm, Bombyx mori, highlighting its use as a model for Lepidoptera, and in sericulture and biotechnology. Dense molecular linkage maps are being integrated with classical linkage maps for positional cloning and marker-assisted selection. Classical mutations have been identified by a candidate gene approach. Cytogenetic and sequence analyses show that the W chromosome is composed largely of nested full-length long terminal repeat retrotransposons. Z-chromosome-linked sequences show a lack of dosage compensation. The downstream sex differentiation mechanism has been studied via the silkworm homolog of doublesex. Expressed sequence tagged databases have been used to discover Lepidoptera-specific genes, provide evidence for horizontal gene transfer, and construct microarrays. Physical maps using large-fragment bacterial artificial chromosome libraries have been constructed, and whole-genome shotgun sequencing is underway. Germline transformation and transient expression systems are well established and available for functional studies, high-level protein expression, and gene silencing via RNA interference.

Citation

http://www.ncbi.nlm.nih.gov/pubmed/15355234 PMID: 15355234 [PubMed - indexed for MEDLINE]

 

Title

A proteomic-based approach for the characterization of some major structural proteins involved in host-parasite relationships from the silkworm parasite Nosema bombycis (Microsporidia).

Authors

Wang JY, Chambon C, Lu CD, Huang KW, Vivarès CP, Texier C.

Equipe Parasitologie Moléculaire et Cellulaire, LBP, UMR CNRS 6023, Université Blaise Pascal, Aubière, France.

Journal

Proteomics. 2007 May;7(9):1461-72.

Abstract

Nosema bombycis is the causative agent of the silkworm Bombyx mori pebrine disease which inflicts severe worldwide economical losses in sericulture. Little is known about host-parasite interactions at the molecular level for this spore-forming obligate intracellular parasite which belongs to the fungi-related Microsporidia phylum. Major microsporidian structural proteins from the spore wall (SW) and the polar tube (PT) are known to be involved in host invasion. We developed a proteomic-based approach to identify few N. bombycis proteins belonging to these cell structures. Protein extraction protocols were optimized and four N. bombycis spore protein extracts were compared by SDS-PAGE and 2-DE to establish complementary proteomic profiles. Three proteins were shown to be located at the parasite SW. Moreover, 17 polyclonal antibodies were raised against major N. bombycis proteins from all extracts, and three spots were shown to correspond to polar tube proteins (PTPs) by immunofluorescent assay and transmission electron microscopy immunocytochemistry on cryosections. Specific patterns for each PTP were obtained by MALDI-TOF-MS and MS/MS. Peptide sequence tags were deduced by de novo sequencing using Peaks Online and DeNovoX, then evaluated by MASCOT and SEQUEST searches. Identification parameters were higher than false-positive hits, strengthening our strategy that could be enlarged to a nongenomic context.

Citation

http://www.ncbi.nlm.nih.gov/pubmed/17407187 PMID: 17407187 [PubMed - indexed for MEDLINE]

 

Title

Genetic characterization of Iranian native Bombyx mori strains using amplified fragment length polymorphism markers.

Authors

Mirhoseini SZ, Dalirsefat SB, Pourkheirandish M.

Department of Sericulture, Faculty of Natural Resources, University of Guilan, Somehe sara 1144, Iran.

Journal

J Econ Entomol. 2007 Jun;100(3):939-45.

Abstract

Genetic relationships within and among seven Iranian native silkworm strains was determined by DNA fingerprinting by using amplified fragment length polymorphism (AFLP) markers. In total, 189 informative AFLP markers were generated and analyzed. Estimates of Nei's gene diversity for all loci in individual strains showed a higher degree of genetic similarity within each studied strain. The highest and the least degrees of gene diversity were related to Khorasan Pink (h = 0.1804) and Baghdadi (h = 0.1412) strains, respectively. The unweighted pair-group method with arithmetic average dendrogram revealed seven strains of silkworm, Bombyx mori (L.), resolving into two major clusters. The highest degree of genetic similarity was related to Baghdadi and Harati White, and the least degree was related to Guilan Orange and Harati Yellow. The genetic similarity estimated within and among silkworms could be explained by the pedigrees, historical and geographical distribution of the strains, effective population size, inbreeding rate, selection intensity, and gene flow. This study revealed that the variability of DNA fingerprints within and among silkworm strains could provide an essential basis for breeders in planning crossbreeding strategies to produce potentially hetrotic hybrids in addition to contributing in conservation programs.

Citation

http://www.ncbi.nlm.nih.gov/pubmed/17598559 PMID: 17598559 [PubMed - indexed for MEDLINE]

 

Title

[The analysis of bro genes of GD isolate of Bombyx mori nucleopolyhedrovirus]

[Article in Chinese]

Authors

Pang M, Pan GQ, Li T, Wang X, Zhou ZY.

The Key Laboratory of Sericulture of Agricultural Ministry, Southwest University, Chongqing 400715, China.

Journal

Bing Du Xue Bao. 2007 Nov;23(6):485-9.

Abstract

BmNPV GD isolate from China was plaque-purified and four bro genes were cloned termed as bro-a,b,c,d. The obtained sequences were aligned to the related sequences in GenBank and the BmNPV CQ1 isolate preserved in our laboratory. Compared with genome sequences of BmNPV T3 isolate, bro genes of GD isolate housed insertion and deletion, and the changes of amino acid mainly occured at the N terminal of corresponding protein. The phylogenetic analysis of bro genes indicated that GD bro-d gene belongs to subgroup A together with T3, CQ1 bro-d and SC7 bro- III; GD bro-a, c genes belong to subgroup B together with T3, CQ1 bro-a, c and SC7 bro-II; GD bro-b gene belongs to subgroup C together with T3, CQ1 bro-b, e and SC7 bro-I. The evolutionary relationship of bro genes showed vague relevance to their geographical location. The distribution character of bro genes in four BmNPV isolates is coincidence with the KANG's theory that the bro-d plays an irreplaceable functional role(s) during viral replication, while bro-a and bro-c functionally complement each other. Meanwhile, we postulate that 3 bro genes in SC7 isolate is probable the most simple form of bro genes.

Citation

http://www.ncbi.nlm.nih.gov/pubmed/18092688 PMID: 18092688 [PubMed - indexed for MEDLINE]

 

Title

Silkworm nucleotide databases--current trends and future prospects. Free PMC Article

Authors

Koshy N, Ponnuvel KM, Sinha RK, Qadri SM.

Biotechnology Laboratory, Central Sericulture and Germplasm research Centre, P.O. Box: 34, Thally road, Hosur-635109, Tamil Nadu, India.

Journal

Bioinformation. 2008 Apr 19;2(7):308-10.

Abstract

The domesticated silkworm, Bombyx mori serves as an ideal representative of lepidopteran species for a variety of scientific studies. As a result, databases have been created to organize information pertaining to the silkworm genome that is subject to constant updating. Of these, four main databases are important for store nucleotide information in the form of genomic data, ESTs and microsatelites. These databases also store data related to other lepidoptera and important insects, which help in insect biological research. Though a considerable amount of nucleotide data is currently available, there is a paucity of data related to silkworm and other lepidopteran proteins. Hence, the focus of this article is to present the current status of nucleotide databases of silkworm, avenues for improvement and possibilities for databases that could be created in the future.

Citation

http://www.ncbi.nlm.nih.gov/pubmed/18478085 PMID: 18478085 [PubMed]PMCID: PMC2374376

 

Title

Identification of a novel spore wall protein (SWP26) from microsporidia Nosema bombycis.

Authors

Li Y, Wu Z, Pan G, He W, Zhang R, Hu J, Zhou Z.

The Key Sericultural Laboratory of Agricultural Ministry, Southwest University, Beibei, Chongqing 400716, PR China.

Journal

Int J Parasitol. 2009 Mar;39(4):391-8. Epub 2008 Sep 27.

Abstract

Microsporidia are obligate intracellular parasites related to fungi with resistant spores against various environmental stresses. The rigid spore walls of these organisms are composed of two major layers, which are the exospore and the endospore. Two spore wall proteins (the endosporal protein-SWP30 and the exosporal protein-SWP32) have been previously identified in Nosema bombycis. In this study, using the MALDI-TOF-MS technique, we have characterised a new 25.7-kDa spore wall protein (SWP26) recognised by monoclonal antibody 2G10. SWP26 is predicted to have a signal peptide, four potential N-glycosylation sites, and a C-terminal heparin-binding motif (HBM) which is known to interact with extracellular glycosaminoglycans. By using a host cell binding assay, recombinant SWP26 protein (rSWP26) can inhibit spore adherence by 10%, resulting in decreased host cell infection. In contrast, the mutant rSWP26 (rDeltaSWP26, without HBM) was not effective in inhibiting spore adherence. Immuno-electron microscopy revealed that this protein was expressed largely in endospore and plasma membrane during endospore development, but sparsely distributed in the exospore of mature spores. The present results suggest that SWP26 is a microsporidia cell wall protein that is involved in endospore formation, host cell adherence and infection in vitro. Moreover, SWP26 could be used as a good prospective target for diagnostic research and drug design in controlling the silkworm, Bombyx mori, pebrine disease in sericulture.

Citation

http://www.ncbi.nlm.nih.gov/pubmed/18854188 PMID: 18854188 [PubMed - indexed for MEDLINE]

 

Title

The UDP-glucosyltransferase multigene family in Bombyx mori. Free PMC Article

Authors

Huang FF, Chai CL, Zhang Z, Liu ZH, Dai FY, Lu C, Xiang ZH.

The Key Sericultural Laboratory of Agricultural Ministry, Institute of Sericulture and Systems Biology, Southwest University, Chongqing 400715, PR China. huangfeifeisd@163.com

Journal

BMC Genomics. 2008 Nov 27;9:563.

Abstract

BACKGROUND: Glucosidation plays a major role in the inactivation and excretion of a great variety of both endogenous and exogenous compounds. A class of UDP-glycosyltransferases (UGTs) is involved in this process. Insect UGTs play important roles in several processes, including detoxication of substrates such as plant allelochemicals, cuticle formation, pigmentation, and olfaction. Identification and characterization of Bombyx mori UGT genes could provide valuable basic information for this important family and explain the detoxication mechanism and other processes in insects. RESULTS: Taking advantage of the newly assembled genome sequence, we performed a genome-wide analysis of the candidate UGT family in the silkworm, B. mori. Based on UGT signature and their similarity to UGT homologs from other organisms, we identified 42 putative silkworm UGT genes. Most of them are clustered on the silkworm chromosomes, with two major clusters on chromosomes 7 and 28, respectively. The phylogenetic analysis of these identified 42 UGT protein sequences revealed five major groups. A comparison of the silkworm UGTs with homologs from other sequenced insect genomes indicated that some UGTs are silkworm-specific genes. The expression patterns of these candidate genes were investigated with known expressed sequence tags (ESTs), microarray data, and RT-PCR method. In total, 36 genes were expressed in tissues examined and showed different patterns of expression profile, indicating that these UGT genes might have different functions. CONCLUSION: B. mori possesses a largest insect UGT gene family characterized to date, including 42 genes. Phylogenetic analysis, genomic organization and expression profiles provide an overview for the silkworm UGTs and facilitate their functional studies in future.

Citation

http://www.ncbi.nlm.nih.gov/pubmed/19038024 PMID: 19038024 [PubMed - indexed for MEDLINE]PMCID: PMC2633020

 

Title

A genomewide survey of homeobox genes and identification of novel structure of the Hox cluster in the silkworm, Bombyx mori.

Authors

Chai CL, Zhang Z, Huang FF, Wang XY, Yu QY, Liu BB, Tian T, Xia QY, Lu C, Xiang ZH.

The Key Sericultural Laboratory of Agricultural Ministry, College of Biotechnology, Institute of Sericulture and Systems Biology, Southwest University, Chongqing, China

Journal

Insect Biochem Mol Biol. 2008 Dec;38(12):1111-20.

Abstract

Homeobox genes encode transcriptional factors that play crucial roles in a variety of developmental pathways from unicellular to multicellular eukaryotes. We have identified 102 homeobox genes in the typical insect of Lepidoptera, Bombyx mori, based on the newly assembled genome sequence with 9X coverage. These identified homeobox genes were categorized into nine classes including at least 74 families. The available ESTs and microarray data at present confirmed that more than half of them were expressed during silkworm developmental processes. Orthologs of pb, zen and ftz were newly identified in the Bombyx Hox cluster on chromosome 6. Interestingly, a special group of 12 tandemly duplicated homeobox genes was found located between Bmpb and Bmzen in the Bombyx Hox cluster, suggesting that Hox cluster might have experienced a lineage-specific expansion in the silkworm. A detailed analysis on genome data reveals that a split exists between Bmlab and Bmpb. Our data provide valuable information for future research on the development and evolution of silkworm.

Citation

http://www.ncbi.nlm.nih.gov/pubmed/19280701 PMID: 19280701 [PubMed - indexed for MEDLINE]

 

Title

Protein profile of Nomuraea rileyi spore isolated from infected silkworm.

Authors

Qin L, Liu X, Li J, Chen H, Yao Q, Yang Z, Wang L, Chen K.

Institute of Life Sciences, Jiangsu University, 301# Xuefu Road, Zhenjiang 212013, Jiangsu Province, People's Republic of China. qinlvgao@163.com

Journal

Curr Microbiol. 2009 Jun;58(6):578-85. Epub 2009 Mar 14.

Abstract

Nomuraea rileyi (N. rileyi) is the causative agent of the silkworm, Bombyx mori, green muscardine which can cause severe worldwide economical loss in sericulture. Little is known about N. rileyi at the protein level for this entomopathogenic parasite which belongs to the Ascomycota. Here, we employed proteomic-based approach to identify proteins of N. rileyi spores collected from the dead silkworm. In all, 252 proteins were separated by two-dimensional gel electrophoresis (2-DE), and were subjected to mass spectrometry (MS) analysis, 121 proteins have good MS signal, and 24 of them were identified due to unavailability of genomic information from N. rileyi. This data will be helpful in understanding the biochemistry of N. rileyi.

Citation

http://www.ncbi.nlm.nih.gov/pubmed/19288155 PMID: 19288155 [PubMed - indexed for MEDLINE]

 

Title

Genetic analysis of Indian mulberry varieties through molecular markers.

Authors

Vijayan K, Awasthi AK, Srivastava PP, Saratchandra B.

Seri-Biotech Research Laboratory, CSB Campus, Carmelram, Kodathi, Bangalore, Karnataka, India. kvijayan01@yahoo.com

Journal

Hereditas. 2004;141(1):8-14.

Abstract

India is one of the countries where sericulture is being practiced traditionally. Due to the higher economic return and the greater employment potential, attempts are being made to increase the productivity by developing high yielding mulberry varieties. At the present, Mysore local, Bomaypiasbari, Kanva-2, Bilidevalaya, Kajli, S1, BC(2)59, C776, RFS-175, S-36 and Victory-1 are being cultivated extensively in different parts of India for rearing the silkworm Bombyx mori L. Using 17 random amplified polymorphic DNA (RAPD) and 11 inter-simple sequence repeat (ISSR) primers the genetic relationships among these varieties were analyzed. The RAPD and ISSR primers revealed more than 75% polymorphism among the varieties. The genetic similarity estimated from RAPD markers varied from 0.645, between Kajli and Victory-1 to 0.887, between Kanva-2 and Bilidevalaya. Similarly, the genetic similarity estimated from the ISSR markers ranged from 0.600, between Kajli and Victory-1, to 0.873 between Kanva-2 and BC(2)59. The dendrogram constructed from these markers grouped the varieties into three major groups comprising the low yielding, medium yielding and high yielding. The low genetic similarity between the group of varieties originating from the eastern regions with that of the southern region encourages formation of extensive breeding programs between these groups as to transfer the high yield potential of the southern varieties to the low yielding but highly adaptive eastern varieties.

Citation

http://www.ncbi.nlm.nih.gov/pubmed/15383066 PMID: 15383066 [PubMed - indexed for MEDLINE]

 

Title

QTL mapping of economically important traits in silkworm (Bombyx mori).

Authors

Lu C, Li B, Zhao A, Xiang Z.

The Key Sericulture Laboratory, Ministry of Agriculture of China, College of Sericulture & Biotechnology, Southwest Agricultural University, Chongqing 400716, China. lucheng@swau.cq.cn

Journal

Sci China C Life Sci. 2004 Oct;47(5):477-84.

Abstract

A backcrossed population (BC1) was derived from a cross between C100 and Dazao. AFLP technique was employed for mapping the QTLs. The QTLs for the whole cocoon weight, cocoon shell weight, ratio of cocoon shell, weight of pupae etc. were analyzed and 11 QTLs were detected based on the constructed linkage map. Two QTLs for whole cocoon weight were localized on linkage group 6 and 19; three QTLs for cocoon shell weight were localized on linkage group 3, 14 and 19; three QTLs for ratio of cocoon shell were localized on the linkage group 2, 11 and 15, and three QTLs for the weight of pupae were localized on linkage 2, 14 and 19. All these have laid an important base for the marker assisted breeding of the silkworm.

Citation

http://www.ncbi.nlm.nih.gov/pubmed/15623161 PMID: 15623161 [PubMed - indexed for MEDLINE]

 

Title

Analysis of cytochrome P450 genes in silkworm genome (Bombyx mori).

Authors

Li B, Xia Q, Lu C, Zhou Z, Xiang Z.

 

Key Sericultural Laboratory of Agricultural Ministry, College of Sericulture & Biotechnology, Southwest Agricultural University, Chongqing, China.

Journal

Sci China C Life Sci. 2005 Aug;48(4):414-8.

Abstract

We have searched the Bombyx mori genome for members of the major enzyme family, the Cytochrome P450s, which carry out multiple reactions to enable organisms to rid themselves of foreign compounds. As a result, 86 putative P450s were discovered in silkworm genome, which are thought to belong to 32 subfamilies. A comparative genomic analysis with Drosophila melanogaster reveals that the two insects have some similar P450 distribution patterns but still have some obvious differences. Especially, the diverse distribution exists in 7 p450 subfamilies, which are CYP4A, CYP4C, CYP4D, CYP6A, CYP6AE, CYP6B and CYP9A. Furthermore, we collected expression sequence tag (EST) evidence for 49 putative P450s genes, which are expressed at the transcriptional level and more likely to be true P450s.

Citation

http://www.ncbi.nlm.nih.gov/pubmed/16248435 PMID: 16248435 [PubMed - indexed for MEDLINE]

 

Title

A cuticle protein gene from the Japanese oak silkmoth, Antheraea yamamai: gene structure and mRNA expression.

Authors

Kim BY, Park NS, Jin BR, Lee BH, Seong SI, Hwang JS, Chang JS, Lee SM.

 

Department of Sericulture and Entomology, Miryang National University, 627-130, Miryang, Korea.

Journal

Biotechnol Lett. 2005 Oct;27(19):1499-504.

Abstract

A cuticle protein gene, AyCP12, from the Japanese oak silkmoth, Antheraea yamamai, was isolated and characterized. The gene spans 1107 bp and consists of one intron and two exons coding for a 112 amino acid polypeptide with a predicted molecular mass of 12,163 Da and a pI of 4.4. The AyCP12 protein contained a type-specific consensus sequence identifiable in other insect cuticle proteins and the deduced amino acid sequence of the AyCP12 cDNA is most homologous to another silkmoth, A. pernyi, cuticle protein ApCP13 (82% protein sequence identity). Northern blot analysis revealed that AyCP12 showed the epidermis-specific expression.

Citation

http://www.ncbi.nlm.nih.gov/pubmed/16231223 PMID: 16231223 [PubMed - indexed for MEDLINE]

 

Title

Gene organization and complete sequence of the Hyphantria cunea nucleopolyhedrovirus genome. Free Article

Authors

Ikeda M, Shikata M, Shirata N, Chaeychomsri S, Kobayashi M.

 

Laboratory of Sericulture and Entomoresources, Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya 464-8601, Japan.

Journal

J Gen Virol. 2006 Sep;87(Pt 9):2549-62.

Abstract

The whole-genome sequence of the Hyphantria cunea nucleopolyhedrovirus (HycuNPV) was analysed. The entire nucleotide sequence of the HycuNPV genome was 132 959 bp long, with a G+C content of 45.1 mol%. A total of 148 open reading frames (ORFs) consisting of more than 50 aa were encoded by the genome. HycuNPV shares more than 122 ORFs with other lepidopteran group I NPVs, including Autographa californica MNPV, Bombyx mori NPV, Choristoneura fumiferana MNPV (CfMNPV), Choristoneura fumiferana defective NPV, Epiphyas postvittana MNPV and Orgyia pseudotsugata MNPV (OpMNPV). Six ORFs are identified as being unique to HycuNPV. Most of the HycuNPV ORFs showed higher similarity to CfMNPV and OpMNPV ORFs than to those of the other group I NPVs. HycuNPV encodes two conotoxin-like homologues (ctls), which are observed only in OpMNPV in group I NPVs. HycuNPV encodes three inhibitors of apoptosis (iaps), hycu-iap-1, hycu-iap-2 and hycu-iap-3, a feature that it shares only with CfMNPV. In addition, six homologous regions (hrs) are identified in the HycuNPV genome. These hrs are located in regions similar to those of the OpMNPV hrs, but different from most of the CfMNPV hrs. Based on the close phylogenetic relationship and conservation of group I NPV-specific genes, such as gp64, ie-2 and ptp-1, it is concluded that HycuNPV belongs to the group I NPVs and is most similar to CfMNPV or OpMNPV.

PMID: 16894193 [PubMed - indexed for MEDLINE]

Citation

http://www.ncbi.nlm.nih.gov/pubmed/16894193

 

Title

A genome-wide survey for host response of silkworm, Bombyx mori during pathogen Bacillus bombyseptieus infection. Free PMC Article

Authors

Huang L, Cheng T, Xu P, Cheng D, Fang T, Xia Q.

 

Institute of Sericulture and Systems Biology, Southwest University, Chongqing, China.

Journal

PLoS One. 2009 Dec 1;4(12):e8098.

Abstract

Host-pathogen interactions are complex relationships, and a central challenge is to reveal the interactions between pathogens and their hosts. Bacillus bombysepticus (Bb) which can produces spores and parasporal crystals was firstly separated from the corpses of the infected silkworms (Bombyx mori). Bb naturally infects the silkworm can cause an acute fuliginosa septicaemia and kill the silkworm larvae generally within one day in the hot and humid season. Bb pathogen of the silkworm can be used for investigating the host responses after the infection. Gene expression profiling during four time-points of silkworm whole larvae after Bb infection was performed to gain insight into the mechanism of Bb-associated host whole body effect. Genome-wide survey of the host genes demonstrated many genes and pathways modulated after the infection. GO analysis of the induced genes indicated that their functions could be divided into 14 categories. KEGG pathway analysis identified that six types of basal metabolic pathway were regulated, including genetic information processing and transcription, carbohydrate metabolism, amino acid and nitrogen metabolism, nucleotide metabolism, metabolism of cofactors and vitamins, and xenobiotic biodegradation and metabolism. Similar to Bacillus thuringiensis (Bt), Bb can also induce a silkworm poisoning-related response. In this process, genes encoding midgut peritrophic membrane proteins, aminopeptidase N receptors and sodium/calcium exchange protein showed modulation. For the first time, we found that Bb induced a lot of genes involved in juvenile hormone synthesis and metabolism pathway upregulated. Bb also triggered the host immune responses, including cellular immune response and serine protease cascade melanization response. Real time PCR analysis showed that Bb can induce the silkworm systemic immune response, mainly by the Toll pathway. Anti-microorganism peptides (AMPs), including of Attacin, Lebocin, Enbocin, Gloverin and Moricin families, were upregulated at 24 hours post the infection.

Citation

http://www.ncbi.nlm.nih.gov/pubmed/19956592

PMID: 19956592 [PubMed - indexed for MEDLINE]PMCID: PMC2780328

 

Title

Natural selection maintains the transcribed LTR retrotransposons in Nosema bombycis.

Authors

Xiang H, Pan G, Zhang R, Xu J, Li T, Li W, Zhou Z, Xiang Z.

 

Institute of Sericulture and Systems Biology, Southwest University, Beibei, Chongqing 400715, China.

Journal

J Genet Genomics. 2010 May;37(5):305-14.

Abstract

Eight intact LTR retrotransposons (Nbr1-Nbr8) have been previously characterized from the genome of Nosema bombycis, a eukaryotic parasite with a compact and reduced genome. Here we describe six novel transcribed Nbr elements (Nbr9-Nbr14) identified through either cDNA library or RT-PCR. Like previously determined ones, all of them belong to the Ty3/Gypsy superfamily. Retrotransposon diversity and incomplete domains with insertions (Nbr12), deletions (Nbr11) and in-frame stop codons in coding regions (Nbr9) were detected, suggesting that both defective and loss events of LTR retrotransposon have happened in N. bombycis genome. Analysis of selection showed that strong purifying selection acts on all elements except Nbr11. This implies that selective pressure keeps both these Nbrs and their functions in genome. Interestingly, Nbr11 is under positive selection and some positively selected codons were identified, indicating that new functionality might have evolved in the Nbr11 retrotransposon. Unlike other transposable elements, Nbr11 has integrated into a conserved syntenic block and probably resulted in the inversion of both flanking regions. This demonstrates that transposable element is an important factor for the reshuffling and evolution of their host genomes, and may be maintained under natural selection. (c) 2010 Institute of Genetics and Developmental Biology and the Genetics Society of China. Published by Elsevier Ltd. All rights reserved.

Citation

http://www.ncbi.nlm.nih.gov/pubmed/20513631 PMID: 20513631 [PubMed - in process]

posted Jul 5, 2010, 1:53 AM by rajesh gk

Title

Endoplasmic reticulum-localized small heat shock protein that accumulates in mulberry t ree (Morus bombycis Koidz.) during seasonal cold acclimation is responsive to abscisic acid.

Authors

Ukaji N, Kuwabara C, Kanno Y, Seo M, Takezawa D, Arakawa K, Fujikawa S.

 

Graduate School of Agriculture, Hokkaido University, Sapporo 060-8589, Japan. ukaji@fsc.hokudai.ac.jp

Journal

Tree Physiol. 2010 Apr;30(4):502-13. Epub 2010 Jan 25.

Abstract

With seasonal changes, several proteins accumulate in the endoplasmic reticulum (ER)-enriched fraction in the bark of mulberry tree (Morus bombycis Koidz.). Results of partial amino acid sequence analysis in our previous study suggested that one of these proteins is the ER-localized small heat shock protein (sHSP), designated 20-kD winter-accumulating protein (WAP20). In the present study, molecular and biochemical properties of WAP20 were investigated in detail. The deduced amino acid sequence of the cDNA has the predicted signal sequence to the ER, retention signal to the ER and two consensus regions conserved in sHSPs. Recombinant WAP20 expressed in Escherichia coli also showed typical biochemical features of sHSPs, including the formation of a high-molecular-mass complex between 200 and 300 kD under native conditions, promotion of the renaturation of chemically denaturated citrate synthase and prevention of heat stress-induced aggregation of the enzyme. Transcript levels of WAP20 in the bark tissue were seasonally changed, showing high expression levels from mid-October to mid-December, and the transcript levels were additionally increased and decreased by cold treatment and warm treatment, respectively. WAP20 transcripts were detected abundantly in bark tissue rather than xylem and winter bud tissues during seasonal cold acclimation. The bark tissue specificity of WAP20 accumulation was also observed by exogenous application of phytohormone abscisic acid (ABA) in de-acclimated twigs, whereas WAP20 transcripts were increased in all of these tissues by heat shock treatment at 37 degrees C in summer twigs. The results suggest that ABA may be involved in the expression of the WAP20 gene in bark tissue of the mulberry tree during seasonal cold acclimation.

Citation

PMID: 20100700 [PubMed - indexed for MEDLINE]

 

Title

Genome-wide identification and expression analysis of serine proteases and h omologs in the silkworm Bombyx mori. Free Article

Authors

Zhao P, Wang GH, Dong ZM, Duan J, Xu PZ, Cheng TC, Xiang ZH, Xia QY.

Journal

BMC Genomics. 2010 Jun 24;11(1):405. [Epub ahead of print]

Abstract

ABSTRACT: BACKGROUND: Serine 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. RESULTS: In 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. mori nucleopolyhedrovirus, 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. CONCLUSION: Silkworm 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.

Citation

PMID: 20576138 [PubMed - as supplied by publisher]

 

Title

Comparative analysis of the genomes of Bombyx mandarina and Bombyx mori nucleopolyhedrovi ruses.

Authors

Xu YP, Ye ZP, Niu CY, Bao YY, Wang WB, Shen WD, Zhang CX.

 

Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, P R China.

Journal

J Microbiol. 2010 Feb;48(1):102-10. Epub 2010 Mar 11.

Abstract

The Bombyx mandarina nucleopolyhedrovirus (BomaNPV) S1 strain can infect the silkworm, Bombyx mori, but is significantly less virulent than B. mori nucleopolyhedrovirus (BmNPV) T3 strain. The complete nucleotide sequence of the S1 strain of BomaNPV was determined and compared with the BmNPV T3 strain. The circular, double stranded DNA genome of the S1 strain was 126,770 nucleotides long (GenBank accession no. FJ882854), with a G+C content of 40.23%. The genome contained 133 potential ORFs. Most of the putative proteins were more than 96% identical to homologs in the BmNPV T3 strain, except for bro-a, lef-12, bro-c, and bro-d. Compared with the BmNPV T3 strain, however, this genome did not encode the bro-b and bro-e genes. In addition, hr1 lacked two repeat units, while hr2L, hr2R, hr3, hr4L, hr4R, and hr5 were similar to the corresponding hrs in the T3 strain. The sequence strongly suggested that BomaNPV and BmNPV are variants with each other, and supported the idea that baculovirus strain heterogeneity may often be caused by variation in the hrs and bro genes.

Citation

PMID: 20221737 [PubMed - indexed for MEDLINE]

 

Title

Shotgun proteomic analysis on the embryos of silkworm Bombyx mori a t the end of organogenesis.

Authors

Li JY, Moghaddam SH, Chen JE, Chen M, Zhong BX.

 

College of Animal Sciences, Zhejiang University, Hangzhou 310029, PR China.

Journal

Insect Biochem Mol Biol. 2010 Apr;40(4):293-302. Epub 2010 Feb 4.

Abstract

Embryonic development of silkworm, Bombyx mori is a process of systematical expression of genes and proteins which is dominated by complex regulatory networks. To gain comprehensive insight into the molecular basis of embryonic development and its regulation mechanisms, the proteome profile of the B. mori embryos at the end of organogenesis (tubercle appearance stage, TA) was characterized using LTQ-Orbitrap mass spectrometer. Totally 963 proteins were identified with a false discovery rate (FDR) of 0.12%. They were involved in embryonic development, chemoreception, and stimuli response and so forth. The proteins with the largest number of identified unique peptides, implying their possibly higher abundance, were involved in heat shock response, lipid transport and metabolism, and apoptosis. It was consistent with the physiological status of embryo at the end of organogenesis. Many functionally important proteins were identified for the first time in B. mori embryo such as the progesterone receptor membrane component 2, antennal binding protein, sericotropin, and molting fluid carboxypeptidase A (MF-CPA). 253 (26.27%) specific proteins in TA versus labrum appearance stage (LA, four days before TA) embryos were identified, which were mainly associated with musculature, nervous system, and chemoreception system. They disclosed the differential temporal and spatial expression of proteins in the process of organogenesis. The relative mRNA levels of fifteen identified proteins in the two experimented stages were also compared using quantitative reverse transcription PCR (qRT-PCR) and showed some inconsistencies with protein expression. Gene Ontology (GO) annotation of the identified proteins showed that the most proteome representations were in the categories of "binding" and "catalytic" in molecular function, and "cellular process" and "metabolic process" in biological process. Copyright (c) 2010 Elsevier Ltd. All rights reserved.

Citation

PMID: 20138214 [PubMed - indexed for MEDLINE]

 

Title

Efficient silkworm expression of single-chain variable fragment antibody against ginsenoside Re using Bombyx mori nucleopolyhedrovirus bacmid DNA system and its application in enzyme-linked immunosorbent assay for quality control of total ginsenosides.

Authors

Sakamoto S, Pongkitwitoon B, Nakamura S, Maenaka K, Tanaka H, Morimoto S.

 

Department of Pharmacognosy, Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan.

Journal

J Biochem. 2010 Jun 30. [Epub ahead of print]

Abstract

A single-chain variable fragment (scFv) antibody against ginsenoside Re (G-Re) have been successfully expressed in the silkworm larvae using Bombyx mori nucleopolyhedrovirus (BmNPV) bacmid DNA system. The baculovirus donor vector for expression of scFv against G-Re (GRe-scFv) was constructed to contain honeybee melittin signal sequence (HMSS) to accelerate secretion of the recombinant GRe-scFv into the hemolymph of silkworm larvae. Functional recombinant GRe-scFv was purified by cation exchange chromatography followed by immobilized metal ion affinity chromatography. The yield of purified GRe-scFv was 6.5 mg per 13 silkworm larvae, which is equivalent to 650 mg/l of the hemolymph, exhibiting extremely higher yield than that expressed in Escherichia coli (1.7 mg per liter of culture medium). It was revealed from characterization that GRe-scFv retained similar characteristic of the parental monoclonal antibody (MAb) against G-Re (MAb-4G10), making it possible to develop indirect competitive enzyme-linked immunosorbent assay (icELISA) for quality control of total ginsenosides in various ginsengs. The detectable range for calibration of G-Re by developed icELISA shows 0.05-10 microg/ml. These results clearly suggested that the silkworm expression system is quite useful for the expression of functional scFv that frequently required time- and cost-consuming refolding when it expressed in Escherichia coli.

Citation

PMID: 20592135 [PubMed - as supplied by publisher]

 

Title

High-efficiency transformation and selective tolerance against biotic and abiotic stress in mulberry, Morus indica cv. K2, by constitutive and inducible expression of tobacco osmotin.

Authors

Das M, Chauhan H, Chhibbar A, Rizwanul Haq QM, Khurana P.

 

Department of Plant Molecular Biology, University of Delhi, South Campus, New Delhi, 110021, India.

Journal

Transgenic Res. 2010 Jun 15. [Epub ahead of print]

Abstract

Osmotin and osmotin-like proteins are stress proteins belonging to the plant PR-5 group of proteins induced in several plant species in response to various types of biotic and abiotic stresses. We report here the overexpression of tobacco osmotin in transgenic mulberry plants under the control of a constitutive promoter (CaMV 35S) as well as a stress-inducible rd29A promoter. Southern analysis of the transgenic plants revealed the stable integration of the introduced genes in the transformants. Real-time PCR analysis provided evidence for the expression of osmotin in the transgenic plants under both the constitutive and stress-inducible promoters. Transgenic plants with the stress-inducible promoter were observed to better tolerate salt and drought stress than those with the constitutive promoter. Transgenic plants when subjected to simulated salinity and drought stress conditions showed better cellular membrane stability (CMS) and photosynthetic yield than non-transgenic plants under conditions of both salinity and drought stress. Proline levels were very high in transgenic plants with the constitutive promoter relative to those with the stress-inducible promoter. Fungal challenge undertaken with three fungal species known to cause serious losses to mulberry cultivation, namely, Fusarium pallidoroseum, Colletotrichum gloeosporioides and Colletotrichum dematium, revealed that transgenic plants with osmotin under control of the constitutive promoter had a better resistance than those with osmotin under the control of the stress-inducible promoter. Evaluation in next generation was undertaken by studying bud break in transgenic and non-transgenic plants under simulated drought (2% polyethylene glycol) and salt stress (200 mM NaCl) conditions. The axillary buds of the selected transgenic lines had a better bud break percentage under stressed conditions than buds from non-transgenic mulberry lines. A biotic assay with Bombyx mori indicated that osmotin protein had no undesirable effect on silkworm rearing and feeding. We therefore conclude that 35S transgenic plants are better suited for both abiotic stress also biotic challenges (fungal), while the rd29A transgenic plants are more responsive to drought.

Citation

PMID: 20549349 [PubMed - as supplied by publisher]

 

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