Pathogen-origin horizontally transferred genes contribute to the evolution of Lepidopteran insects

<p>Abstract</p> <p>Background</p> <p>Horizontal gene transfer (HGT), a source of genetic variation, is generally considered to facilitate hosts' adaptability to environments. However, convincing evidence supporting the significant contribution of the transferred genes to the evolution of metazoan recipients is rare.</p> <p>Results</p> <p>In this study, based on sequence data accumulated to date, we used a unified method consisting of similarity search and phylogenetic analysis to detect horizontally transferred genes (HTGs) between prokaryotes and five insect species including <it>Drosophila melanogaster</it>, <it>Anopheles gambiae</it>, <it>Bombyx mori</it>, <it>Tribolium castaneum </it>and <it>Apis mellifera</it>. Unexpectedly, the candidate HTGs were not detected in <it>D. melanogaster</it>, <it>An. gambiae </it>and <it>T. castaneum</it>, and 79 genes in <it>Ap. mellifera </it>sieved by the same method were considered as contamination based on other information. Consequently, 14 types of 22 HTGs were detected only in the silkworm. Additionally, 13 types of the detected silkworm HTGs share homologous sequences in species of other Lepidopteran superfamilies, suggesting that the majority of these HTGs were derived from ancient transfer events before the radiation of Ditrysia clade. On the basis of phylogenetic topologies and BLAST search results, donor bacteria of these genes were inferred, respectively. At least half of the predicted donor organisms may be entomopathogenic bacteria. The predicted biochemical functions of these genes include four categories: glycosyl hydrolase family, oxidoreductase family, amino acid metabolism, and others.</p> <p>Conclusions</p> <p>The products of HTGs detected in this study may take part in comprehensive physiological metabolism. These genes potentially contributed to functional innovation and adaptability of Lepidopteran hosts in their ancient lineages associated with the diversification of angiosperms. Importantly, our results imply that pathogens may be advantageous to the subsistence and prosperity of hosts through effective HGT events at a large evolutionary scale.</p

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

<p>Abstract</p> <p>Background</p> <p>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.</p> <p>Results</p> <p>Taking advantage of the newly assembled genome sequence, we performed a genome-wide analysis of the candidate sHSP genes in the silkworm, <it>Bombyx mori</it>. 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 <it>B. mori</it>, <it>Drosophila melanogaster</it>, <it>Apis mellifera</it>, <it>Tribolium castaneum</it>, and <it>Anopheles gambiae </it>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.</p> <p>Conclusion</p> <p><it>B. mori </it>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.</p

Burst expansion, distribution and diversification of MITEs in the silkworm genome

<p>Abstract</p> <p>Background</p> <p>Miniature inverted-repeat transposable elements (MITEs) are widespread in plants and animals. Although silkworm (<it>Bombyx mori</it>) has a large amount of and a variety of transposable elements, the genome-wide information of the silkworm MITEs is unknown.</p> <p>Results</p> <p>We used structure-based and homology approaches to search for MITEs in the silkworm genome. We identified 17 MITE families with a total of 5785 members, accounting for ~0.4% of the genome. 7 of 17 MITE families are completely novel based on the nucleotide composition of target site duplication (TSD) and/or terminal inverted repeats (TIR). Silkworm MITEs were widely and nonrandom distributed in the genome. One family named BmMITE-2 might experience a recent burst expansion. Network and diversity analyses for each family revealed different diversification patterns of the silkworm MITEs, reflecting the signatures of genome-shocks that silkworm experienced. Most silkworm MITEs preferentially inserted into or near genes and BmMITE-11 that encodes a germline-restricted small RNA might silence its the closest genes in silkworm ovary through a small RNA pathway.</p> <p>Conclusions</p> <p>Silkworm harbors 17 MITE families. The silkworm MITEs preferred to reside in or near genes and one MITE might be involved in gene silence. Our results emphasize the exceptional role of MITEs in transcriptional regulation of genes and have general implications to understand interaction between MITEs and their host genome.</p

The UDP-glucosyltransferase multigene family in Bombyx mori

<p>Abstract</p> <p>Background</p> <p>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 <it>Bombyx mori </it>UGT genes could provide valuable basic information for this important family and explain the detoxication mechanism and other processes in insects.</p> <p>Results</p> <p>Taking advantage of the newly assembled genome sequence, we performed a genome-wide analysis of the candidate UGT family in the silkworm, <it>B. mori</it>. 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.</p> <p>Conclusion</p> <p><it>B. mori </it>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.</p

Analyzing Gene Expression Profile in K562 Cells Exposed to Sodium Valproate Using Microarray Combined with the Connectivity Map Database

To explore the mechanism underlying antileukaemia effect of sodium valproate, the growth and survival of the K562 cell line were investigated. Global profiles of gene expression in K562 cells exposed to sodium valproate were assessed and validated. The differentially expressed genes identified were further used to query the connectivity map database to retrieve a ranked list of compounds that act on the same intracellular targets as sodium valproate. A significant increase in cell apoptosis and a change in gene expression profile were observed in valproate-exposed K562 cells. The significant enrichment analysis of gene ontology terms for the differentially expressed genes showed that these genes were involved in many important biological processes. Eight differentially expressed genes involved in apoptosis were verified by quantitative real-time PCR. The connectivity map analysis showed gene expression profile in K562 cells exposed to sodium valproate was most similar to that of HDACi and PI3K inhibitors, suggesting that sodium valproate might exert antileukaemic action by inhibiting HDAC as well as inhibiting PI3K pathway. In conclusion, our data might provide clues to elucidate the molecular and therapeutic potential of VPA in leukaemia treatment, and the connectivity map is a useful tool for exploring the molecular mechanism of drug action

Protection effect of Emodin pretreatment on intestinal I-RI damage of intestinal mucosa in ratsa

AbstractObjectiveTo tinvestigate the protective effect and mechanism of emodin pretreatment on intestinal mucosa of rats with intestinal ischemia-reperfusion injury.MethodsA total of 50 SD rats were randomly divided into control group, model group, emodin groups of low, medium and high dose, with 10 in each group. Ischemia-reperfusion injury (I-RI) mode was established by using noninvasive clamp on superior mesentericartery (SMA). Control group and model group were pretreated with 0.5% sodium carboxymethyl cellulose solution lavage 2 h before operation, emodin groups of low, medium and high dose were given emodin lavage with 20, 40, 60 mg/kg pretreatment, femoral venous blood before the lavage pretreatment (T0) and 1 h ischemia (T1), and inferior vena venous blood after 1 h of reperfusion (T2) were extracted from each group of rats for detection of serum level of intestinal fatty acid binding protein (I-FABP), tumor necrosis factor (TNF-α), endotoxin, interleukin 6 (IL-6), and the content of diamine oxidase (DAO); After model establishment, the rats were sacrificed, intestine homogenate was prepared by using blind intestinal tissue to detect intestinal tissue myeloperoxidase (MPO), malondialdehyde (MDA) and superoxide dismutase (SOD) levels. And upper small intestine tissue was retrieved, followed by fixation and conventional HE staining to observe intestinal tissue morphology under light microscopy.ResultsIn emodin groups of low, medium and high dose at T1 and T2, I-FABP, TNF-α, endotoxin, IL-6 and DAO level were significantly lower than that of model group (P<0.05); in emodin group of low, medium and high dose, MPO and MDA content in intestinal tissue homogenate was significantly lower than that in model group (P<0.05), SOD level was significantly higher than that of model group (P<0.05). Intestinal damage of emodin low, medium and high dose groups were significantly lighter than model group.ConclusionsEmodin pretreatment has certain protective effect on intestinal mucosa in ischemia reperfusion injury

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

<p>Abstract</p> <p>Background</p> <p>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.</p> <p>Results</p> <p>In this study, 51 SP genes and 92 SPH genes were systematically identified in the genome of the silkworm <it>Bombyx mori</it>. 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 <it>Escherichia coli</it>, <it>Bacillus bombysepticus</it>, <it>Batrytis bassiana </it>and <it>B. mori </it><it>nucleopolyhedrovirus</it>, 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 <it>B. mori</it>.</p> <p>Conclusion</p> <p>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.</p