Capturing candidate drought tolerance traits in two native Andean potato clones by transcription profiling of field grown plants under water stress.

Candidate traits for drought tolerance were targeted by analyzing water stress responses in two moderately drought-tolerant native Andean potato clones, SA2563 and Sullu (Solanum tuberosum L. subsp, andigena (Juz, Bukasov) Hawkes) under field conditions. SA2563 exhibited increased root growth under drought, while Sullu retained a higher relative leaf water content. Gene expression profiling using the TIGR 10 K microarray revealed 1713 significantly differentially expressed genes, 186 of these genes were up-regulated in both clones. In addition to these commonly up-regulated genes, each clone induced a specific gene set in response to drought. Gene expression and metabolite analysis pinpointed candidate traits for drought tolerance present either in one or both of the clones under investigation. These traits included osmotic adjustment, changes in carbohydrate metabolism, membrane modifications, strengthening of cuticle and cell rescue mechanisms, such as detoxification of oxygen radicals and protein stabilization. Many of the up-regulated genes have been identified previously in laboratory studies on model plants using shock treatments, and the present study confirms the importance of these factors under field conditions.     

Analysis of Differential Expression of Barley ESTs during Cold Acclimatization Using Microarray Technology

Abstract: Genomics adds a new dimension to genetic analysis, shifting the focus from the study of a single gene to the whole genome. We have successfully applied the genomics approach based on microarray to the study of genes involved in barley responses to cold stress. About 900 EST clones from barley were obtained from a cDNA library of cold acclimatized leaves of cv. Nure and arrayed, and gene expression analysis done on cold acclimatized vs. control plants. The system allowed for reliable detection of differences in mRNA expression levels, and was confirmed by the finding that numerous previously reported cold-related genes were differentially expressed in treated and untreated plants when evaluated in our arrays. The expression profiles of a sample of genes analysed by the array were confirmed by quantitative RT-PCR.
Previously, identification of novel plant genes was achieved considering a few genes at a time; now many genes can be found as up- or down-regulated based on a one step procedure. Many of the genes we found to be up- or down-regulated do not have an assigned function. This includes 15 of the 78 up-regulated and 8 of the 45 down-regulated clones. Our results add new genes to the group of cold-regulated genes and provide the opportunity to better understand the complex mechanism of stress tolerance.     

Differential gene expression in response to brown planthopper feeding in rice

Plant responses to herbivores are complex. 108 cDNA clones representing genes relating to plant responses to chewing insect-feeding, pathogen infection, wounding and other stresses were collected. Northern blot and cDNA array analysis were employed to investigate gene expression regulated by piercing-sucking insect, brown planthopper (BPH), Nilaparvata lugens (Homoptera: Dephacidae) on both the resistant and susceptible rice genotypes. After BPH feeding in rice for 72 h, the expression of most tested genes was affected. 14 genes in resistant rice variety B5 and 44 genes in susceptible MH63 were significantly up- or down-regulated. Most of the well-regulated genes were grouped in the categories of signaling pathways, oxidative stress/apoptosis, wound-response, drought-inducible and pathogen-related proteins. Those related to the flavonoid pathway, aromatic metabolidsm and the octadecanoid pathway were mostly kept unchanged or down-regulated. Our results indicate that BPH feeding induces plant responses which would take part in a jasmonic acid-independent pathway and crosstalk with those related to abiotic stress, pathogen invasion and phytohormone signaling pathways.     

Temporary effect of postharvest UV-C irradiation on gene expression profile in tomato fruit

To obtain an overall view on gene expression during the early stage (24 h) of tomato fruit in response to postharvest UV-C irradiation (4 kJ/m(2)), we performed a microarray analysis by using Affymetrix Tomato Genechip. The results showed that 274 and 403 genes were up- or down-regulated, respectively, more than two folds in postharvest tomato fruit irradiated with UV-C as compared with that in control fruit. The up-regulated genes mainly involve in signal transduction, defense response and metabolism. Conversely, genes related to cell wall disassembly, photosynthesis and lipid metabolism were generally down-regulated. These results opened ways to probe into the molecular mechanisms of the effects of postharvest UV-C irradiation on increased disease resistance, delayed softening, better quality maintenance and prolonged postharvest life in tomato fruit.     

Next-generation sequencing-based transcriptome analysis of l-lysine-producing Corynebacterium glutamicum ATCC 21300 strain

In the present study, 151 genes showed a significant change in their expression levels in Corynebacterium glutamicum ATCC 21300 compared with those of C. glutamicum ATCC 13032. Of these 151 genes, 56 genes (2%) were up-regulated and 95 genes (3%) were down-regulated. RNA sequencing analysis also revealed that 11 genes, involved in the L-lysine biosynthetic pathway of C. glutamicum, were up- or down-regulated compared with those of C. glutamicum ATCC 13032. Of the 151 genes, 10 genes were identified to have mutations including SNP (9 genes) and InDel (1 gene). This information will be useful for genome breeding of C. glutamicum to develop an industrial amino acid-producing strain with minimal mutation.     

雷公藤甲素对结肠癌细胞SW480 的基因表达谱的影响

目的:探讨雷公藤甲素对结肠癌SW480细胞的基因表达谱的影响。方法:雷公藤甲素处理结肠癌SW480细胞24h后,分别提取给药组和空白对照组SW480细胞总RNA,纯化并逆转录成用Cy3和Cy5标记的cDNA探针,经全基因芯片杂交,洗涤,通过生物信息学方法分析雷公藤甲素处理组和空白对照组SW480细胞基因表达谱的差异。结果:与空白对照组比较,共发现了902个差异基因,雷公藤甲素处理组有196个基因上调,706个基因下调。上调基因主要涉及细胞代谢。下调基因主要涉及wnt通路、细胞周期通路、Toll样受体通路以及MAPK等通路。结论:雷公藤甲素能导致结肠癌细胞基因表达谱的改变,这些基因改变可能参与了细胞增殖、分化、凋亡等过程。这些信息可能为探讨雷公藤抗结肠癌作用机制提供线索。     

Integrative genomics revealed RAI3 is a cell growth-promoting gene and a novel P53 transcriptional target

In this study, differential gene expression between normal human mammary epithelial cells and their malignant counterparts (eight well established breast cancer cell lines) was studied using Incyte GeneAlbum 1-6, which contains 65,873 cDNA clones representing 33,515 individual genes. 3,152 cDNAs showed a > or =3.0-fold expression level change in at least one of the human breast cancer cell lines as compared with normal human mammary epithelial cells. Integration of breast tumor gene expression data with the genes in the tumor suppressor p53 signaling pathway yielded 128 genes whose expression is altered in breast tumor cell lines and in response to p53 expression. A hierarchical cluster analysis of the 128 genes revealed that a significant portion of genes demonstrate an opposing expression pattern, i.e. p53-activated genes are down-regulated in the breast tumor lines, whereas p53-repressed genes are up-regulated. Most of these genes are involved in cell cycle regulation and/or apoptosis, consistent with the tumor suppressor function of p53. Follow-up studies on one gene, RAI3, suggested that p53 interacts with the promoter of RAI3 and repressed its expression at the onset of apoptosis. The expression of RAI3 is elevated in most tumor cell lines expressing mutant p53, whereas RAI3 mRNA is relatively repressed in the tumor cell lines expressing wild-type p53. Furthermore, ectopic expression of RAI3 in 293 cells promotes anchorage-independent growth and small interfering RNA-mediated depletion of RAI3 in AsPc-1 pancreatic tumor cells induces cell morphological change. Taken together, these data suggest a role for RAI3 in tumor growth and demonstrate the predictive power of integrative genomics.     

Combined transcript and metabolite analysis reveals genes involved in spider mite induced volatile formation in cucumber plants

Many plants have an indirect defense against herbivores by emitting volatiles that attract carnivorous enemies of the herbivores. In cucumber (Cucumis sativus) the production of carnivore attractants can be induced by herbivory or jasmonic acid spraying. From the leaves of cucumber plants with and without spider mite infestation, two subtractive cDNA libraries were made that were enriched in cDNA fragments up- or down-regulated by spider mite infestation. A total of 713 randomly selected clones from these libraries were used to make a cDNA microarray. Subsequently, cucumber plants were sprayed with jasmonic acid, mechanically damaged, infested with spider mites, or left untreated (control). Leaf samples were taken at a range of different time points, and induced volatile compounds and mRNA (from the same leaves) were collected. cDNAs prepared from the mRNA were hybridized to the clones on the microarray. The resulting gene expression profiles were analyzed in combination with volatile production data in order to gain insight in the possible involvement of the studied genes in the synthesis of those volatiles. The clones on the microarray and the induced cucumber volatiles could be grouped into a number of clusters in which specific biosynthetic genes clustered with the product of that pathway. For example, lipoxygenase cDNA clones clustered with the volatile (Z)-3-hexenyl acetate and the volatile sesquiterpene (E,E)- alpha-farnesene clustered with an up-regulated sesquiterpene synthase fragment. This fragment was used to screen a cDNA library which resulted in the cloning of the cucumber (E,E)-alpha-farnesene and (E)-beta-caryophyllene synthases. The use of combined global gene expression analysis and metabolite analysis for the discovery of genes involved in specific biosynthetic processes is discussed.     

Systems genetics approach reveals candidate genes for parasite resistance from quantitative trait loci studies in agricultural species

A systems genetics approach combining pathway analysis of quantitative trait loci (QTL) and gene expression information has provided strong evidence for common pathways associated with genetic resistance to internal parasites. Gene data, collected from published QTL regions in sheep, cattle, mice, rats and humans, and microarray data from sheep, were converted to human Entrez Gene IDs and compared to the KEGG pathway database. Selection of pathways from QTL data was based on a selection index that ensured that the selected pathways were in all species and the majority of the projects overall and within species. Pathways with either up- and down-regulated genes, primarily up-regulated genes or primarily down-regulated genes, were selected from gene expression data. After comparing the data sets independently, the pathways from each data set were compared and the common set of pathways and genes was identified. Comparisons within data sets identified 21 pathways from QTL data and 66 pathways from gene expression data. Both selected sets were enriched with pathways involved in immune functions, disease and cell responses to signals. The analysis identified 14 pathways that were common between QTL and gene expression data, and four directly associated with IFNγ or MHCII, with 31 common genes, including three MHCII genes. In conclusion, a systems genetics approach combining data from multiple QTL and gene expression projects led to the discovery of common pathways associated with genetic resistance to internal parasites. This systems genetics approach may prove significant for the discovery of candidate genes for many other multifactorial, economically important traits.     

Global Gene Expression Analysis of Long-Term Stationary Phase Effects in E. coli K12 MG1655

Global gene expression was monitored in long-term stationary phase (LSP) cells of E. coli K12 MG1655 and compared with stationary phase (SP) cells that were sub-cultured without prolonged delay to get an insight into the survival strategies of LSP cells. The experiments were carried out using both LB medium and LB supplemented with 10% of glycerol. In both the media the LSP cells showed decreased growth rate compared to SP cells. DNA microarray analysis of LSP cells in both the media resulted in the up- and down-regulation of several genes in LSP cells compared to their respective SP cells in the corresponding media. In LSP cells grown in LB 204 genes whereas cells grown in LB plus glycerol 321 genes were differentially regulated compared to the SP cells. Comparison of these differentially regulated genes indicated that irrespective of the medium used for growth in LSP cells expression of 95 genes (22 genes up-regulated and 73 down-regulated) were differentially regulated. These 95 genes could be associated with LSP status of the cells and are likely to influence survival and growth characteristics of LSP cells. This is indeed so since the up- and down-regulated genes include genes that protect E. coli LSP cells from stationary phase stress and genes that would help to recover from stress when transferred into fresh medium. The growth phenotype in LSP cells could be attributed to up-regulation of genes coding for insertion sequences that confer beneficial effects during starvation, genes coding for putative transposases and simultaneous down-regulation of genes coding for ribosomal protein synthesis, transport-related genes, non-coding RNA genes and metabolic genes. As yet we still do not know the role of several unknown genes and genes coding for hypothetical proteins which are either up- or down-regulated in LSP cells compared to SP cells.     

Effect of sucA or sucC gene knockout on the metabolism in Escherichia coli based on gene expressions, enzyme activities, intracellular metabolite concentrations and metabolic fluxes by C-labeling experiments

The effect of sucA or sucC gene knockout on the metabolism in Escherichia coli was investigated for the aerobic cell growth in batch and continuous cultivations based on gene expressions, enzyme activities, intracellular metabolite concentrations and metabolic flux analysis. In the batch cultivation, the cell growth rate and the glucose uptake rate were lower for sucA mutant as compared with the parent strain, while it was not the case for sucC mutant. A significantly higher amount of acetate was produced, and it was not utilized in sucC mutant, while a little less acetate was produced in sucA mutant as compared with the parent strain. Unlike the parent strain and sucC mutant, sucA mutant excreted a little amount of l-glutamate. Enzyme activity results show that some of the glycolytic enzymes such as Tpi and Pgk were up-regulated, while Pfk, Fba and Pyk activities were down-regulated for sucA mutant as compared with the parent strain. For sucC mutant, the activities of Pfk, Fba, Tpi, GAPDH, Pgk and Pyk activities were down-regulated. As for the TCA cycle enzymes, the activities of CS and ICDH were down-regulated, while those of Icl, MS, Fum and MDH were up-regulated for sucA mutant. The activities of the oxidative pentose phosphate (PP) pathway enzymes such as G6PDH and 6PGDH and the gluconeogenic pathway enzyme such as Mez were up-regulated in sucA mutant. The Ack activity was down-regulated for sucA mutant, but not for sucC mutant. In continuous cultivation, the gene expression results indicate that the global regulatory genes such as fadR and iclR were slightly down-regulated in sucA mutant, which enhanced the expression of aceA gene and caused the up-regulation of the isocitrate lyase activity in sucA mutant, while fadR and iclR of sucC mutant changed little and no isocitrate lyase activation was observed for sucC mutant. Some other global regulatory genes such as arcA and fnr genes were down-regulated in both mutants, which caused some of the TCA cycle genes to be up-regulated. The effect of the sucA gene knockout on the metabolic flux distributions was investigated based on ¹H–¹³C NMR spectra and GC–MS signals obtained from ¹³C-labeling experiments. Flux analysis results indicate that the knockout of sucA gene caused the activation of PP pathway and the glyoxylate shunt. The fluxes through glycolysis and the TCA cycle were down-regulated in the sucA mutant. On the other hand, the fluxes through PP pathway and the anaplerotic reactions of Ppc-Pck and Mez increased.