Diverse expression profiles of 21 rice peroxidase genes

Secretory class III plant peroxidases (POXs) catalyze the oxidation of various reductants, and are encoded by a large multigene family. In rice, 42 independent expressed sequence tags for POXs have been identified. By RNA gel blot analysis using specific probes, we show here that 21 rice POX genes are unique in their developmental, organ specific and external stimuli-responsive expression. This would suggest that encoded POX isoenzymes are involved in a broad range of physiological processes in rice plants, individually.     

Four rice genes encoding NADP malic enzyme exhibit distinct expression profiles

In plants, the NADP malic enzymes (NADP-MEs) are encoded by small gene families. These NADP-ME gene families are relatively well described in C4 plants but not well studied in C3 plants. In this study, we investigated the NADP-ME gene family in a model C3 monocot plant (rice, Oryza sativa) based on its recently released genomic DNA sequence. We found that the rice NADP-ME family is composed of four members, one plastidic NADP-ME and three cytosolic versions. Although the rice NADP-ME genes identified share a high degree of similarity with one another, one cytosolic NADP-ME (OscytME3) contains several unique amino acid substitutions within highly conserved amino acid regions. Phylogenetic analysis showed that OscytME3 might be derived from a different evolutionary branch than the other three rice genes. Expression analysis of the four rice NADP-ME genes indicated that each had a different tissue-specific and developmental profile, although all four responded to stress stimuli.     

Characterization and expression profiles of miRNAs in rice seeds

Small RNAs (sRNAs) are common and effective modulators of gene expression in eukaryotic organisms. To characterize the sRNAs expressed during rice seed development, massively parallel signature sequencing (MPSS) was performed, resulting in the obtainment of 797 399 22-nt sequence signatures, of which 111 161 are distinct ones. Analysis on the distributions of sRNAs on chromosomes showed that most sRNAs originate from interspersed repeats that mainly consist of transposable elements, suggesting the major function of sRNAs in rice seeds is transposon silencing. Through integrative analysis, 26 novel miRNAs and 12 miRNA candidates were identified. Further analysis on the expression profiles of the known and novel miRNAs through hybridizing the generated chips revealed that most miRNAs were expressed preferentially in one or two rice tissues. Detailed comparison of the expression patterns of miRNAs and corresponding target genes revealed the negative correlation between them, while few of them are positively correlated. In addition, differential accumulations of miRNAs and corresponding miRNA*s suggest the functions of miRNA*s other than being passenger strands of mature miRNAs, and in regulating the miRNA functions.     

Metabolite profiles of rice cultivars containing bacterial blight-resistant genes are distinctive from susceptible rice

The metabolic changes of bacterial blight-resistant line C418/Xa23 generated by molecular marker-assisted selection (n= 12), transgenic variety C418-Xa21 generated by using the Agrobacterium-mediated system (n= 12), and progenitor cultivar C418 (n= 12) were monitored using gas chromatography/mass spectrometry. The validation, discrimination, and establishment of correlative relationships between metabolite signals were performed by cluster analysis, principal component analysis, and partial least squares-discriminant analysis. Significant and unintended changes were observed in 154 components in C418/Xa23 and 48 components in C418-Xa21 compared with C418 (P< 0.05, Fold change > 2.0). The most significant decreases detected (P< 0.001) in both C418/Xa23 and C418-Xa21 were in three amino acids: glycine, tyrosine, and alanine, and four identified metabolites: malic acid, ferulic acid, succinic acid, and glycerol. Linoleic acid was increased specifically in C418/Xa23 which was derived from traditional breeding. This line, possessing a distinctive metabolite profile as a positive control, shows more differences vs. the parental than the transgenic line. Only succinic acid that falls outside the boundaries of natural variability between the two non-transgenic varieties C418 and C418/Xa23 should be further investigated with respect to safety or nutritional impact.     

Gene expression profiles in rice roots under low phosphorus stress

Phosphorus (P), an important plant macronutrient, is a component of key molecules such as nucleic acids, phospholipids and ATP. P is often the limiting nutrient for crop yield potential because of the low concentration of soluble P that can be absorbed directly by plant. Plants have evolved a series of molecular and morphological adaptations to cope with P limitation. However, the molecular bases of these responses to P deficiency have not been thoroughly elucidated. In this report, the gene expression profiles of low-P-tolerant rice Zhongzao 18 (Oryza sativa ssp. Indica) and not-low-P-tolerant rice Lagrue (Oryza sativa ssp. Indica) roots at 6 h, 24 h and 72 h under low P stress were investigated and compared with a control (normal P conditions) profile, using a DNA chip of 60,000 oligos (70 mer) that represented all putative genes of the rice genome. A total of 1,518 and 2,358 genes exhibited alterations in expression in response to low P stress in at least one of the three time points in rice Zhongzao 18 and rice Lagrue, respectively. The differentially expressed genes included those involved in phosphate (Pi) transportation, transportations except for Pi transportation, phosphatase, enzymes other than phosphatase, primary metabolism, secondary metabolism and so on. Several genes involved in glycolysis and TCA cycle were up-regulated during the early stages of low P treatment in rice Zhongzao 18 roots, but not in rice Lagrue roots. The results may provide useful information to further studies of the molecular mechanism of plant adaptation to low P and thus facilitate research in improving P utilization in crop species.     

Defining the gene repertoire and spatiotemporal expression profiles of adhesion G protein-coupled receptors in zebrafish

Background

Adhesion G protein-coupled receptors (aGPCRs) are the second largest of the five GPCR families and are essential for a wide variety of physiological processes. Zebrafish have proven to be a very effective model for studying the biological functions of aGPCRs in both developmental and adult contexts. However, aGPCR repertoires have not been defined in any fish species, nor are aGPCR expression profiles in adult tissues known. Additionally, the expression profiles of the aGPCR family have never been extensively characterized over a developmental time-course in any species.

Results

Here, we report that there are at least 59 aGPCRs in zebrafish that represent homologs of 24 of the 33 aGPCRs found in humans; compared to humans, zebrafish lack clear homologs of GPR110, GPR111, GPR114, GPR115, GPR116, EMR1, EMR2, EMR3, and EMR4. We find that several aGPCRs in zebrafish have multiple paralogs, in line with the teleost-specific genome duplication. Phylogenetic analysis suggests that most zebrafish aGPCRs cluster closely with their mammalian homologs, with the exception of three zebrafish-specific expansion events in Groups II, VI, and VIII. Using quantitative real-time PCR, we have defined the expression profiles of 59 zebrafish aGPCRs at 12 developmental time points and 10 adult tissues representing every major organ system. Importantly, expression profiles of zebrafish aGPCRs in adult tissues are similar to those previously reported in mouse, rat, and human, underscoring the evolutionary conservation of this family, and therefore the utility of the zebrafish for studying aGPCR biology.

Conclusions

Our results support the notion that zebrafish are a potentially useful model to study the biology of aGPCRs from a functional perspective. The zebrafish aGPCR repertoire, classification, and nomenclature, together with their expression profiles during development and in adult tissues, provides a crucial foundation for elucidating aGPCR functions and pursuing aGPCRs as therapeutic targets.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1296-8) contains supplementary material, which is available to authorized users.     

稻纵卷叶螟羧酸酯酶基因的鉴定与表达谱分析

【目的】鉴定稻纵卷叶螟Cnaphalocrocis medinalis的羧酸酯酶基因,并检测这些基因在成虫不同组织中的表达模式。【方法】从稻纵卷叶螟转录组中搜索羧酸酯酶基因,使用生物信息学软件对所获得的基因序列进行分析,使用荧光定量PCR检测这些基因在各组织中的相对表达水平。【结果】获得了15个羧酸酯酶基因,分别命名为Cm Car E1~Cm Car E15。其中Cm Car E12缺少3′区域,其余14个序列均含有完整的开放阅读框。除Cm Car E11外,其余14个基因编码的蛋白均具有羧酸酯酶的典型特征,如保守的五肽结构域,催化三联体和氧阴离子穴等。系统进化分析显示15个Cm Car Es被聚在不同的进化支内,Cm Car E13、Cm Car E14和Cm Car E15聚在"胞内催化类"进化支,其余12个Cm Car Es聚在"分泌催化类"进化支。Cm Car E1、Cm Car E2、Cm Car E3、Cm Car E7、Cm Car E8、Cm Car E10和Cm Car E13特异表达于成虫腹部,而Cm Car E9特异表达于雌雄成虫触角。其他基因的表达没有组织特异性。【结论】Cm Car E1、Cm Car E2、Cm Car E3、Cm Car E7、Cm Car E8、Cm Car E10和Cm Car E13编码的酯酶可能参与了内外源化合物的代谢,而Cm Car E9编码的酯酶可能参与了气味分子的降解。     

The expression of iron homeostasis-related genes during rice germination

To characterize Fe homeostasis during the early stages of seed germination, a microarray analysis was performed. mRNAs extracted from fully mature seeds or seeds harvested 1–3 days after sowing were hybridized to a rice microarray containing approximately 22,000 cDNA oligo probes. Many Fe deficiency-inducible genes were strongly expressed throughout early seed germination. These results suggest that the demand for Fe is extremely high during germination. Under Fe-deficient conditions, rice produces and secretes a metal-cation chelator called deoxymugineic acid (DMA) to acquire Fe from the soil. In addition, DMA and its intermediate nicotianamine (NA) are thought to be involved in long distance Fe transport in rice. Using promoter-β-glucuronidase (GUS) analysis, we investigated the expression patterns during seed germination of the Fe deficiency-inducible genes OsNAS1, OsNAS2, OsNAS3, OsNAAT1, and OsDMAS1, which encode enzymes that participate in the biosynthesis of DMA, and the transporter genes OsYSL2 and OsIRT1, which are involved in Fe transport. All of these genes were expressed in germinating seeds prior to protrusion of the radicle. These results suggest that DMA and NA are produced and involved in Fe transport during germination. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Identification and expression profiles of genes and protens in SMMC-7721 cells

In the study presented here, we first evaluated effect of CDDP on liver cancer cells SMMC-7721 apoptosis and motility capacity. Then, we evaluate inhibitory effect of CDDP on tumour growth and its possible molecular mechanism in liver cancer mice model. Results showed that the apoptosis rate of cells decreased with increasing CDDP. Analysis of the effect of the CDDP on cell cycle was performed by flow cytometry and results show a dose-dependent increase in the percentage of cells in the S-phase of the cell cycle, with a decrease in the percentage of cells in the G1 and G2/M phases. CDDP did not close the wound even after 48 h, as opposed to untreated cells (0 mg/l). Similarly, the migratory and invasion capacity of SMMC-7721 cells was also reduced after treatment with CDDP, as evaluated by a transwell assay. Animal experiment indicated that CDDP administration could increase blood WBC, total protein, albumin and A/G, decrease blood alanine aminotransferase, aspartate aminotransferase and alkaline phosphatase levels in hepatocellular carcinomas mice. Immunohistochemistry analysis showed that positive expression of Fas and Bax proteins in the medicine-treated (II, III) group was significantly higher, whereas the expression of NF-κB, P53, Bcl-2 proteins was significantly lower than those of the control group. Gene expression analysis using Real time PCR methods revealed a significant up-regulation in the expression levels of Bax mRNA in the medicne-treated (II, III) group when compared to untreated control. In contrast, CDDP-treated group showed a significant down regulation in the expression levels of Bcl-2 mRNA as compared to untreated control group. These results are in agreement with immunohistochemistry data. Our observations indicate that CDDP has damaged effects on liver tumour cells SMMC-7721 including apoptosis, motility and cell cycle under in vitro. CDDP can enhance pro-apoptosis gene Fas, Bax expression, decrease anti-apoptosis genes Bcl-2 expression, and mutant genes P53, NF-κB proteins expression.     

异源表达古菌TRAM基因增强水稻的耐旱性

干旱会直接影响水稻的生长发育,导致其产量和品质下降。在水稻中异源表达细菌RNA分子伴侣Csp能够显著提高水稻的耐旱能力,并且不影响水稻的正常生长。古菌中也发现具有类似细菌分子伴侣Csp功能的TRAM (TRM2 and MiaB)蛋白,且古菌的DNA复制、转录和翻译等过程与真核生物有着更为相似的调控方式,然而,古菌中RNA分子伴侣蛋白能否调控植物耐旱能力还未见报道。我们选取了嗜冷甲烷古菌Methanolobus psychrophilus R15中两个TRAM蛋白在水稻中进行研究,发现在水稻中过量表达Mpsy_3066和Mpsy_0643两个TRAM蛋白均能显著提高水稻苗期和成株期时对干旱胁迫的耐受能力。同时,我们在水稻原生质体中验证了TRAM蛋白可以发挥其分子伴侣的功能消除RNA的错误折叠对翻译的影响,这可能是TRAM转基因植物发挥其耐旱能力的作用机制。该工作初步展示了异源表达古菌TRAMs可以作为提高水稻耐旱能力的一种有效手段。     

Characterization and expression analyses of two plastidic enolase genes in rice

To verify the presence of enolase related to the chloroplastic glycolysis in rice, database search was carried out and identified seven putative enolase genes in the rice genome. Among them, OsEno1 and OsEno3 encode long proteins with N-terminal extensions. GFP protein fusions of these N-terminal extensions were both targeted to plastids of onion epidermal cell. Promoter::GUS analysis showed that OsEno3 was highly expressed in young developing leaves, but its expression was drastically decreased during leaf development and greening. On the other hand, the expression of OsEno1 was low and detected in limited portions such as leaf sheath at the tiller base. Recombinant OsEno1 protein showed enolase activity with a pH optimum at pH 8.0, whereas OsEno3 did not exhibit detectable activity. Although it remains obscure if OsEno3 encodes a functional enolase in vivo, our results demonstrate that the entire glycolytic pathway does not operate in rice chloroplasts.     

Selecting informative genes for discriminant analysis using multigene expression profiles

Background

Gene expression data extracted from microarray experiments have been used to study the difference between mRNA abundance of genes under different conditions. In one of such experiments, thousands of genes are measured simultaneously, which provides a high-dimensional feature space for discriminating between different sample classes. However, most of these dimensions are not informative about the between-class difference, and add noises to the discriminant analysis.

Results

In this paper we propose and study feature selection methods that evaluate the "informativeness" of a set of genes. Two measures of information based on multigene expression profiles are considered for a backward information-driven screening approach for selecting important gene features. By considering multigene expression profiles, we are able to utilize interaction information among these genes. Using a breast cancer data, we illustrate our methods and compare them to the performance of existing methods.

Conclusion

We illustrate in this paper that methods considering gene-gene interactions have better classification power in gene expression analysis. In our results, we identify important genes with relative large p-values from single gene tests. This indicates that these are genes with weak marginal information but strong interaction information, which will be overlooked by strategies that only examine individual genes.