Dissecting the molecular basis of the contribution of source strength to high fructan accumulation in wheat

Fructans represent the major component of water soluble carbohydrates (WSCs) in the maturing stem of temperate cereals and are an important temporary carbon reserve for grain filling. To investigate the importance of source carbon availability in fructan accumulation and its molecular basis, we performed comparative analyses of WSC components and the expression profiles of genes involved in major carbohydrate metabolism and photosynthesis in the flag leaves of recombinant inbred lines from wheat cultivars Seri M82 and Babax (SB lines). High sucrose levels in the mature flag leaf (source organ) were found to be positively associated with WSC and fructan concentrations in both the leaf and stem of SB lines in several field trials. Analysis of Affymetrix expression array data revealed that high leaf sucrose lines grown in abiotic-stress-prone environments had high expression levels of a number of genes in the leaf involved in the sucrose synthetic pathway and photosynthesis, such as Calvin cycle genes, antioxidant genes involved in chloroplast H₂O₂ removal and genes involved in energy dissipation. The expression of the majority of genes involved in fructan and starch synthetic pathways were positively correlated with sucrose levels in the leaves of SB lines. The high level of leaf fructans in high leaf sucrose lines is likely attributed to the elevated expression levels of fructan synthetic enzymes, as the mRNA levels of three fructosyltransferase families were consistently correlated with leaf sucrose levels among SB lines. These data suggest that high source strength is one of the important genetic factors determining high levels of WSC in wheat.     

Differential gene expression during seed germination in barley (Hordeum vulgare L.)

A barley cDNA macroarray comprising 1,440 unique genes was used to analyze the spatial and temporal patterns of gene expression in embryo, scutellum and endosperm tissue during different stages of germination. Among the set of expressed genes, 69 displayed the highest mRNA level in endosperm tissue, 58 were up-regulated in both embryo and scutellum, 11 were specifically expressed in the embryo and 16 in scutellum tissue. Based on Blast X analyses, 70% of the differentially expressed genes could be assigned a putative function. One set of genes, expressed in both embryo and scutellum tissue, included functions in cell division, protein translation, nucleotide metabolism, carbohydrate metabolism and some transporters. The other set of genes expressed in endosperm encodes several metabolic pathways including carbohydrate and amino acid metabolism as well as protease inhibitors and storage proteins. As shown for a storage protein and a trypsin inhibitor, the endosperm of the germinating barley grain contains a considerable amount of residual mRNA which was produced during seed development and which is degraded during early stages of germination. Based on similar expression patterns in the endosperm tissue, we identified 29 genes which may undergo the same degradation process. Electronic Publication     

Molecular dissection of variation in carbohydrate metabolism related to water-soluble carbohydrate accumulation in stems of wheat

Water-soluble carbohydrates (WSCs; composed of mainly fructans, sucrose [Suc], glucose [Glc], and fructose) deposited in wheat (Triticum aestivum) stems are important carbon sources for grain filling. Variation in stem WSC concentrations among wheat genotypes is one of the genetic factors influencing grain weight and yield under water-limited environments. Here, we describe the molecular dissection of carbohydrate metabolism in stems, at the WSC accumulation phase, of recombinant inbred Seri/Babax lines of wheat differing in stem WSC concentrations. Affymetrix GeneChip analysis of carbohydrate metabolic enzymes revealed that the mRNA levels of two fructan synthetic enzyme families (Suc:Suc 1-fructosyltransferase and Suc:fructan 6-fructosyltransferase) in the stem were positively correlated with stem WSC and fructan concentrations, whereas the mRNA levels of enzyme families involved in Suc hydrolysis (Suc synthase and soluble acid invertase) were inversely correlated with WSC concentrations. Differential regulation of the mRNA levels of these Suc hydrolytic enzymes in Seri/Babax lines resulted in genotypic differences in these enzyme activities. Down-regulation of Suc synthase and soluble acid invertase in high WSC lines was accompanied by significant decreases in the mRNA levels of enzyme families related to sugar catabolic pathways (fructokinase and mitochondrion pyruvate dehydrogenase complex) and enzyme families involved in diverting UDP-Glc to cell wall synthesis (UDP-Glc 6-dehydrogenase, UDP-glucuronate decarboxylase, and cellulose synthase), resulting in a reduction in cell wall polysaccharide contents (mainly hemicellulose) in the stem of high WSC lines. These data suggest that differential carbon partitioning in the wheat stem is one mechanism that contributes to genotypic variation in WSC accumulation.     

Microarray analysis of differentially expressed genes engaged in fruit development between table and wine grape

Microarray analysis of genes can provide individual gene-expression profiles and new insights for elucidating biological mechanisms responsible for fruit development. To obtain an overall view on expression profiles of metabolism-related genes involved in fruit development of table and wine grapes, a microarray system comprising 15,403 ESTs was used to compare the expressed genes. The expression patterns from the microarray analysis were validated with quantitative real-time polymerase chain reaction analysis of 18 selected genes of interest. During the entire fruit development stage, 2,493 genes exhibited at least 2.0-fold differences in expression levels with 1,244 genes being up-regulated and 1,249 being down-regulated. Following gene ontology analysis, only 929 differentially expressed (including 403 up-regulated and 526 down-regulated) genes were annotated in table and wine grapes. These differentially expressed genes were found to be mainly involved in carbohydrate metabolism, biosynthesis of secondary metabolites as well as energy, lipid and amino acid metabolism via KEGG. Our results provide new insights into the molecular mechanisms and expression profiles of genes in the fruit development stage of table and wine grapes.     

Relationships between the severity of leaf blotch (Rhynchosporium secalis) and the water-soluble carbohydrate and nitrogen contents of barley plants

Water-soluble carbohydrate (WSC) and total nitrogen (N) contents of leaves of field-grown barley plants were measured in 1966 and 1967. Consistent differences were found between cultivars. The susceptibility of cultivars to leaf blotch was correlated negatively with WSC content and positively with N content at G.S. 10.4. Application of nitrogen fertiliser (which increased N and decreased WSC) also increased the severity of leaf blotch. The occurrence of primary lesions on seedlings does not seem to be affected by their WSC and N contents and the relation between WSC and N contents of leaves and severity of leaf blotch possibly depends on differences in growth and sporulation of the pathogen on substrates containing different amounts of carbohydrate and nitrogen.     

茶足柄瘤蚜茧蜂碳水化合物代谢相关的滞育关联基因差异表达分析

为明确糖代谢相关途径在茶足柄瘤蚜茧蜂Lysiphlebustestaceipes蛹滞育过程中的作用,揭示滞育调控的分子机制,本试验利用转录组测序技术,对滞育组与非滞育组的茶足柄瘤蚜茧蜂蛹进行转录组测序,并结合生物信息学方法对糖代谢相关途径中的差异表达基因进行了筛选与分析.GO注释到的与碳水化合物代谢条目相关的差异基因共1 050个,KEGG注释到的与碳水化合物代谢相关的差异表达基因共149个,糖酵解/糖异生、淀粉与蔗糖代谢及柠檬酸循环三条途径的差异表达基因分别为18个、10个和18个.这些在滞育过程中与碳水化合物代谢相关的差异基因呈现不同程度的上调或下调表达,发现PFK,PGK,ALDO,GAPDH,PGAM,PEPCK,GYS,TreS,TreH,MDH,IDH等基因与茶足柄瘤蚜茧蜂滞育密切相关,共同影响茶足柄瘤蚜茧蜂的滞育.碳水化合物代谢相关途径可能对茶足柄瘤蚜茧蜂的滞育起着非常重要的作用,糖类物质的合成与分解为昆虫在滞育过程中提供能量.     

Genetic, proteomic and metabolic analysis of the regulation of energy storage in rice seedlings in response to drought

We used proteomic analysis to determine the response of rice plant seedlings to drought-induced stress. The expression of 71 protein spots was significantly altered, and 60 spots were successfully identified. The greatest down-regulated protein functional category was translation. Up-regulated proteins were mainly related to protein folding and assembly. Additionally, many proteins involved in metabolism (e.g. carbohydrate metabolism) also showed differences in expression. cDNA microarray and GC-MS analysis showed 4756 differentially expressed mRNAs and 37 differentially expressed metabolites. Once these data were integrated with the proteomic analysis, we were able to elucidate the metabolic pathways affected by drought-induced stress. These results suggest that increased energy consumption from storage substances occurred during drought. In addition, increased expression of the enzymes involved in anabolic pathways corresponded with an increase in the content of six amino acids. We speculated that energy conversion from carbohydrates and/or fatty acids to amino acids was increased. Analysis of basic metabolism networks allowed us to understand how rice plants adjust to drought conditions.     

Seasonal shifts in dormancy status, carbohydrate metabolism, and related gene expression in crown buds of leafy spurge

Crown buds of field-grown leafy spurge (Euphorbia esula L.) were examined to determine relationships between carbohydrate metabolism and gene expression throughout para-, endo-, and eco-dormancy during the transition from summer, autumn, and winter, respectively. The data indicates that endo-dormancy plays a role in preventing new shoot growth during the transition from autumn to winter. Cold temperature was involved in breaking endo-dormancy, inducing flowering competence, and inhibiting shoot growth. An inverse relationship developed between starch and soluble sugar (mainly sucrose) content in buds during the shift from para- to endo-dormancy, which continued through eco-dormancy. Unlike starch content, soluble sugars were lowest in crown buds during para-dormancy but increased over two- to three-fold during the transition to endo-dormancy. Several genes (AGPase, HK, SPS, SuSy, and UGPase) coding for proteins involved in sugar metabolism were differentially regulated in conjunction with well-defined phases of dormancy in crown buds. Marker genes for S-phase progression, cell wall biochemistry, or responsive to auxin were also differentially regulated during transition from para-, endo-, and eco-dormancy. The results were used to develop a model showing potential signalling pathways involved in regulating seasonal dormancy status in leafy spurge crown buds.     

草菇耐低温突变菌株Vtlt-1和原始菌株V23转录组差异的研究

为了培育草菇耐低温菌株与解析其耐低温的分子机制,采用紫外诱变的方法,选育出耐低温草菇菌株Vtlt-1,并利用表达谱芯片技术,比较突变菌株Vtlt-1与原始菌株V23的表达差异基因,筛选差异显著基因后利用GO（gene ontology）功能注释和KEGG（kyoto encyclopedia of genes and genomes）通路富集等方法分析,结果发现与V23相比Vtlt-1表达显著差异基因共有1 600个,其中704个基因上调表达,896个基因下调表达。针对差异基因的GO功能分类结果发现：生物学过程方面,差异基因主要分布在金属离子结合、氧化还原过程、碳水化合物的代谢与核酸的结合。细胞组分方面主要与细胞核相关;分子功能中,氧化还原活性以及解旋酶活性,依赖于ATP 的解旋酶活性、DNA指导的RNA聚合酶活性。KEGG注释结果发现差异表达基因主要富集在氨基酸与氮类物质的代谢、脂肪酸与生物碱的合成这两方面,此外还富集到核糖体的生物合成、细胞色素P450、RNA聚合酶、硫和氨基酸的代谢、核酸的修复等通路。这些结果为解析草菇耐低温机制提供分子依据和理论基础。     

巴氏蘑菇子实体不同发育阶段的转录组分析

为探讨巴氏蘑菇子实体不同发育阶段基因的表达情况,本研究对巴氏蘑菇子实体不同发育时期（原基、采收期和开伞期）进行转录组测序,以本实验室已获得的巴氏蘑菇JA菌株的不育单孢菌株JA-15036基因组为参考基因组研究原基与采收期及开伞期样本间差异表达基因,并对差异表达基因进行了GO功能和Pathway富集分析。GO功能分析结果显示,差异表达基因主要富集在跨膜转运、碳水化合物代谢途径和膜组分,它们协同调控为子实体生长发育提供稳定的内环境。KEGG富集分析结果表明,原基期上调的差异表达基因主要富集在核糖体蛋白和DNA复制,表明原基期细胞代谢旺盛,其中核糖体蛋白基因上调为后期蛋白质合成提供重要场所;采收期和开伞期子实体时期差异表达基因主要富集在碳水化合物代谢、脂肪酸降解和氨基酸代谢等途径,为巴氏蘑菇子实体的生长发育与成熟提供营养与能量。     

蓝标型核不育小麦花药转录物组学及花色素苷合成相关基因的表达分析

为了揭示蓝标型小麦核雄性不育的分子机制,更好地利用隐性核不育小麦杂种优势,本研究以蓝标型白粒小麦WS（不育）和浅蓝粒小麦WF（育性正常）植株花药为试验材料,利用转录物组学技术对两者差异表达基因进行了分析,并对其中涉及花色素苷合成相关基因进行了验证。结果表明： WF与WS相比,共检测到2 352个差异表达基因,这些基因经GO功能注释分为3大类43个小类,主要涉及生物合成、苯丙烷代谢、L-苯丙氨酸分解代谢、膜组成部分、质膜、细胞质、ATP结合和蛋白质丝氨酸/苏氨酸激酶活性等。 KEGG通路分析结果显示,苯丙烷类生物合成通路富集基因最多,有159个,其次是苯丙氨酸代谢通路,包含136个显著差异表达基因,其他还涉及多种氨基酸代谢、嘌呤代谢、嘧啶代谢及糖代谢通路;与花青素代谢直接相关的通路中,多个控制关键酶结构基因存在差异表达,且大多数在WF中上调表达,只有黄烷酮3-羟化酶基因（flavanone 3-hydroxylase,F3H）和无色花青素双加氧酶基因（anthocyanin dioxygenase,ANS）下调表达;实时荧光定量分析显示,10个与花青素代谢相关基因实际表达情况和转录物组测序数据中基因表达情况具有相同的上下调趋势;差异基因序列同源性分析显示,筛选出的2个转录因子（DN48762c2g1、DN25944c0g1）与玉米、水稻及拟南芥花色素苷合成调控转录因子聚为同一簇,可能是蓝标型小麦浅蓝粒植株蓝色糊粉层性状的候选基因。并且荧光定量分析表明,DN48762c2g1和DN25944c0g1在WF中的表达量要明显高于WS。综上认为,花青素的生物合成途径相关基因不仅与籽粒蓝色性状有关,而且可能参与了蓝标型核不育系的花药败育。