Identification and characterization of differential gene expression in the mesocarp and kernel of oil palm nuts using suppression subtractive hybridization

Suppression subtracted hybridization (SSH) and dot blotting were used to identify differential gene expression in the mesocarp and kernel of oil palm nuts. The different types of nut tissue show differences in fatty acid anabolism and the synthesis of other important compounds. In total, 302 clones from forward SSH libraries and 238 clones from reverse SSH libraries were identified following differential screening, respectively. Among these, 120 clones from the forward SSH library and 81 clones from the reverse SSH library, showed tenfold or more differential expression levels, and were sequenced. Sequence analysis revealed that 76 clones (28 from the forward SSH library and 48 from the reverse SSH library) represent non-redundant cDNA inserts. The differential expression of 39 subset genes in the two different tissues was further confirmed by RT-PCR analysis. Functionally annotated blasting against the GenBank non-redundant protein database classified all 76 candidate genes into six categories, according to their putative functions. Interestingly, our results show that a group of significantly differentially expressed genes are involved in processes associated with oil palm nut maturation, such as the synthesis of medium-chain saturated fatty acids and phytic acid, nut development, and stress/defense responses. This study describes some relationships between gene expression and metabolic pathways in mature oil palm nuts, and contributes to our understanding of oil palm nut ESTs.     

Identification of ESTs differentially expressed in green and albino mutant bamboo (Bambusa edulis) by suppressive subtractive hybridization (SSH) and microarray analysis

To gain a better understanding of gene expression in bamboo (Bambusa edulis Murno), we have used a combination of suppressive subtractive hybridization (SSH), microarray hybridization analysis, sequencing, and bioinformatics to identify bamboo genes differentially expressed in a bamboo albino mutant. Ten expressed sequence tags (ESTs) were found to be differentially expressed; these were isolated and sequenced. RT-PCR analysis of these ESTs supported the results of the microarray analysis. Six ESTs that were nucleus-encoded exhibited differential expression patterns in the green wild-type bamboo relative to the albino mutant. These genes (exception being the Rubisco small subunit) were non-photosynthesis-related genes. The development of a specific SSH cDNA library in which most of the chloroplast-encoded or photosynthesis-related genes had been subtracted proved to be useful for studying the function of non-photosynthesis-related genes in the albino bamboo mutants with aberrant chloroplast genome. The combined use of this SSH library with microarray analysis will provide a powerful analytical tool for future studies of the bamboo genome.     

Identification and characterization of differentially expressed ESTs of <Emphasis Type="Italic">Gossypium barbadense</Emphasis> infected by <Emphasis Type="Italic">Verticillium dahliae</Emphasis> with suppression subtractive hybridization

The wilt defense reaction of cotton is a complicated continuous process and involves a battery of genes. In this study, we adopted the suppression subtractive hybridization (SSH) technique to isolate differentially expressed ESTs from Gossypium barbadense variety 7124 during the Verticillium wilt defense process. An array of 1165 clones from the subtractive library has been screened with reverse northern blotting, of which 131 ESTs were considered as overexpressed and 16 ESTs were downregulated. Sequence analysis and blast search showed that 83 ESTs were homologous to 45 unique sequences in the databases. Among all these differentially expressed ESTs, at least three kinds of genes were characterized. The majority of ESTs with a deduced identity as aerobic metabolism enzymes were strongly expressed in the infection process. Likewise, ESTs similar to those reported for pathogen-related protein genes were also picked out in this study. These ESTs, in combination with other kinase-like genes and a defensin-like EST, constituted an assembly of genes which responded during pathogenic infection. These results imply that sea-island cotton undergoes strong oxidative stress and results in a series of defense responses when attacked by V. dahliae. To our knowledge, this is the first report on the isolation of global ESTs during the sea-island cotton defense reaction.__________From Molekulyarnaya Biologiya, Vol. 39, No. 2, 2005, pp. 214–223.Original English Text Copyright © 2005 by Zuo, Wang, Wu, Chai, Sun, Tang.This article was submitted by the authors in English.     

Identification and characterization of differentially expressed ESTs of Gossypium barbadense infected by Verticillium dahliae with suppression subtractive hybridization

Cotton wilt defense reaction is a complicated continuous process and involves a battery of genes. In this study, we adopted suppression subtractive hybridization (SSH) technique to isolate differentially expressed ESTs from Gossypium barbadense variety 7124 during Verticillium wilt defense process. An array of 1165 clones from the subtractive library has been screened with reverse northern blotting, of which 131 ESTs were considered as over-expressed and 16 ESTs were down-regulated. Sequence analysis and blast search showed that 83 ESTs were homologous to 45 unique sequences in the databases. Among all these differentially expressed ESTs, at least three kinds of genes were characterized. The majority of ESTs with deduced identity to aerobic metabolism enzymes strongly expressed in the infection process. Likewise, ESTs similar to those reported for pathogen-related protein genes were also picked out in this study. These ESTs in combination with other kinase-like genes and a defensin-like EST constituted an assembly of genes responded during pathogens' infection. These results imply that sea-island cotton undergoes strong oxidative stress and results in a series of defense responses when attacked by V. dahliae. To our knowledge, this is the first report on the isolation of global ESTs during sea-island cotton defense reaction.     

性逆转石斑鱼性腺差异表达基因的克隆和筛选

以 17α 甲基睾丸酮 (17α MT)饲喂 2～ 4龄赤点石斑鱼 (Epinephelusakaara) ,成功地促使其性转变为具有生殖功能的雄鱼 .应用抑制性差减杂交 (SSH)技术构建了石斑鱼性反转前后性腺组织的SMARTcDNA文库及其cDNA差减文库 ,从中随机挑取 12 0 0个克隆进行了PCR和斑点杂交筛选 ,得到 12 0个差异表达cDNA片段 .挑选 71个cDNA克隆测序 ,将所测序列经GenBank检索和生物信息学比较 ,发现有 5 1个cDNA片段序列无明显的同源性 ,2 0个片段与报道的基因有较高同源性 .在这 2 0个具同源性的片段中有 3个片段可能是与性别分化密切相关的重要功能基因 ,它们是钙调蛋白基因、活性蛋白激酶C受体基因和一氧化氮合酶蛋白抑制剂基因 .这 3个基因被分别命名为鱼钙调蛋白基因 (GenBankaccession :AY2 8136 3)、鱼活性蛋白激酶C受体基因 (GenBankaccession :AY2 8136 4)和鱼一氧化氮合酶蛋白抑制剂基因 (GenBankaccession :AY2 8136 5 ) .     

Differential gene expression profile in Pseudomonas putida NBRIC19-treated wheat (Triticum aestivum) plants subjected to biotic stress of Parthenium hysterophorus

The inoculation of Pseudomonas putida NBRIC19 protected wheat plant from phytotoxic effect of Parthenium hysterophorus (Parthenium) and enhanced root length, shoot length, dry weight, spike length and chlorophyll content. With the aim to screen for genes differentially expressed in P. putida NBRIC19-inoculated wheat grown along with Parthenium (WPT), the suppression subtractive hybridization (SSH) methodology was employed. The SSH analysis was performed with WPC (uninoculated wheat grown along with Parthenium) as driver and WPT as tester. The cDNA library, enriched with differentially expressed ESTs (expressed sequence tags), were constructed from WPT. Following an initial screen of 165 ESTs in our library, 32 ESTs were identified, annotated and further validated by semiquantitative RT-PCR. The differentially expressed ESTs were associated with general stress response, defense response, growth and development, metabolic process, photosynthesis, signal transduction, and some other with unknown function. Five ESTs showing downregulation in expression level in response to Parthenium got upregulated due to P. putida NBRIC19 inoculation and further validated by quantitative real time PCR analysis at different time intervals viz. 15, 30, 45 and 90 days. SSH has been implemented for the first time to gain insights into molecular events underlying successful role of P. putida NBRIC19 in providing protection to wheat against Parthenium. The information generated in this study provides new clues to aid the understanding of genes corresponding to differentially expressed ESTs putatively involved in allelopathic interactions. Further characterization and functional analysis of these genes may provide valuable information for future studies of the molecular mechanism by which plants adapt to allelopathic effect of Parthenium.     

Elongation of Stem Internodes in the Japanese Morning Glory (Pharbitis nil) in Relation to Auxin Destruction

The relationship between auxin destruction and stem internode elongation was investigated in the vines of the Japanese morning glory (Pharbitis nil Choisy). In young plants an age-dependent gradient was demonstrated in which the decreasing rate of elongation of older internodes correlated with an increasing ability of such tissue to destroy indoleacetic acid. Fragments of tissue from old internodes when incubated with indoleacetic acid (IAA), destroyed the hormone immediately and rapidly; in contrast, young, rapidly elongating internode tissue destroyed IAA only after a lag of several hours. In older plants the gradient was more erratic towards the middle of the plant but old and young tissue behaved as in young plants, i.e., old internodes destroyed IAA rapidly whereas young internodes did not. It appears reasonable to conclude that cessation of elongation in maturing internodes is brought about by developing an internal environment in which auxin is rapidly destroyed.     

西藏八角莲与桃儿七根及根茎SSH文库的建立

以西藏八角莲(Dysosma tsayuensis Ying)和桃儿七[Sinopodophyllum hexandrum(Royle)Ying]为材料,构建其根及根茎的SSH文库,从中筛选鬼臼类植物属种间与鬼臼毒素生物合成相关的差异表达基因。从文库中随机挑取201个阳性克隆测序后得到183条ESTs。去除载体序列和冗余序列,聚类拼接得到17个西藏八角莲的unique ESTs。经BLAST同源比较和功能查寻,有功能注释的unique ESTs共12个,占70.6%,所编码的蛋白涉及光合作用、合成代谢、转录调控等功能;无功能注释和匹配结果的共5个,占29.4%。该研究成功构建了西藏八角莲和桃儿七SSH文库,为进一步揭示鬼臼毒素生物合成途径及其调控机制奠定了基础。     

The role of nodal regions in growth of Xanthium (Compositae) stem

Vegetative Xanthium plants grown under noninductive conditions were marked with India ink along the stem and photographed at three consecutive time intervals. Relative elemental rates (d[dX/dt]/dX) of stem elongation were estimated from displacement of marks during stem elongation. Young internodes elongated with constant relative elemental rates of 0.2 day^-1. Older internodes displayed an acropetal pattern of elongation in which the basal segments of an internode stopped elongating first and the apical portion last. Nodal regions elongated with very small relative elemental rates of 0.05 day^-1. Rates decreased as the age of the internodes and nodes increased and stopped shortly after Leaf Plastochron Index 9.     

STEM ELONGATION OF XANTHIUM PLANTS PRESENTED IN TERMS OF RELATIVE ELEMENTAL RATES

Vegetative Xanthium plants grown under noninductive conditions were marked along the stem with India ink and photographed during three successive days. The relative elemental rates of stem elongation [d(dX/dt)/dX] were estimated for 18 plants between 15 and 18 plastochrons. On the average, only the 8.0 cm terminal part of the stem was elongating in this group of plants. Young internodes were elongating at constant relative elemental rates ([d(dX/dt)/dX] was about 0.2 days^–1); nodal portions of the stem beteween two young internodes were not elongating. Internodes longer than 2 cm displayed an acropetal pattern of elongation in which the basal part of an internode stopped elongating and matured first and the apical portion last. The pattern of elongation of the stem could be best approximated to a set of cascading waterfalls with declining plateaus in the direction of the water flow. The acropetal pattern of individual internode elongation observed in Xanthium was similar to those reported for Helianthus and Phaseolus internode growth.     

Identification of genes associated with fruit ripening in Ziziphus jujuba using suppression subtractive hybridization approach

Owing to the high nutritional value and extensive medicinal use of its products, Chinese jujube (Ziziphus jujuba Mill) is one of the most important fruit crops in China. However, jujube fruits are highly perishable and thus have a short shelf life, which is a serious hindrance to the industry. Better understanding of the molecular mechanisms underlying jujube fruit softening is fundamental to overcome the problem. Thus, both forward and reverse suppression subtractive hybridization (SSH) cDNA libraries were constructed to identify differentially expressed genes for fruit at half-red ripening stage and complete red stage. As a result of dot blot confirmation, a total of 154 differentially expressed genes were identified. After removed low-quality regions and screened for vector contamination, blasted with the non-redundant NCBI databases, 78.6 % of sequences exhibited high homology to previously identified or putative proteins. All the ESTs were annotated and classified according to the terms of the three main Gene Ontology vocabularies using the Blast2GO software. Furthermore, the quantitative real-time PCR was carried out for 17 genes to validate the genes differentially expressed from the SSH libraries. And the full-length sequences of galactose oxidase and aldehyde dehydrogenase genes were obtained. It is the first step to explore the functional genomics and regulatory networks during the storage period of jujube fruit. The identification of the genes differentially expressed is helpful to understand the ripening and softening of the jujube fruit at the molecular level.     

Cuticle Biosynthesis in Rapidly Growing Internodes of Deepwater Rice

Submergence induces rapid elongation of deepwater rice (Oryza sativa L.) internodes. This adaptive feature allows deepwater rice to grow out of the water and to survive flooding. The growth response of submerged deepwater rice plants is, ultimately, elicited by gibberellin (GA). Little attention has been given to the synthesis and role of the cuticle during plant growth. We investigated two questions regarding the cuticle in rapidly elongating deepwater rice internodes: (a) how does cuticle formation keep pace with internodal growth, which can reach rates of up to 5 mm/h; and (b) does the cuticle contribute to tissue stress in rice internodes? Treatment with GA for 48 h caused an up to 60-fold increase in the incorporation of [14C]palmitic acid and an up to 6-fold increase in the incorporation of [14C]oleic acid into the cuticle of growing internodes. GA also caused a qualitative change in the incorporation pattern of palmitic acid into several cutin monomers, the most prominent of which was tentatively identified by thin-layer chromatography as a derivative of dihydroxyhexadecanoic acid. Rapidly growing plant organs exhibit longitudinal tissue stress: the epidermal cell layer is under tension with a tendency to contract, whereas the internal cells are under compression with a tendency to expand. As a result of tissue stress, longitudinally sliced sections of elongating internodes bend outward upon isolation from the plant. Treating rapidly growing rice internodes with cutinase reduced such outward bending, indicating that the cuticle contributes to tissue stress. Based on these results, we propose that rapidly elongating structures such as deepwater rice internodes constitute an excellent system to study cuticle formation at the biochemical and cellular level.     

Identification of the unfolded protein response (UPR)-related genes from Bombyx mori cell lines by a subtractive hybridization approach

The baculovirus expression vector system (BEVS) is one of the powerful insect cell systems for heterologous protein expression. However, over-expression of heterologous proteins in this system sometimes results in protein misfolding and aggregation because of insufficient levels of folding catalysts. In previous study using the differential screening (DS) method, we isolated only 40 differentially expressed genes after treatment with tunicamycin, an unfolded protein response (UPR) inducer. To isolate more protein folding catalysts from insect, we performed suppressive subtractive hybridization (SSH) with untreated and tunicamycin-treated Bm5 cell lines in this study. We could isolate 366 differentially expressed clones by SSH method and produced expressed sequence tags (ESTs). ESTs included the UPR pathway-related genes involved in protein folding, including heat shock proteins, molecular chaperones, foldases, as well as glycosylation and secretory pathway related genes. Identification of the tunicamycin responsive genes using SSH provides more information about the UPR-related genes in insect cells, and will facilitate modifications of the protein folding pathway in the ER to improve heterologous protein expression.     

Suppression subtractive hybridization identifies differentially expressed genes in Brassica napus chlorophyll-reduced mutant

Suppressive subtraction hybridization (SSH) was used to identify differentially expressed genes caused by a chlorophyll-reduced mutation in B. napus. The cDNA fragments, derived from SSH positive subtractive library (tester: normal wild type, driver: mutant) were cloned into pMD18-T vector. Two hundred SSH cDNA clones were screened by dot blot array, and 151 clones were identified as differentially expressed cDNA fragments in Cr3529 line. Thirty-six positive clones which showed marked expression differences were selected and sequenced. After redundant cDNAs were removed, 33 differentially expressed unique cDNA section clones were obtained. Among the 33 clones, two clones possess different parts of the cDNA sequence of the same gene coding geranylgeranyl reductase, four clones belong to unknown proteins, and the rest share homology to genes of diverse class. Sequence analysis showed that at least 12 genes were discovered to be related to the photosynthesis, seven of them coded the proteins which belong to the subunit of photosystem 2. RNA gel blot analysis showed that compared with 3529, the gene expression of the chlorophyll a/b-binding protein Lhcb2 in photosystem 2 declined markedly in the cotyledons and seedling leaves of Cr3529, indicating that the reduced light-harvesting complex 2 accumulation in thylakoid membrane of Cr3529 was due to the decrease of the related gene mRNA level for translation.     

落叶松体细胞胚成熟阶段差异表达的基因及部分基因的表达谱分析

摘要: 为研究落叶松体细胞胚胎发生的分子机理, 文章以日本落叶松×华北落叶松杂种无性系胚性细胞系Y35体细胞胚成熟阶段培养物的cDNA为实验组, 继代培养阶段胚性愈伤组织的cDNA为对照组, 利用抑制性消减杂交技术(Suppression subtractive hybridization, SSH)构建了体细胞胚成熟阶段的差异表达基因文库。随机选取800个阳性克隆进行测序, 共获得468个UniGenes, 共将其分为19类, 功能分析结果表明: 这些UniGenes可能参与代谢、转录、信号转导、转运、细胞生长分裂、细胞结构、细胞命运、蛋白质合成与降解、防御等与个体发育密切相关的生物学过程。对部分ESTs的表达谱进行分析, 结果表明这些ESTs均在落叶松体细胞胚胎发生的不同阶段特异表达。     

Identification of differentially expressed genes in seeds of two near-isogenic Brassica napus lines with different oil content

The regulation of seed oil synthesis in rapeseed is largely unknown. In this study, we compared the gene expression during seed development between two lines of Brassica napus with a 10% difference in oil content. We isolated the immature seeds 15 and 25 days after flowering at periods preceding and including the major accumulation of storage oils and proteins. The differentially expressed gene clones between the two rape lines were isolated by subtractive suppression hybridization (SSH). All SSH clones were arrayed and screened by dot blot hybridization, followed by RT-PCR analysis for selected clones. A total of 217 cDNA clones corresponding to 30 genes were found to have a high expression in seeds with high oil content. Six genes were highly expressed in seeds with low oil content. Northern blot and enzyme activity analysis demonstrated a change in expression pattern of several genes. The results provide information on gene-encoding factors responsible for the regulation of oil synthesis. The possible role of these genes in seeds is discussed. The genes in this study may be suitable as novel targets for genetic improvement of seed oil content and may also provide molecular markers for studies of rape breeding.