Heterologous microarray experiments allow the identification of the early events associated with potato tuber cold sweetening.
Heterologous microarray experiments allow the identification of the early events associated with potato tuber cold sweetening.
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DOI：
10.1186/1471-2164-9-176
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发表时间：
2008-04-16
期刊：
影响因子：
4.4
通讯作者：
Perata P
中科院分区：
文献类型：
--
作者：
Bagnaresi P;Moschella A;Beretta O;Vitulli F;Ranalli P;Perata P
马铃薯块茎冷诱导甜味（CIS）自100多年前被发现以来，一直受到广泛的研究。一些碳水化合物相关基因似乎参与了这一过程。然而，许多不确定性仍然存在，因为每个基因对该过程的相对贡献往往是不清楚的，可能是实验系统的异质性的结果。一些与CIS相关的酶，如β-淀粉酶和转化酶，仍有待在序列水平上鉴定。此外，很少有人知道的早期事件，触发CIS和参与/协会与CIS的基因不同的碳水化合物相关基因。这些不确定性中的许多可以通过分析实验来解决，但是没有用于马铃薯的基因芯片，并且马铃薯cDNA斑点阵列（TIGR）的生产最近已经停止。为了获得与CIS相关的早期转录事件的全貌，我们研究了市售的番茄Affyssin基因芯片是否可用于识别哪些马铃薯冷响应基因家族成员应通过实时（RT）-PCR（qPCR）进行进一步详细研究。生成番茄-马铃薯全局匹配文件用于解释异源数据集的各个方面，包括检索最佳匹配马铃薯对应物和注释，以及建立高度同源基因的核心集。鉴定了几个冷响应基因，并通过qPCR在26天内详细研究了它们的表达模式。我们检测了碳水化合物相关基因mRNA积累的双相行为，并且我们的组合GeneChip-qPCR数据在序列水平上鉴定了先前报道参与CIS的酶活性，如β-淀粉酶和转化酶。基因芯片数据还揭示了伴随CIS的重要过程，例如诱导氧化还原和乙烯相关基因。我们的全局匹配文件策略被证明是准确解释异源数据集的关键，并表明类似的方法可能对其他物种也有成效。与CIS相关的早期事件的转录谱分析揭示了涉及糖、氧化还原和激素信号传导的事件的复杂网络，这些事件可以串联或平行地起作用。在序列水平上鉴定长期以来被认为在CIS中起作用的各种酶为进一步理解这种现象提供了分子工具。
Since its discovery more than 100 years ago, potato (Solanum tuberosum) tuber cold-induced sweetening (CIS) has been extensively investigated. Several carbohydrate-associated genes would seem to be involved in the process. However, many uncertainties still exist, as the relative contribution of each gene to the process is often unclear, possibly as the consequence of the heterogeneity of experimental systems. Some enzymes associated with CIS, such as β-amylases and invertases, have still to be identified at a sequence level. In addition, little is known about the early events that trigger CIS and on the involvement/association with CIS of genes different from carbohydrate-associated genes. Many of these uncertainties could be resolved by profiling experiments, but no GeneChip is available for the potato, and the production of the potato cDNA spotted array (TIGR) has recently been discontinued. In order to obtain an overall picture of early transcriptional events associated with CIS, we investigated whether the commercially-available tomato Affymetrix GeneChip could be used to identify which potato cold-responsive gene family members should be further studied in detail by Real-Time (RT)-PCR (qPCR). A tomato-potato Global Match File was generated for the interpretation of various aspects of the heterologous dataset, including the retrieval of best matching potato counterparts and annotation, and the establishment of a core set of highly homologous genes. Several cold-responsive genes were identified, and their expression pattern was studied in detail by qPCR over 26 days. We detected biphasic behaviour of mRNA accumulation for carbohydrate-associated genes and our combined GeneChip-qPCR data identified, at a sequence level, enzymatic activities such as β-amylases and invertases previously reported as being involved in CIS. The GeneChip data also unveiled important processes accompanying CIS, such as the induction of redox- and ethylene-associated genes. Our Global Match File strategy proved critical for accurately interpretating heterologous datasets, and suggests that similar approaches may be fruitful for other species. Transcript profiling of early events associated with CIS revealed a complex network of events involving sugars, redox and hormone signalling which may be either linked serially or act in parallel. The identification, at a sequence level, of various enzymes long known as having a role in CIS provides molecular tools for further understanding the phenomenon.
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影响因子：
12.3
作者：
Gentleman RC;Carey VJ;Bates DM;Bolstad B;Dettling M;Dudoit S;Ellis B;Gautier L;Ge Y;Gentry J;Hornik K;Hothorn T;Huber W;Iacus S;Irizarry R;Leisch F;Li C;Maechler M;Rossini AJ;Sawitzki G;Smith C;Smyth G;Tierney L;Yang JY;Zhang J
通讯作者：
Zhang J
影响因子：
7.4
作者：
Gilmour, SJ;Sebolt, AM;Thomashow, MF
通讯作者：
Thomashow, MF
影响因子：
14.9
作者：
Fei Z;Tang X;Alba R;Giovannoni J
通讯作者：
Giovannoni J
影响因子：
6.9
作者：
Balmer, Y;Vensel, WH;Hurkman, WJ
通讯作者：
Hurkman, WJ
DOI：
10.1073/pnas.0511040103
发表时间：
2006-02-21
影响因子：
11.1
作者：
Balmer, Y;Vensel, WH;Buchanan, BB
通讯作者：
Buchanan, BB