Genome-wide identification and functional analyses of calmodulin genes in Solanaceous species.
Genome-wide identification and functional analyses of calmodulin genes in Solanaceous species.
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DOI：
10.1186/1471-2229-13-70
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发表时间：
2013-04-27
影响因子：
5.3
通讯作者：
Cai XZ
中科院分区：
文献类型：
--
作者：
Zhao Y;Liu W;Xu YP;Cao JY;Braam J;Cai XZ
钙调素（CaM）是真核生物中一种主要的钙感受器。它结合钙并调节多种下游蛋白质的活性以响应钙信号。然而，对茄科物种中的CaM基因家族知之甚少，包括经济上重要的物种番茄（Solanum lycopersicum）和基因沉默模式植物本氏烟草（Nicotiana benthamiana）。此外，CaM在植物抗病性中的潜在功能在很大程度上仍不清楚。我们在茄科物种中进行了全基因组的CaM基因家族鉴定。利用生物信息学方法，从番茄、N. benthamiana和马铃薯（S. tuberosum）基因组，番茄有6个CaM基因，N.本塞姆亚那有7个CaM基因，马铃薯有4个CaM基因。序列比较分析表明，3个番茄基因SlCaM 3/4/5、2个马铃薯基因StCaM 2/3和2组N.本塞姆氏菌基因NbCaM 1/2/3/4和NbCaM 5/6编码相同的CaM蛋白，但基因含有不同的内含子/外显子结构，并且位于不同的染色体上。进一步的序列比较、基因结构分析和系统发育分析表明，茄科植物在进化过程中获得了一组新的CaM基因。这些新的钙调素基因是不寻常的，因为它们含有三个内含子，而不是只有一个典型的已知的钙调素基因在植物中的内含子。番茄CaM基因（SlCaM）在所有器官中都有表达。5'上游顺式作用元件的预测和表达分析表明，SlCaM基因具有对各种生物和非生物刺激高度响应的潜力。此外，SlCaM 2和SlCaM 6的沉默改变了一组信号和防御相关基因的表达，并导致对烟草脆裂病毒和卵菌病原体腐霉的抗性显著降低。CaM基因家族在茄科植物番茄、N.通过全基因组分析鉴定了benthamiana和马铃薯。这三种植物都有一小部分基因编码相同的CaM蛋白，这可能是植物保留冗余或增强数量基因功能的一种策略。此外，茄科植物在进化过程中还进化出一组新的CaM基因。CaM基因在植物对多种病原菌的抗病性中起重要作用。
Calmodulin (CaM) is a major calcium sensor in all eukaryotes. It binds calcium and modulates the activity of a wide range of downstream proteins in response to calcium signals. However, little is known about the CaM gene family in Solanaceous species, including the economically important species, tomato (Solanum lycopersicum), and the gene silencing model plant, Nicotiana benthamiana. Moreover, the potential function of CaM in plant disease resistance remains largely unclear. We performed genome-wide identification of CaM gene families in Solanaceous species. Employing bioinformatics approaches, multiple full-length CaM genes were identified from tomato, N. benthamiana and potato (S. tuberosum) genomes, with tomato having 6 CaM genes, N. benthamiana having 7 CaM genes, and potato having 4 CaM genes. Sequence comparison analyses showed that three tomato genes, SlCaM3/4/5, two potato genes StCaM2/3, and two sets of N. benthamiana genes, NbCaM1/2/3/4 and NbCaM5/6, encode identical CaM proteins, yet the genes contain different intron/exon organization and are located on different chromosomes. Further sequence comparisons and gene structural and phylogenetic analyses reveal that Solanaceous species gained a new group of CaM genes during evolution. These new CaM genes are unusual in that they contain three introns in contrast to only a single intron typical of known CaM genes in plants. The tomato CaM (SlCaM) genes were found to be expressed in all organs. Prediction of cis-acting elements in 5' upstream sequences and expression analyses demonstrated that SlCaM genes have potential to be highly responsive to a variety of biotic and abiotic stimuli. Additionally, silencing of SlCaM2 and SlCaM6 altered expression of a set of signaling and defense-related genes and resulted in significantly lower resistance to Tobacco rattle virus and the oomycete pathogen, Pythium aphanidermatum. The CaM gene families in the Solanaceous species tomato, N. benthamiana and potato were identified through a genome-wide analysis. All three plant species harbor a small set of genes that encode identical CaM proteins, which may manifest a strategy of plants to retain redundancy or enhanced quantitative gene function. In addition, Solanaceous species have evolved one new group of CaM genes during evolution. CaM genes play important roles in plant disease resistance to a variety of pathogens.
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