Comparative genomics of bacterial and plant folate synthesis and salvage: predictions and validations.
Comparative genomics of bacterial and plant folate synthesis and salvage: predictions and validations.
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DOI：
10.1186/1471-2164-8-245
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发表时间：
2007-07-23
期刊：
影响因子：
4.4
通讯作者：
Hanson AD
中科院分区：
文献类型：
--
作者：
de Crécy-Lagard V;El Yacoubi B;de la Garza RD;Noiriel A;Hanson AD
叶酸合成和挽救途径在经典生物化学和遗传学中相对众所周知，但尚未进行比较基因组分析。来自数百种不同细菌和拟南芥的基因组序列的可用性使得能够使用 SEED 数据库及其工具进行此类分析。这项研究报告了分析结果，并将其与新的和现有的实验数据相结合。基于序列相似性以及基因的聚类、融合和系统发育分布，该分析得出了一些功能预测。对于细菌来说，这些因素包括存在新型 GTP 环化水解酶 I 和叶酰聚谷氨酸合酶基因家族，以及三功能对氨基苯甲酸合成基因。对于植物和细菌，预测包括“缺失”叶酸合成基因（folQ）和叶酸转运蛋白的身份，以及植物中叶酸回收酶的缺失。基因和生化测试证实了这些预测。对于细菌来说，这些结果表明，可以从比较基因组学中学到很多东西，甚至对于经过充分探索的主要代谢途径也是如此。对于植物来说，这些发现特别说明了通过分析哪些基因与原核同源基因相关，对具有原核同源基因的未知基因进行快速功能分配的潜力。更一般地说，我们的数据表明，植物和原核生物的组合基因组分析比单独对任一组进行单独检查更有效。
Folate synthesis and salvage pathways are relatively well known from classical biochemistry and genetics but they have not been subjected to comparative genomic analysis. The availability of genome sequences from hundreds of diverse bacteria, and from Arabidopsis thaliana, enabled such an analysis using the SEED database and its tools. This study reports the results of the analysis and integrates them with new and existing experimental data. Based on sequence similarity and the clustering, fusion, and phylogenetic distribution of genes, several functional predictions emerged from this analysis. For bacteria, these included the existence of novel GTP cyclohydrolase I and folylpolyglutamate synthase gene families, and of a trifunctional p-aminobenzoate synthesis gene. For plants and bacteria, the predictions comprised the identities of a 'missing' folate synthesis gene (folQ) and of a folate transporter, and the absence from plants of a folate salvage enzyme. Genetic and biochemical tests bore out these predictions. For bacteria, these results demonstrate that much can be learnt from comparative genomics, even for well-explored primary metabolic pathways. For plants, the findings particularly illustrate the potential for rapid functional assignment of unknown genes that have prokaryotic homologs, by analyzing which genes are associated with the latter. More generally, our data indicate how combined genomic analysis of both plants and prokaryotes can be more powerful than isolated examination of either group alone.
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影响因子：
15.9
作者：
FAN, HZ;BRUNHAM, RC;MCCLARTY, G
通讯作者：
MCCLARTY, G
影响因子：
2.7
作者：
Hyde, JE
通讯作者：
Hyde, JE
影响因子：
14.9
作者：
Chenna, R;Sugawara, H;Thompson, JD
通讯作者：
Thompson, JD
DOI：
10.1038/88584
发表时间：
2001-06-01
期刊：
NATURE STRUCTURAL BIOLOGY
影响因子：
--
作者：
Gourley, DG;Schüttelkopf, AW;Hunter, WN
通讯作者：
Hunter, WN
DOI：
10.1073/pnas.0404208101
发表时间：
2004-09-21
影响因子：
11.1
作者：
de la Garza, RD;Quinlivan, EP;Hanson, AD
通讯作者：
Hanson, AD