Proteins of Unknown Biochemical Function: A Persistent Problem and a Roadmap to Help Overcome It
Proteins of Unknown Biochemical Function: A Persistent Problem and a Roadmap to Help Overcome It
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DOI：
10.1104/pp.15.00959
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发表时间：
2015-11-01
期刊：
影响因子：
7.4
通讯作者：
Hanson, Andrew D.
中科院分区：
文献类型：
--
作者：
Niehaus, Thomas D.;Thamm, Antje M. K.;Hanson, Andrew D.
测序的基因组数量正在迅速增加，但这些基因组中基因的功能注释远远落后。即使在拟南芥（Arabidopsis thaliana）中，也只有大约40%的酶和转运蛋白编码基因具有可靠的功能注释，而在非模式植物中这个数字甚至更低。未知基因的功能表征是一个挑战，但可以挖掘各种数据库（例如蛋白质定位和共表达）以提供线索。如果存在同源微生物基因，并且拟南芥中编码未知酶和转运蛋白的基因中约有一半具有微生物同源物，那么跨王国比较基因组学可以有力地补充基于植物的数据。多线证据可以加强预测和保证实验表征。在某些情况下，对基因上易处理的微生物进行相对快速的测试可以确定预测是否值得生化验证，这是昂贵的，需要专业技能。
The number of sequenced genomes is rapidly increasing, but functional annotation of the genes in these genomes lags far behind. Even in Arabidopsis (Arabidopsis thaliana), only approximately 40% of enzyme-and transporter-encoding genes have credible functional annotations, and this number is even lower in nonmodel plants. Functional characterization of unknown genes is a challenge, but various databases (e.g. for protein localization and coexpression) can be mined to provide clues. If homologous microbial genes exist-and about one-half the genes encoding unknown enzymes and transporters in Arabidopsis have microbial homologs-cross-kingdom comparative genomics can powerfully complement plant-based data. Multiple lines of evidence can strengthen predictions and warrant experimental characterization. In some cases, relatively quick tests in genetically tractable microbes can determine whether a prediction merits biochemical validation, which is costly and demands specialized skills.