用从头预测蛋白结构的方法注释嗜盐古菌Halobacterium sp. NRC-1的基因组

  随着基因组全序列的不断测定，对基因组的注释工作也在不断展开，但是，无论是面对那个生物的基因组，基因组中的未知功能基因任然占有相当大的比例。这也是系统生物学发展的一个瓶颈。

  这篇文章介绍了这个研究领域的一些研究，作者利用Rosetta这个蛋白结构从头预测工具，预测了嗜盐古菌Halobacterium sp. NRC-1基因组中1185个蛋白或结构域的三维结构。然后将这些预测的结构检索Protein Data Bank数据库，鉴别它们的折叠类型，并推测它们可能的功能。然后，作者结合其他几种蛋白功能预测的方法，如蛋白质相互作用，预测操纵子，系统发生图谱相似性以及结构域融合等，对这些蛋白进行了进一步分析。结果证明，这些方法组合起来对我们对Halobacterium sp. NRC-1的化学分类，潜在的原噬菌体，古菌的转录调控的认识起了很大的作用。

Halobacterium NRC-1简介：
The archaeon Halobacterium NRC-1 is an extreme halophile that thrives in saturated brine environments such as the Dead Sea and solar salterns. It offers a versatile and easily assayed system for an array of well-coordinated physiologies that are necessary for survival in its harsh environment. It has robust DNA repair systems that can efficiently reverse the damages caused by a variety of mutagens including UV radiation and desiccation/re-hydration cycles. Halobacterium NRC-1 adapts its metabolism to anaerobic conditions with the synthesis of bacterorhodopsin, which facilitates the conversion of energy from light into ATP. The completely sequenced genome of Halobacterium NRC-1 (containing ~2,600 genes) has provided insights into many of its physiological capabilities, however nearly half of all genes encoded in the halobacterial genome have no known function.

参考文献：

Richard Bonneau, Nitin S Baliga, EricW Deutsch, Paul Shannon and Leroy Hood.
Comprehensive de novo structure prediction in a systems-biology context for the archaea Halobacterium sp. NRC-1.
Genome Biology 2004, 5:R52.
http://genomebiology.com/2004/5/8/R52