Resolving the Problem of Orphan Enzyme Activities

描述(由申请人提供)：一个新测序的基因组的价值直接取决于我们为该基因组中的基因分配功能的能力。在这样一个时代，病原体基因组可能会在分离出病原体后不久就被完全测序，而且测序能力已经超过了实验者在实验室检查每个单独生物体内的大量基因的能力，这一点尤其正确。不幸的是，分配基因功能的能力没有跟上测序结果的步伐，许多新基因组中的很大一部分基因仍然没有分配。我们的团队和其他人还发现了另一个与无法分配基因功能有关的问题，即先前表征的酶活性没有分配的序列数据。事实上，超过三分之一的具有指定E.C.编号的活动没有与它们相关的基因或蛋白质序列信息。这些“孤儿酶活性”代表着生物医学研究中的一个重大问题和机遇。最值得注意的是，只要这些活动仍然是“孤立的”，并且没有序列，它们就永远不会被预测为新测序基因组中任何基因的功能。我们的假设是，在这些孤儿活动和许多目前没有指定功能的基因之间可能存在显著的重叠。因此，对于现代基因组驱动的生物学来说，寻找孤儿活动的序列至关重要。我们建议开发一种系统的方法来解决孤儿活动的问题，方法是识别与每个此类活动相关的基因序列。我们将进行初步的文献评估阶段，确认每个活动的孤立状态，我们预计这一阶段将产生200-300个人工孤儿，立即将大量与序列相关的活动添加到公共数据库中。随后将开展实验室工作，以确定21项主要的孤儿活动，并帮助为今后大规模和小规模的孤儿识别工作奠定基础，最终目标是能够为每项活动确定至少一个基因。公共卫生相关性：该项目将生成一份显示缺乏序列的孤儿活动清单，捕获与这些孤儿相关的文献和其他关键数据，解决数百项人工孤儿活动，确定21项主要孤儿活动的序列，并为其他调查人员提供识别其他孤儿的指南。200-300个人工孤儿活动和21个真正的孤儿活动的解决将有助于减少酶学上浪费的重复工作，并将提高未来所有基因组注释的质量。

DESCRIPTION (provided by applicant): The value of a newly sequenced genome is directly dependent on our ability to assign function to the genes within that genome. This is especially true in an era in which pathogen genomes may be fully sequenced shortly after a pathogen is isolated, and in which sequencing capacity has already outstripped the ability of experimentalists to examine a large number of genes within each individual organism in the lab. Unfortunately, the ability to assign gene functions has not kept pace with sequencing output, and a significant fraction of the genes in many new genomes remain unassigned. Our group and others have also identified another problem related to the inability to assign gene functions, that of previously characterized enzyme activities that have no assigned sequence data. In fact, over a third of activities with assigned E.C. numbers have neither gene nor protein sequence information associated with them. These "orphan enzyme activities" represent a significant problem and opportunity in biomedical research. Most notably, as long as these activities remain "orphan" and devoid of sequence, they will never be predicted as functions for any genes in newly sequenced genomes. It is our hypothesis that there is likely to be significant overlap between these orphan activities and many of the genes that currently have no assigned function. As a consequence, it is critically important for modern, genome-driven biology to find sequences for orphan activities. We propose to develop a systematic approach for resolving the problem of orphan activities by identifying a gene sequence associated with each such activity. We will carry out an initial literature evaluate stage that will confirm the orphan status of each activity, a phase that we expect will yield 200-300 artifactual orphans, immediately adding a large body of activities associated with sequence to public databases. This will be followed by laboratory work that will identify 21 major orphan activities and help lay the groundwork for future large- and small-scale orphan identifications, with the eventual goal of enabling the identification of at least one gene for each activity. PUBLIC HEALTH RELEVANCE: This project will generate a list of orphan activities with a demonstrated lack of sequence, capture literature and other key data related to those orphans, resolve hundreds of artifactual orphan activities, identify sequences for 21 major orphan activities, and provide guidelines for other investigators to identify additional orphans. The resolution of 200-300 artifactual orphan activities and 21 genuine orphan activities will help reduce wasteful duplicated efforts in enzymology and will enhance the quality of all future genome annotations.