Metagenomic gene discovery: How far have we moved into novel sequence space?
Metagenomic gene discovery: How far have we moved into novel sequence space?
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DOI：
10.1002/biot.200900235
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发表时间：
2009-12-01
影响因子：
4.7
通讯作者：
Cowan, Don
中科院分区：
文献类型：
--
作者：
Tuffin, Marla;Anderson, Dominique;Cowan, Don
宏基因组学出现在20世纪90年代末，作为一种工具，用于访问和研究环境中的集体微生物遗传物质。这项技术的出现引起了极大的兴奋，因为它为研究环境中丰富的微生物遗传多样性提供了新的机会和技术。宏基因组学已被广泛预测为进入蛋白质序列空间的新维度。十年过去了，我们回顾了我们使用宏基因组工具实际上已经进入新序列空间（以及蛋白质空间的其他方面）的程度。虽然已经通过宏基因组策略鉴定了几种新的酶活性和蛋白质结构，但在分离新蛋白质序列方面取得了最大的进展，其中一些没有近亲，形成了深分支谱系，甚至代表了新的家族。这对于糖基水解酶和脂肪酶/酯酶尤其如此，尽管事实上这些活性经常在宏基因组研究中筛选。然而，所采用的方法还有很大的改进余地，需要加以解决，以便扩大新的生物催化活动的范围。
Metagenomics emerged in the late 1990s as a tool for accessing and studying the collective microbial genetic material in the environment. The advent of the technology generated great excitement, as it has provided new opportunities and technologies for studying the wealth of microbial genetic diversity in the environment. Metagenomics has been widely predicted to access new dimensions of protein sequence space. A decade on, we review how far we have actually moved into new sequence space (and other aspects of protein space) using metagenomic tools. While several novel enzyme activities and protein structures have been identified through metagenomic strategies, the greatest advancement has been made in the isolation of novel protein sequences, some of which have no close relatives, form deeply branched lineages and even represent novel families. This is particularly true for glycosyl hydrolases and lipase/esterases, despite the fact that these activities are frequently screened for in metagenomic studies. However, there is much room for improvement in the methods employed and they will need to be addressed so that access to novel biocatalytic activities can be widened.