The essential gene set of a photosynthetic organism
The essential gene set of a photosynthetic organism
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DOI：
10.1073/pnas.1519220112
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发表时间：
2015-12-01
影响因子：
11.1
通讯作者：
Golden, Susan S.
中科院分区：
文献类型：
--
作者：
Rubin, Benjamin E.;Wetmore, Kelly M.;Golden, Susan S.
长聚球菌PCC 7942是一种用于研究光合作用和生物钟的模式生物，目前正在开发用于生产燃料、工业化学品和药品。为了鉴定一组影响长形螺适合度的基因和基因间区域，我们创建了一个类似于25万个转座子突变体的集合文库，并使用测序来确定插入位置。通过分析这些突变体的分布和存活，我们确定了生物体2,723个基因中的718个是在实验室条件下存活所必需的。关键基因集的有效性由其与保守基因的紧密重叠和核心生物过程的富集所支持。然而，我们的数据集与这些本质预测因子之间的差异导致了令人惊讶的生物学见解。其中一个发现是，大部分TCA循环中的基因是可缺性的，这表明S. elongatus不需要一个循环的TCA过程。此外，转座子突变文库的密度使得对非编码rna、调控元件和其他基因间区域的重要性的个人和整体陈述成为可能。通过这种方式，位于tRNALeu的I组内含子被广泛用于系统发育研究，在这里被证明对S. elongatus的生存至关重要。我们对长形丝瓜基因组中每个基因座的重要性进行了调查，为了解生物体的生理机能提供了强大的资源，并定义了光合生物生长所需的基本基因集。
Synechococcus elongatus PCC 7942 is a model organism used for studying photosynthesis and the circadian clock, and it is being developed for the production of fuel, industrial chemicals, and pharmaceuticals. To identify a comprehensive set of genes and intergenic regions that impacts fitness in S. elongatus, we created a pooled library of similar to 250,000 transposon mutants and used sequencing to identify the insertion locations. By analyzing the distribution and survival of these mutants, we identified 718 of the organism's 2,723 genes as essential for survival under laboratory conditions. The validity of the essential gene set is supported by its tight overlap with well-conserved genes and its enrichment for core biological processes. The differences noted between our dataset and these predictors of essentiality, however, have led to surprising biological insights. One such finding is that genes in a large portion of the TCA cycle are dispensable, suggesting that S. elongatus does not require a cyclic TCA process. Furthermore, the density of the transposon mutant library enabled individual and global statements about the essentiality of noncoding RNAs, regulatory elements, and other intergenic regions. In this way, a group I intron located in tRNALeu, which has been used extensively for phylogenetic studies, was shown here to be essential for the survival of S. elongatus. Our survey of essentiality for every locus in the S. elongatus genome serves as a powerful resource for understanding the organism's physiology and defines the essential gene set required for the growth of a photosynthetic organism.