Computational prediction and experimental verification of the gene encoding the NAD+/NADP+-dependent succinate semialdehyde dehydrogenase in Escherichia coli
Computational prediction and experimental verification of the gene encoding the NAD+/NADP+-dependent succinate semialdehyde dehydrogenase in Escherichia coli
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DOI：
10.1128/jb.01027-07
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发表时间：
2007-11-01
影响因子：
3.2
通讯作者：
Vitkup, Dennis
中科院分区：
文献类型：
--
作者：
Fuhrer, Tobias;Chen, Lifeng;Vitkup, Dennis
虽然NAD（+）依赖的琥珀酸半醛脱氢酶活性在25年前首次在大肠杆菌中被描述，但迄今为止，负责基因仍然难以捉摸。作为早期开发的代谢网络间隙填充算法的概念实验证明，我们在这里证明了E。coli基因yneI负责该活性。我们的生化结果表明，yneI编码的琥珀酸半醛脱氢酶可以使用NAD（+）或NADP（+）将琥珀酸半醛氧化为琥珀酸。该基因受琥珀酸半醛诱导，表达数据表明yneI在大肠杆菌的一般氮代谢中起独特的生理作用。杆菌特别是，我们证明了使用突变体生长实验，yneI基因具有重要的，但不是必需的，精氨酸生长过程中的作用，并可能具有腐胺作为氮源生长过程中的重要功能。由功能同源物gabD编码的NADP（+）依赖性琥珀酸半醛脱氢酶活性似乎对氮限制条件下的氮代谢很重要。与此相反，yneI编码的活性主要起着防止琥珀酸半醛毒性积累的阀门的作用。可用的基因组序列的分析表明，直向同源的yneI和gabD广泛分布在整个系统发育空间。
Although NAD(+)-dependent succinate semialdehyde dehydrogenase activity was first described in Escherichia coli more than 25 years ago, the responsible gene has remained elusive so far. As an experimental proof of concept for a gap-filling algorithm for metabolic networks developed earlier, we demonstrate here that the E. coli gene yneI is responsible for this activity. Our biochemical results demonstrate that the yneI-encoded succinate semialdehyde dehydrogenase can use either NAD(+) or NADP(+) to oxidize succinate semialdehyde to succinate. The gene is induced by succinate semialdehyde, and expression data indicate that yneI plays a unique physiological role in the general nitrogen metabolism of E. coli. In particular, we demonstrate using mutant growth experiments that the yneI gene has an important, but not essential, role during growth on arginine and probably has an essential function during growth on putrescine as the nitrogen source. The NADP(+)-dependent succinate semialdehyde dehydrogenase activity encoded by the functional homolog gabD appears to be important for nitrogen metabolism under N limitation conditions. The yneI-encoded activity, in contrast, functions primarily as a valve to prevent toxic accumulation of succinate semialdehyde. Analysis of available genome sequences demonstrated that orthologs of both yneI and gabD are broadly distributed across phylogenetic space.