Minor Isozymes Tailor Yeast Metabolism to Carbon Availability
Minor Isozymes Tailor Yeast Metabolism to Carbon Availability
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DOI：
10.1128/msystems.00170-18
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发表时间：
2019-01-01
期刊：
影响因子：
6.4
通讯作者：
Rabinowitz, Joshua D.
中科院分区：
文献类型：
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作者：
Bradley, Patrick H.;Gibney, Patrick A.;Rabinowitz, Joshua D.
同工酶是序列不同但催化相同化学反应的酶。尽管它们明显冗余，同工酶往往保留在进化的时间，这表明他们有助于健身。我们开发了一种无监督的计算方法，以确定环境条件下，同工酶可能作出健身的贡献。该方法分析已发表的基因表达数据，以找到诱导差异同工酶表达的特定实验扰动。在酵母中，我们发现，同工酶强烈富集在中央碳代谢的途径，许多同工酶对呼吸发酵转变过程中表现出相关的表达。基于这些观察结果，我们将功能分配给两种次要的中心碳同工酶，乌头酸酶2（ACO2）和丙酮酸激酶2（PYK2）。ACO2在发酵过程中表达，并在葡萄糖受限时证明是有利的。PYK2在呼吸过程中表达，并证明有利于在三碳基质上生长。只有当主要丙酮酸激酶携带反映PYK2变构调节的突变时，PYK2的缺失才能通过表达该酶来挽救。因此，中央碳同工酶有助于优化变构代谢调节下广泛的潜在营养条件下，而只需要少量的转录states.IMPORTANCE基因复制是一个主要的进化途径，以新的蛋白质功能。通常情况下，重复的基因要么积累突变并降解为假基因，要么被保留并在功能上发生分歧。然而，一些重复的基因表现出长期的持续性，而没有明显获得新的功能。一类重要的同工酶由在相同区室中催化相同反应的那些同工酶组成，其中一种同工酶的敲除不会引起已知的功能缺陷。在这里，我们提出了一种方法来分配特定的功能角色，看似多余的同工酶。首先，通过计算分析基因表达数据以确定同工酶表达发散的条件。然后，在这些条件下比较敲除。这种方法表明，许多酵母同工酶的表达发散响应碳的可用性和碳源操作可以诱导健身表型看似多余的同工酶。这些适应性表型的驱动因素是差异变构酶调节，表明同工酶趋异以实现更优化的代谢控制。
Isozymes are enzymes that differ in sequence but catalyze the same chemical reactions. Despite their apparent redundancy, isozymes are often retained over evolutionary time, suggesting that they contribute to fitness. We developed an unsupervised computational method for identifying environmental conditions under which isozymes are likely to make fitness contributions. This method analyzes published gene expression data to find specific experimental perturbations that induce differential isozyme expression. In yeast, we found that isozymes are strongly enriched in the pathways of central carbon metabolism and that many isozyme pairs show anticorrelated expression during the respirofermentative shift. Building on these observations, we assigned function to two minor central carbon isozymes, aconitase 2 (ACO2) and pyruvate kinase 2 (PYK2). ACO2 is expressed during fermentation and proves advantageous when glucose is limiting. PYK2 is expressed during respiration and proves advantageous for growth on three-carbon substrates. PYK2's deletion can be rescued by expressing the major pyruvate kinase only if that enzyme carries mutations mirroring PYK2's allosteric regulation. Thus, central carbon isozymes help to optimize allosteric metabolic regulation under a broad range of potential nutrient conditions while requiring only a small number of transcriptional states.IMPORTANCE Gene duplication is one of the main evolutionary paths to new protein function. Typically, duplicated genes either accumulate mutations and degrade into pseudogenes or are retained and diverge in function. Some duplicated genes, however, show long-term persistence without apparently acquiring new function. An important class of isozymes consists of those that catalyze the same reaction in the same compartment, where knockout of one isozyme causes no known functional defect. Here we present an approach to assigning specific functional roles to seemingly redundant isozymes. First, gene expression data are analyzed computationally to identify conditions under which isozyme expression diverges. Then, knockouts are compared under those conditions. This approach revealed that the expression of many yeast isozymes diverges in response to carbon availability and that carbon source manipulations can induce fitness phenotypes for seemingly redundant isozymes. A driver of these fitness phenotypes is differential allosteric enzyme regulation, indicating isozyme divergence to achieve more-optimal control of metabolism.