The number of catalytic cycles in an enzyme's lifetime and why it matters to metabolic engineering.
The number of catalytic cycles in an enzyme's lifetime and why it matters to metabolic engineering.
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DOI：
10.1073/pnas.2023348118
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发表时间：
2021-03-30
影响因子：
11.1
通讯作者：
Millar AH
中科院分区：
文献类型：
--
作者：
Hanson AD;McCarty DR;Henry CS;Xian X;Joshi J;Patterson JA;García-García JD;Fleischmann SD;Tivendale ND;Millar AH
酶和其他蛋白质的持续替代占用了微生物和植物维持能量预算的一半。因此，较高的酶替代率降低了从微生物发酵到农作物的各种生物系统的生产率。然而，缺乏评估是什么驱动酶蛋白替代的标准，以及如何减少酶蛋白替代的指导方针。因此，我们使用一种新的标准(直到替换的催化循环[Ccr])比较了酶的寿命跨度，并将Ccr与酶反应化学相关联。我们的结论是：1)许多酶的失效是由于它们催化的反应造成的附带损害，2)这种损害和随之而来的酶替代成本是可以通过工程来减轻的，因此是合成生物学的有希望的目标。代谢工程使用酶作为部分，为特定的任务建立生物系统。虽然部件的工作寿命和故障模式是关键的工程性能指标，但在代谢工程中还不是这样，因为还不知道酶在体内保持多长时间的功能，也不知道是否累积恶化(磨损)、突然的随机故障或其他原因导致更换。因此，无法对酶进行改造以延长寿命和降低更换所需的高昂能源成本。在催化剂工程学的指导下，我们采用了直到替换的催化循环(CCR)作为体内酶功能寿命的度量。Ccr是一种酶在失效或替换之前在体内介导的催化循环的数量，即代谢通量速率/蛋白质周转率。我们使用估计的通量和测量的蛋白质周转率来计算∼100-200酶的CCR，每个酶来自乳酸乳球菌、酵母和拟南芥。这些生物的Ccr具有相似的范围(<；103到>；107)，但不同的中位数(乳酸菌和酵母为3-4×104，拟南芥为4×105)。在所有生物体中，底物、产物或机制可以攻击反应性氨基酸残基的酶的Ccr值中值明显低于其他酶。结合机理失活的文献，后者的发现支持这样的假设：1)反应化学造成的随机活性中心损伤是酶失效的重要原因，2)活性中心区域的反应性非催化残基可能是损伤易感性的贡献者。因此，通过酶工程来提高CCR和降低替代成本可能是有益和可行的。
The continuous replacement of enzymes and other proteins appropriates up to half the maintenance energy budget in microorganisms and plants. High enzyme replacement rates therefore cut the productivity of biosystems ranging from microbial fermentations to crops. However, yardsticks to assess what drives enzyme protein replacement and guidelines on how to reduce it are lacking. Accordingly, we compared enzymes’ life spans across kingdoms using a new yardstick (catalytic cycles until replacement [CCR]) and related CCR to enzyme reaction chemistry. We concluded that 1) many enzymes fail due to collateral damage from the reaction they catalyze, and 2) such damage and its attendant enzyme replacement costs are mitigable by engineering and are therefore promising targets for synthetic biology. Metabolic engineering uses enzymes as parts to build biosystems for specified tasks. Although a part’s working life and failure modes are key engineering performance indicators, this is not yet so in metabolic engineering because it is not known how long enzymes remain functional in vivo or whether cumulative deterioration (wear-out), sudden random failure, or other causes drive replacement. Consequently, enzymes cannot be engineered to extend life and cut the high energy costs of replacement. Guided by catalyst engineering, we adopted catalytic cycles until replacement (CCR) as a metric for enzyme functional life span in vivo. CCR is the number of catalytic cycles that an enzyme mediates in vivo before failure or replacement, i.e., metabolic flux rate/protein turnover rate. We used estimated fluxes and measured protein turnover rates to calculate CCRs for ∼100–200 enzymes each from Lactococcus lactis, yeast, and Arabidopsis. CCRs in these organisms had similar ranges (<103 to >107) but different median values (3–4 × 104 in L. lactis and yeast versus 4 × 105 in Arabidopsis). In all organisms, enzymes whose substrates, products, or mechanisms can attack reactive amino acid residues had significantly lower median CCR values than other enzymes. Taken with literature on mechanism-based inactivation, the latter finding supports the proposal that 1) random active-site damage by reaction chemistry is an important cause of enzyme failure, and 2) reactive noncatalytic residues in the active-site region are likely contributors to damage susceptibility. Enzyme engineering to raise CCRs and lower replacement costs may thus be both beneficial and feasible.
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影响因子：
64.8
作者：
Chatterjee, Abhishek;Abeydeera, N. Dinuka;Bale, Shridhar;Pai, Pei-Jing;Dorrestein, Pieter C.;Russell, David H.;Ealick, Steven E.;Begley, Tadhg P.
通讯作者：
Begley, Tadhg P.
DOI：
10.1099/mic.0.067975-0
发表时间：
2013-07
期刊：
Microbiology (Reading, England)
影响因子：
--
作者：
Arpino JAJ;Hancock EJ;Anderson J;Barahona M;Stan GV;Papachristodoulou A;Polizzi K
通讯作者：
Polizzi K
影响因子：
4.1
作者：
Bramski, Julia;Dick, Markus;Classen, Thomas
通讯作者：
Classen, Thomas
影响因子：
5.2
作者：
Hanson, Andrew D.;Amthor, Jeffrey S.;Ding, Yousong
通讯作者：
Ding, Yousong
DOI：
10.1073/pnas.1514240113
发表时间：
2016-03-22
影响因子：
11.1
作者：
Davidi, Dan;Noor, Elad;Milo, Ron
通讯作者：
Milo, Ron