Computational modeling and evolutionary implications of biochemical reactions in bacterial microcompartments
Computational modeling and evolutionary implications of biochemical reactions in bacterial microcompartments
复制标题
细菌微区室生化反应的计算模型和进化意义
DOI：
10.1016/j.mib.2021.10.001
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发表时间：
2022
影响因子：
5.4
通讯作者：
Cameron, Jeffrey C
中科院分区：
文献类型：
--
作者：
Huffine, Clair A;Wheeler, Lucas C;Wing, Boswell;Cameron, Jeffrey C
BMC的计算建模启发了实验上难以测量的特征。对分解代谢BMC能力的重要探索仍然存在。氧气敏感性在包含BMC的酶中相对常见。BMC壳蛋白对带负电荷的代谢物具有选择性渗透性。细菌微区室（BMC）是至少在23个细菌门中发现的蛋白质封装区室。BMC包含多种代谢过程，这些代谢过程具有毒性或挥发性中间体、氧敏感性酶和辅因子或增加底物浓度以放大反应速率的共性。这些区室化的反应已经被计算建模，以探索封装的动力学，提出基于进化的问题，并开发新的BMC工程所需的更系统的理解。这些系统的许多关键方面仍然是未知的或未测量的，如底物透过蛋白质壳的渗透性，pH梯度的可行性，以及相关底物进入细胞的转运速率。这篇评论探讨了现有的BMC模型，占主导地位的蓝藻carboxysomes在文献中，并强调了潜在的重要领域的探索。
HighlightsComputational modeling of BMCs enlightens experimentally hard-to-measure features.Significant exploration remains of catabolic BMC capabilities.Oxygen sensitivity is relatively common across BMC-contained enzymes.BMC shell proteins are selectively permeable to negatively charged metabolites.Bacterial microcompartments (BMCs) are protein-encapsulated compartments found across at least 23 bacterial phyla. BMCs contain a variety of metabolic processes that share the commonality of toxic or volatile intermediates, oxygen-sensitive enzymes and cofactors, or increased substrate concentration for magnified reaction rates. These compartmentalized reactions have been computationally modeled to explore the encapsulated dynamics, ask evolutionary-based questions, and develop a more systematic understanding required for the engineering of novel BMCs. Many crucial aspects of these systems remain unknown or unmeasured, such as substrate permeabilities across the protein shell, feasibility of pH gradients, and transport rates of associated substrates into the cell. This review explores existing BMC models, dominated in the literature by cyanobacterial carboxysomes, and highlights potentially important areas for exploration.