Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology and Business University, Beijing, 100048, China.
Department of Engineering Science, University of Oxford, Parks Road, Oxford, OX1 3PJ, UK.
BMC Bioinformatics. 2021 Sep 28;22(1):467. doi: 10.1186/s12859-021-04382-3.
The rising consensus that the cell can dynamically allocate its resources provides an interesting angle for discovering the governing principles of cell growth and metabolism. Extensive efforts have been made in the past decade to elucidate the relationship between resource allocation and phenotypic patterns of microorganisms. Despite these exciting developments, there is still a lack of explicit comparison between potentially competing propositions and a lack of synthesis of inter-related proposals and findings.
In this work, we have reviewed resource allocation-derived principles, hypotheses and mathematical models to recapitulate important achievements in this area. In particular, the emergence of resource allocation phenomena is deciphered by the putative tug of war between the cellular objectives, demands and the supply capability. Competing hypotheses for explaining the most-studied phenomenon arising from resource allocation, i.e. the overflow metabolism, have been re-examined towards uncovering the potential physiological root cause. The possible link between proteome fractions and the partition of the ribosomal machinery has been analysed through mathematical derivations. Finally, open questions are highlighted and an outlook on the practical applications is provided. It is the authors' intention that this review contributes to a clearer understanding of the role of resource allocation in resolving bacterial growth strategies, one of the central questions in microbiology.
We have shown the importance of resource allocation in understanding various aspects of cellular systems. Several important questions such as the physiological root cause of overflow metabolism and the correct interpretation of 'protein costs' are shown to remain open. As the understanding of the mechanisms and utility of resource application in cellular systems further develops, we anticipate that mathematical modelling tools incorporating resource allocation will facilitate the circuit-host design in synthetic biology.
细胞可以动态分配其资源的这一共识为发现细胞生长和代谢的控制原则提供了一个有趣的角度。在过去的十年中，人们做出了广泛的努力来阐明资源分配与微生物表型模式之间的关系。尽管这些令人兴奋的发展，但仍然缺乏对潜在竞争命题的明确比较，也缺乏对相关命题和发现的综合。
在这项工作中，我们回顾了资源分配衍生的原则、假设和数学模型，以回顾该领域的重要成就。特别是，通过细胞目标、需求和供应能力之间的潜在拔河，解释资源分配现象的出现。为了揭示潜在的生理根本原因，我们重新检查了解释最受研究的资源分配现象，即溢出代谢的竞争假设。通过数学推导分析了蛋白质分数与核糖体机械分配之间的可能联系。最后，突出了开放性问题并提供了实际应用的展望。作者希望这篇综述有助于更清楚地理解资源分配在解决细菌生长策略中的作用，这是微生物学的核心问题之一。
我们表明资源分配在理解细胞系统的各个方面的重要性。几个重要的问题，如溢出代谢的生理根本原因和“蛋白质成本”的正确解释，仍然存在。随着对细胞系统中资源应用机制和效用的理解进一步发展，我们预计纳入资源分配的数学建模工具将有助于合成生物学中的电路宿主设计。
