Mahdavi Sara, Salmon Gabriel L, Daghlian Patill, Garcia Hernan G, Phillips Rob
bioRxiv. 2023 Apr 13:2023.04.11.536490. doi: 10.1101/2023.04.11.536490.
UNLABELLED: Cells adapt to environments and tune gene expression by controlling the concentrations of proteins and their kinetics in regulatory networks. In both eukaryotes and prokaryotes, experiments and theory increasingly attest that these networks can and do consume bio-chemical energy. How does this dissipation enable cellular behaviors unobtainable in equilibrium? This open question demands quantitative models that transcend thermodynamic equilibrium. Here we study the control of a simple, ubiquitous gene regulatory motif to explore the consequences of departing equilibrium in kinetic cycles. Employing graph theory, we find that dissipation unlocks nonmonotonicity and enhanced sensitivity of gene expression with respect to a transcription factor's concentration. These features allow a single transcription factor to act as both a repressor and activator at different levels or achieve outputs with multiple concentration regions of locally-enhanced sensitivity. We systematically dissect how energetically-driving individual transitions within regulatory networks, or pairs of transitions, generates more adjustable and sensitive phenotypic responses. Our findings quantify necessary conditions and detectable consequences of energy expenditure. These richer mathematical behaviors-feasibly accessed using biological energy budgets and rates-may empower cells to accomplish sophisticated regulation with simpler architectures than those required at equilibrium. SIGNIFICANCE STATEMENT: Growing theoretical and experimental evidence demonstrates that cells can (and do) spend biochemical energy while regulating their genes. Here we explore the impact of departing from equilibrium in simple regulatory cycles, and learn that beyond increasing sensitivity, dissipation can unlock more flexible input-output behaviors that are otherwise forbidden without spending energy. These more complex behaviors could enable cells to perform more sophisticated functions using simpler systems than those needed at equilibrium.
未标注:细胞通过控制蛋白质浓度及其在调控网络中的动力学来适应环境并调节基因表达。在真核生物和原核生物中,实验和理论越来越证明这些网络能够且确实消耗生物化学能量。这种能量耗散如何使细胞在平衡状态下无法实现的行为成为可能?这个开放性问题需要超越热力学平衡的定量模型。在这里,我们研究一个简单且普遍存在的基因调控基序的控制,以探索在动力学循环中偏离平衡的后果。利用图论,我们发现能量耗散解锁了基因表达相对于转录因子浓度的非单调性和增强的敏感性。这些特性允许单个转录因子在不同水平上既作为阻遏物又作为激活物起作用,或者在局部增强敏感性的多个浓度区域实现输出。我们系统地剖析了在调控网络中能量驱动单个转变或一对转变如何产生更可调节和敏感的表型反应。我们的发现量化了能量消耗的必要条件和可检测的后果。这些更丰富的数学行为——使用生物能量预算和速率可以切实实现——可能使细胞能够用比平衡状态所需更简单的架构完成复杂的调控。 意义声明:越来越多的理论和实验证据表明,细胞在调节基因时能够(且确实)消耗生物化学能量。在这里,我们探讨在简单调控循环中偏离平衡的影响,并了解到除了提高敏感性之外,能量耗散还可以解锁更灵活的输入 - 输出行为,而这些行为在不消耗能量的情况下是被禁止的。这些更复杂的行为可以使细胞使用比平衡状态所需更简单的系统来执行更复杂的功能。
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