LaBoone Perry A, Assis Raquel
Department of Electrical Engineering and Computer Science, Florida Atlantic University, Boca Raton, FL, 33431, USA.
Institute for Human Health and Disease Intervention, Florida Atlantic University, Boca Raton, FL, 33431, USA.
J Mol Evol. 2024 Dec;92(6):834-841. doi: 10.1007/s00239-024-10211-x. Epub 2024 Oct 11.
Gene expression is an inherently noisy process that is constrained by natural selection. Yet the condition dependence of constraint on expression noise remains unclear. Here, we address this problem by studying constraint on expression noise of E. coli genes in eight diverse growth conditions. In particular, we use variation in expression noise as an analog for constraint, examining its relationships to expression level and to the number of regulatory inputs from transcription factors across and within conditions. We show that variation in expression noise is negatively associated with expression level, implicating constraint to minimize expression noise of highly expressed genes. However, this relationship is condition dependent, with the strongest constraint observed when E. coli are grown in the presence of glycerol or ciprofloxacin, which result in carbon or antibiotic stress, respectively. In contrast, we do not observe evidence of constraint on expression noise of highly regulated genes, suggesting that highly expressed and highly regulated genes represent distinct classes of genes. Indeed, we find that essential genes are often highly expressed but not highly regulated, with elevated expression noise in glycerol and ciprofloxacin conditions. Thus, our findings support the hypothesis that selective constraint on expression noise is condition dependent in E. coli, illustrating how it may play a critical role in ensuring expression stability of essential genes in unstable environments.
基因表达是一个受自然选择限制的内在有噪声的过程。然而，限制对表达噪声的条件依赖性仍不清楚。在这里，我们通过研究大肠杆菌基因在八种不同生长条件下的表达噪声限制来解决这个问题。具体而言，我们将表达噪声的变化用作限制的模拟物，研究其与表达水平以及跨条件和条件内转录因子调控输入数量的关系。我们表明，表达噪声的变化与表达水平呈负相关，这意味着存在限制以最小化高表达基因的表达噪声。然而，这种关系取决于条件，在大肠杆菌分别在甘油或环丙沙星存在下生长时观察到最强的限制，这分别导致碳或抗生素应激。相比之下，我们没有观察到对高度调控基因的表达噪声存在限制的证据，这表明高表达基因和高度调控基因代表不同类别的基因。事实上，我们发现必需基因通常高度表达但调控程度不高，在甘油和环丙沙星条件下表达噪声升高。因此，我们的研究结果支持这样的假设，即大肠杆菌中对表达噪声的选择性限制取决于条件，说明了它如何在确保不稳定环境中必需基因的表达稳定性方面发挥关键作用。
