Gabalda-Sagarra Marçal, Carey Lucas B, Garcia-Ojalvo Jordi
Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona Biomedical Research Park, 08003 Barcelona, Spain.
Chaos. 2018 Oct;28(10):106313. doi: 10.1063/1.5039861.
Cellular information processing is generally attributed to the complex networks of genes and proteins that regulate cell behavior. It is still unclear, however, what are the main features of those networks that allow a cell to encode and interpret its ever changing environment. Here, we address this question by studying the computational capabilities of the transcriptional regulatory networks of five evolutionary distant organisms. We identify in all cases a cyclic recurrent structure, formed by a small core of genes, that is essential for dynamical encoding and information integration. The recent history of the cell is projected nonlinearly into this recurrent reservoir of nodes, where it is encoded by its transient dynamics, while the rest of the network forms a readout layer devoted to decode and interpret the high-dimensional dynamical state of the recurrent core. In that way, gene regulatory networks act as echo-state networks that perform optimally in standard memory-demanding tasks, with most of their memory residing in the recurrent reservoir. The biological significance of these results is analyzed in the particular case of the bacterium Escherichia coli. Our work thus suggests that recurrent nonlinear dynamics is a key element for the processing of complex time-dependent information by cells.
细胞信息处理通常归因于调节细胞行为的复杂基因和蛋白质网络。然而，这些网络的哪些主要特征使细胞能够编码和解读其不断变化的环境，目前仍不清楚。在这里，我们通过研究五种进化距离较远的生物体的转录调控网络的计算能力来解决这个问题。我们在所有情况下都识别出一种由一小部分核心基因形成的循环递归结构，它对于动态编码和信息整合至关重要。细胞的近期历史被非线性地投射到这个由节点组成的循环储备中，在那里它由其瞬态动力学进行编码，而网络的其余部分则形成一个读出层，专门用于解码和解读循环核心的高维动态状态。通过这种方式，基因调控网络就像回声状态网络一样，在标准的需要记忆的任务中表现最佳，其大部分记忆都存在于循环储备中。我们在大肠杆菌的具体案例中分析了这些结果的生物学意义。因此，我们的工作表明，循环非线性动力学是细胞处理复杂时间相关信息的关键要素。
