Simulating a growing minimal cell: Integrating experiment and theory

所有细胞都共享一套普遍的、最小的生命必需的生物学过程。对该集合的搜索导致了最小细菌细胞JCVI-syn3A的构建。JCVI-syn3A的基因组长543 kbp，有493个基因，其基因组比自然界中发现的任何独立复制的细胞的基因组都小，形态健壮，可以在无压力的实验室生长介质中每两小时分裂一次。在这个最小的细胞中，几乎所有的基因都是必不可少的，而且细胞足够小，可以通过利用图形处理单元(GPU)计算来尝试在生物相关的长度、时间和浓度范围内对所有细胞功能进行完整的描述。最近在GPU计算和3D成像方面的成功使得现在有可能为这个最小的细菌细胞建立一个完整的细胞计算模型，并研究什么是生命规则允许这个细胞生长和分裂。在这个项目中，研究人员构建了一个耦合所有细胞功能的全细胞模型。该项目的结果将使研究团队能够预测细胞在各种扰动下的行为，从而解释完整细胞是如何工作的。更广泛的教育影响包括对学生和博士后研究人员的培训，以及通过研讨会和YouTube/VR平台扩大到更广泛的社区，促进科学的公开传播。该研究项目解决了为不断增长的最小细胞建立更完整的计算模型所需的关键组成部分。在493个基因中，大约有90个∼编码细胞背景不明的蛋白质，其中30个是转座子轰击实验确定的必需蛋白质。为了将现有的三维空间模型扩展到涵盖整个细胞周期，需要在基于GPU的Lattice Microbe软件和成像实验中实现新的随机-确定性混合算法。MINFLUX显微镜将被用来提供增强的空间和时间分辨率的数据，这是构建细胞生长、分裂和DNA复制的准确模型所需的。最近的工作表明，为了保持Syn3A的形态和分裂的一致性，需要对功能不明确的蛋白质进行结构和功能表征，以扩展该模型，并有望揭示新的相互作用和生化反应。为了实现这些目标，将对Syn3A的细胞过程进行实验测量。与细胞形状和生长相关的未知基因的功能将被识别。转录单位的组织以及细胞分裂和DNA复制启动的MINFLUX成像研究将得到确定。通过开发和实施生长和细胞分裂动力学模型，将新的异质数据整合到现有的全细胞计算模型中。此外，还将确定30种基本蛋白质的结构。最后，基因表达动力学模型将被告知测量的转录单位，以确定对蛋白质生产和细胞的整体影响。计划中的研究将与伊利诺伊大学香槟分校(UIUC)、约翰霍普金斯大学(JHU)、JCVI合成生物学小组以及德累斯顿理工大学、莱顿大学和格罗宁根大学的合作者一起进行，该奖项反映了NSF的法定使命，并通过使用基金会的智力优势和更广泛的影响审查标准进行评估，被认为值得支持。

All cells share a universal, minimal set of biological processes essential for life. The search for this set led to the construction of the minimal bacterial cell JCVI-syn3A. With 493 genes in a genome of 543 kbp, JCVI-syn3A has a genome smaller than that of any independently-replicating cell found in nature, a robust morphology, and can divide every two hours in a stress-free laboratory growth medium. Nearly all genes in this minimal cell are essential, and the cell is small enough that a complete description of all cellular functions can be attempted over biological relevant length, time, and concentrations scales by exploiting graphics processing unit (GPU) computing. Recent successes in GPU computing, and 3D imaging have made it now possible to build a whole-cell computational model of this minimal bacterial cell and to investigate what are the rules of life allowing this cell to grow and divide. In this project the investigators construct a whole-cell model coupling all the cellular functions. The outcome of this project will allow the research team to predict cellular behavior under a variety of perturbations, and thus explain how a complete cell works. The educational broader impacts include the training of students and postdoctoral investigators, and outreach to the broader community through workshops and YouTube/VR platforms facilitating the public dissemination of the science.This research project addresses key components needed to make a more complete computational model of a growing minimal cell. Approximately ∼90 out of the 493 genes encode proteins of unclear cellular context, of which 30 were determined to be essential from transposon bombardment experiments. Extension of the current 3D spatial model to encompass the full cell cycle requires new hybrid stochastic-deterministic algorithms to be implemented in the GPU-based Lattice Microbe software and imaging experiments. MINFLUX microscopy will be used to provide data at the enhanced spatial and temporal resolutions needed to construct accurate models of cell growth, division, and DNA replication. The structural and functional characterization of proteins of unclear function, which recent work indicates are required for consistent morphology and division of Syn3A, are needed to extend the model and promise to reveal novel interactions and biochemical reactions. To achieve these goals, the cellular processes of Syn3A will be experimentally measured. The function of unknown genes associated with cell shape and growth will be identified. The organization of transcriptional units and MINFLUX imaging studies of cell division and initiation of DNA replication will be determined. The integration of new heterogeneous data into the existing whole-cell computational models will occur through the develop and implementation growth and cell division kinetic models. In addition, the structure of the 30 essential proteins will be identified. Finally, the gene expression kinetic model will be informed with measured transcriptional units to determine the overall impacts on protein production and the cell. The planned research will be conducted with postdocs and graduate students at the University of Illinois at Urbana-Champaign (UIUC), Johns Hopkins University (JHU), the Synthetic Biology group at JCVI, and collaborators at TU Dresden, Leiden University, and University of GroningenThis award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.