Investigating Carboxysome Morphology Dynamics with a Rotationally Invariant Variational Autoencoder
Investigating Carboxysome Morphology Dynamics with a Rotationally Invariant Variational Autoencoder
复制标题
DOI：
10.1021/acs.jpca.2c02179
复制
发表时间：
2022-07-26
影响因子：
2.9
通讯作者：
Ziatdinov, Maxim
中科院分区：
文献类型：
--
作者：
Fuentes-Cabrera, Miguel;Sakkos, Jonathan K.;Ziatdinov, Maxim
羧基体是一类细菌微区室，在蓝藻细胞质内形成蛋白质细胞器，并通过定义允许二氧化碳固定的细胞微环境在光合代谢中发挥核心作用。羧基体组装的关键方面仍然相对未知，特别是关于该微室的动力学。理解羧基体动力学的进展受到阻碍，部分原因是用显微镜对羧基体形态的微妙变化进行分析仍然是一个低通量和主观的过程。在这里，我们使用深度学习技术，特别是旋转不变变分自动编码器（rVAE），来分析带有羧基体报告基因的蓝细菌的荧光显微镜图像，并定量评估羧基体壳重塑如何影响微区室形态随时间的微妙趋势。为了实现这一目标，我们使用最近开发的工具来控制蓝细菌Synechococcous elongatus PCC 7942模型中的内源蛋白质水平，包括羧基体成分。通过利用该系统，可以实时调整组成羧基体的蛋白质，作为检查羧基体动力学的方法。我们发现 rVAE 能够帮助定量评估羧基体数量、形状和大小随时间的变化。我们认为，rVAE 可能是加速分析羧基体组装和响应遗传或环境扰动的动力学的有用工具，并且可能更普遍地用于探测涉及更广泛的细菌微区室的调控过程。
Carboxysomes are a class of bacterial microcompart-ments that form proteinaceous organelles within the cytoplasm of cyanobacteria and play a central role in photosynthetic metabolism by defining a cellular microenvironment permissive to CO2 fixation. Critical aspects of the assembly of the carboxysomes remain relatively unknown, especially with regard to the dynamics of this micro-compartment. Progress in understanding carboxysome dynamics is impeded in part because analysis of the subtle changes in carboxysome morphology with microscopy remains a low-throughput and subjective process. Here we use deep learning techniques, specifically a Rotationally Invariant Variational Autoencoder (rVAE), to analyze fluorescence microscopy images of cyanobacteria bearing a carboxysome reporter and quantitatively evaluate how carboxysome shell remodelling impacts subtle trends in the morphology of the microcompartment over time. Toward this goal, we use a recently developed tool to control endogenous protein levels, including carboxysomal components, in the model cyanobacterium Synechococcous elongatus PCC 7942. By utilization of this system, proteins that compose the carboxysome can be tuned in real time as a method to examine carboxysome dynamics. We find that rVAEs are able to assist in the quantitative evaluation of changes in carboxysome numbers, shape, and size over time. We propose that rVAEs may be a useful tool to accelerate the analysis of carboxysome assembly and dynamics in response to genetic or environmental perturbation and may be more generally useful to probe regulatory processes involving a broader array of bacterial microcompartments.