Supplementary Material for: Assessing combinatorial diversity of aureochrome bZIPs through genome-wide screening

Aureochromes are unique blue light-responsive LOV (Light Oxygen Voltage) photoreceptors cum basic leucine zipper (bZIP) transcription factors (TFs), present exclusively in photosynthetic marine stramenopiles. Considering the availability of the complete genome sequence, this study focuses on aureochromes from Ectocarpus siliculosus. Aureochromes mediate light-regulated developmental responses in this brown photosynthetic algae. Both the LOV sensor and the bZIP effector shows overall sequence-structure conservation. The structurally similar LOV+bZIP modules of aureochrome homologs/paralogs prefer a dimeric state. Besides a heterogeneous linker connecting the sensor-effector and a flexible N-terminal region, the sequence composition of both domains is vital. Aureochromes execute diverse cellular responses in different photosynthetic stramenopiles – though their activities can vary even within a given algal species. Therefore, it is important to understand whether aureochromes select dimerization partners from the same family or interact with other bZIPs as well. To regulate multifarious biological activities, it is possible that aureochromes activate the global TF interaction network. Following homo/heterodimer modeling, we address the compatibility of dimerization partners by screening through heptad repeats. We evaluate the dimer interface area in terms of gain in solvation energy and the number of hydrogen bonds/salt bridge interactions. We further explore the relative stability of these structures from a graph-theoretic perspective through well-studied measures such as the energy of the graph, average participation coefficient, and betweenness centrality. Furthermore, we also conduct an information-theoretic analysis using hitherto understudied measures such as network information centrality and Kullback-Leibler divergence. We find that all our investigations into the relative stability of the dimers using diverse methods from bioinformatics, network science, and, information theory are in harmonious agreement. Coupling preferences of monomers in aureochromes can be further translated to design novel optogenetic tools useful for understanding human development and disease.

黄金素（aureochromes）是一类独特的蓝光响应型光氧电压（Light Oxygen Voltage，LOV）感受器兼碱性亮氨酸拉链（basic leucine zipper，bZIP）转录因子（transcription factors，TFs），仅存在于光合海洋不等鞭毛类生物中。鉴于完整基因组序列已完成测定，本研究聚焦于皱纹马尾藻（Ectocarpus siliculosus）中的黄金素。黄金素可介导该光合褐藻的光调控发育响应。LOV感应结构域与bZIP效应结构域均整体呈现序列与结构层面的保守性。黄金素同源/旁系同源蛋白中结构相似的LOV+bZIP模块倾向于以二聚体形式存在。除了连接感应与效应结构域的异质性接头区域以及柔性N端区域外，两个结构域的序列组成均至关重要。黄金素在不同的光合不等鞭毛类生物中可介导多种细胞响应——即便在同一藻类物种内，其活性也可能存在差异。因此，明确黄金素的二聚化伴侣是否仅选自同一转录因子家族，抑或也可与其他bZIP家族蛋白发生相互作用，具有重要研究价值。为调控多样的生物学活动，黄金素可能会激活全局转录因子相互作用网络。在完成同源/异源二聚体建模后，我们通过七肽重复（heptad repeats）序列筛选，以探究二聚化伴侣的兼容性。我们从溶剂化能增益、氢键/盐桥相互作用数量两个维度，对二聚体界面面积进行评估。我们进一步从图论视角出发，通过一系列已被广泛研究的量化指标——如图能量、平均参与系数以及介数中心性（betweenness centrality），探究这些二聚体结构的相对稳定性。此外，我们还采用此前较少被应用的信息论分析方法，以网络信息中心性（network information centrality）与库勒贝克-莱布勒散度（Kullback-Leibler divergence，KL散度）作为量化指标开展研究。我们发现，借助生物信息学、网络科学以及信息论领域的多种方法对二聚体相对稳定性开展的所有探究，均得到了一致的结论。黄金素单体的偶联偏好性可进一步应用于新型光遗传学工具的开发，助力人类发育与疾病相关研究。