Data_Sheet_1_Multifaceted Stoichiometry Control of Bacterial Operons Revealed by Deep Proteome Quantification.zip

More than half of the protein-coding genes in bacteria are organized in polycistronic operons composed of two or more genes. It remains under debate whether the operon organization maintains the stoichiometric expression of the genes within an operon. In this study, we performed a label-free data-independent acquisition hyper reaction monitoring mass-spectrometry (HRM-MS) experiment to quantify the Escherichia coli proteome in exponential phase and quantified 93.6% of the cytosolic proteins, covering 67.9% and 56.0% of the translating polycistronic operons in BW25113 and MG1655 strains, respectively. We found that the translational regulation contributes largely to the proteome complexity: the shorter operons tend to be more tightly controlled for stoichiometry than longer operons; the operons which mainly code for complexes is more tightly controlled for stoichiometry than the operons which mainly code for metabolic pathways. The gene interval (distance between adjacent genes in one operon) may serve as a regulatory factor for stoichiometry. The catalytic efficiency might be a driving force for differential expression of enzymes encoded in one operon. These results illustrated the multifaceted nature of the operon regulation: the operon unified transcriptional level and gene-specific translational level. This multi-level regulation benefits the host by optimizing the efficiency of the productivity of metabolic pathways and maintenance of different types of protein complexes.

超过一半的细菌编码蛋白质的基因以多顺反子操纵子形式组织，操纵子由两个或多个基因组成。关于操纵子组织是否维持操纵子内基因的化学计量表达的稳定性，尚存在争议。在本研究中，我们通过无标记的数据无关采集超反应监测质谱（HRM-MS）实验，对指数生长期的埃希氏菌（Escherichia coli）蛋白质组进行了定量分析，并量化了93.6%的细胞质蛋白，分别覆盖了BW25113和MG1655菌株中67.9%和56.0%的翻译多顺反子操纵子。研究发现，翻译调控对蛋白质组复杂性的贡献显著：较短的操纵子相较于较长的操纵子，在化学计量稳定性方面受到更严格的调控；主要编码复合物的操纵子相较于主要编码代谢途径的操纵子，在化学计量稳定性方面受到更严格的调控。基因间隔（操纵子中相邻基因之间的距离）可能作为化学计量调控的调节因子。催化效率可能是同一操纵子中编码的酶差异表达的一个驱动因素。这些结果揭示了操纵子调控的多面性：操纵子统一了转录水平与基因特异性翻译水平。这种多层次调控有助于宿主通过优化代谢途径的生产效率和不同类型蛋白质复合物的维持，从而获得益处。