Characterization of structurally atypical sigma factors carrying fused domains of unknown function in the plant endosymbiont, Sinorhizobium meliloti

转录是所有生物体基因表达的第一个主要步骤。在细菌中，所有的基因表达都受到一个称为sigma（）因子的通用转录因子家族的调节。每个因子控制基因的子集（其调节子）的表达，并且取决于因子，调节子可以由一到数千个基因组成。这些蛋白质中的一个重要组由细胞质外功能（ECF）因子组成，并且这些因子中的许多的活性由包括拮抗性抗因子蛋白的信号转导途径负调节。ECF因子及其相关调节因子构成了主要的感觉系统，其沿着特异性转录因子和双组分调节系统，介导细胞对细胞内外变化的物理化学条件进行适当基因表达应答的能力。 从机制上讲，因子执行两个主要功能：它们将RNAP全酶靶向基因启动子，并将转录起始位点捕获在称为开放复合物的单链状态中。开放复合物的稳定化是转录起始途径中的重要步骤，并且因子活性部分类似于TFIIB在古细菌和真核RNAP II中的活性。了解因子函数的机制细节是一个非常活跃的研究领域，涉及一些特征良好的模型系统。然而，基因组序列数据的分析显示，在许多细菌中存在结构不寻常的ECF因子相关蛋白，这些非典型或非规范系统仍然研究不足。ECF因子的几个亚组意外地携带未知或不完全表征功能的融合蛋白结构域。新出现的证据表明这些融合结构域的调控功能，我的研究计划的长期目标是研究细菌中非经典转录系统的机制细节。对非经典系统的研究有望揭示转录起始的新途径以及基因表达调控与其他细胞过程之间意想不到的生理关系。 值得注意的是，重要的内共生细菌苜蓿中华根瘤菌合成了两个独特的非典型融合域因子的例子。目前的建议描述了这些蛋白质之一（RpoE9）对S的生理重要性的研究。草蛉生物学为此，我们提出了一系列的研究追求，主要集中在辨别RpoE9活性和其他细胞调节和稳态系统之间的意想不到的交叉点。我们要强调的是，虽然这种结构上的非典型因素的研究本身是重要的，我们也认为它是一个工具，建立和完善的研究，所有ECF因素从一个更全球和系统范围的角度。

Transcription is the first major step in gene expression in all organisms. In bacteria, all gene expression is regulated by a family of general transcription factors called sigma () factors. Each factor controls the expression of a subset (its regulon) of genes and regulons may consist of between one and thousands of genes depending on the factor. An important group of these proteins is comprised of Extracytoplasmic Function (ECF) factors and the activity of many of these is negatively regulated by a signal transduction pathway that includes an antagonistic anti- factor protein. ECF factors and their associated regulators constitute a major sensory system that, along with specific transcription factors and two-component regulatory systems, mediate the cellular ability to mount appropriate gene expression responses to changing physicochemical conditions inside and outside of the cell. Mechanistically, factors carry out two major functions: they target RNAP holoenzyme to the gene promoter and they trap the transcription start site in a single-stranded state called an open-complex. Stabilization of the open-complex is an essential step in the transcription initiation pathway and factor activity is partially analogous to the activity of TFIIB in archaeal and eukaryotic RNAP II. Understanding mechanistic detail of factor function is a very active area of research that involves a few well-characterized model systems. However, the analysis of genome sequence data has revealed the presence of structurally unusual ECF factor-related proteins in many bacteria and these atypical or non-canonical systems remain understudied. Several sub-groups of ECF factors unexpectedly carry fused protein domains of unknown or incompletely characterized function. Emerging evidence points to regulatory functions for these fused domains and the long term objective of my research program is to study mechanistic details of non-canonical transcription systems in bacteria. The study of non-canonical systems carries the promise of uncovering novel pathways to transcription initiation and unexpected physiological relationships between the regulation of gene expression and other cellular processes. Remarkably, the important endosymbiotic bacterium Sinorhizobium meliloti synthesizes two unique examples of non-canonical fused domain factors. This current proposal describes the study of the physiological importance of one of these proteins (RpoE9) to S. meliloti biology. To these ends, we are proposing a series of research pursuits mainly focused on discerning unexpected intersections between RpoE9 activity and other cellular regulatory and homeostatic systems. We wish to emphasize that while the study of this structurally atypical factor is important in itself, we also view it as a vehicle to establish and refine the study of all ECF factors from a more global and systems-wide perspective.