Modular interplay of transcription and translation

该项目通过调节关键细胞过程之间的相互作用，促进了对微生物适应不同生态位的非凡成功的理解。这一理解对于利用从生物能源生产到环境可持续性和人类健康的各种应用来操纵微生物过程至关重要。例如，有了这样的理解，就有可能修改病原体在遇到潜在致命环境时如何迅速转变为类似持久性的状态，或者改造用于生物技术应用和生物修复的微生物菌株。此外，该项目让妇女、少数群体和被系统边缘化的学生和教师参与，以开发和传播关于极端环境中的适应和进化的符合标准的高中课程模块。新高中课程的开发为教师提供了优化的教学工具，与当前的世界问题相关，美国所有50个州和全球144个国家都可以使用。转录和翻译的模块化相互作用是所有生物体进化的基础。虽然核糖体在蛋白质合成中的基本重要性早已被认识到，但到目前为止，它作为基因表达调控元件的能力大多被忽视。为了在表型中表现出来，转录调控程序的模块化的变化必须直接影响蛋白质(即转录因子、酶等)的协调合成和作用。同样，核糖体的专门化需要转录调控的平行变化，因此专门化的核糖体亚基是在正确的环境背景下产生的，以及需要选择性翻译的转录本。本研究旨在阐明通过转录因子家族的扩大而产生的转录模块调节如何促进专门的核糖体协调地招募到转录库中，转录库编码适应新环境所需的功能。第一个目的是研究在相关的环境变化过程中盐碱藻野生型和转录因子突变体的转录、核糖体足迹和蛋白质水平的全基因组变化。第二个目的是绘制转录因子的全基因组结合位置和蛋白质-蛋白质相互作用图，并量化在相同环境下组装的核糖体复合体的组成和亚单位化学计量比。第三个目的是通过对特定核糖体亚单位转录共调控的合理重组，表征转录组范围内和环境特有的对核糖体招募和翻译效率的影响。最后，第四个目标是通过开发一个关于极端环境中的适应和进化的课程模块，将这个项目的结果转化为高中课堂。这些目标的成功实现有助于阐明翻译系统中异质性是如何产生的，以及不同的核糖体群体如何调节与环境相关的细胞表型和生理状态转换。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。

This project advances the understanding of the extraordinary success of microbes in adapting to diverse niches by modulating the interplay between the key cellular processes. This understanding is essential to manipulate microbial processes with applications ranging from bioenergy production to environmental sustainability and human health. For example, with such understanding the modification of how pathogens rapidly transition into a persistent-like state upon encountering a potentially lethal environment or the engineering of microbial strains for biotechnology applications and bioremediation, would be possible. Additionally, this project engages women, minorities, and systematically marginalized students and teachers, to develop and disseminate a standards-aligned high school curriculum module on adaptation and evolution in extreme environments. The development of a new high-school curriculum provides teaching with instruments optimized for teachers and relevant to current world issues and is accessible across all 50 states in the US and 144 countries worldwide. The modular interplay of transcription and translation is foundational to the evolution of all organisms. Although the fundamental importance of ribosomes in protein synthesis has long been recognized, its capability as a regulatory element in gene expression has thus far been mostly overlooked. In order to manifest in phenotype, changes to modularity of a transcriptional regulatory program must have direct consequences on the coordinated synthesis and action of proteins (i.e., transcription factors, enzymes, etc.). Similarly, specialization of ribosomes requires parallel changes in transcriptional regulation so the specialized ribosomal subunits are made in the right environmental context, together with the pool of transcripts that need to be selectively translated. This research aims to elucidate how modular regulation of transcription generated through the expansion of a transcription factor family facilitates the coordinated recruitment of specialized ribosomes to pools of transcripts that encode functions required for adaptation to a new environment. The first aim investigates genome-wide changes in transcription, ribosome footprints and protein levels in the wild type and transcription factor mutants of H. salinarum during relevant environmental shifts. The second aim maps genome-wide binding locations and protein-protein interactions of transcription factors, and quantifies the composition and subunit stoichiometry of assembled ribosomal complexes in the same environmental contexts. The third aim characterizes transcriptome-wide and environment-specific consequences on ribosome recruitment and translation efficiency through rational reengineering of the transcriptional co-regulation of specialized ribosomal subunits. Finally, the fourth aim translates findings from this project to a high school classroom by developing a curriculum module on adaptation and evolution in environmental extremes. The successful execution of these aims allows elucidation of how heterogeneity is generated within the translation system and how a diverse population of ribosomes mediates environmentally relevant cellular phenotypes and physiological state transitions.This 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.