Modular interplay of transcription and translation

这个项目推进了对微生物通过调节关键细胞过程之间的相互作用来适应不同生态位的非凡成功的理解。这种理解对于从生物能源生产到环境可持续性和人类健康等应用中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持久状态，或者为生物技术应用和生物修复而设计微生物菌株。此外，该项目还吸引了妇女、少数民族和被系统边缘化的学生和教师，开发和传播一套关于极端环境下的适应和进化的标准高中课程模块。新高中课程的开发为教师提供了优化的教学工具，并与当前的世界问题相关，并且在美国所有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，但其作为基因表达调控元件的能力迄今为止大多被忽视。为了在表型中表现出来，转录调控程序的模块化变化必须对蛋白质（即转录因子、酶等）的协调合成和作用产生直接影响。类似地，核糖体的特化需要转录调控的平行变化，因此特化的核糖体亚基是在适当的环境背景下产生的，以及需要选择性翻译的转录本库。本研究旨在阐明通过转录因子家族的扩展产生的转录的模块化调节如何促进特化核糖体的协调招募到转录库中，这些转录库编码适应新环境所需的功能。第一个目的是研究野生型和转录因子突变体在相关环境变化中转录、核糖体足迹和蛋白质水平的全基因组变化。第二个目标是绘制转录因子的全基因组结合位置和蛋白-蛋白相互作用，并量化在相同环境下组装的核糖体复合物的组成和亚基化学计量。第三个目标是通过对特定核糖体亚基的转录协同调控进行合理的重组，表征转录组范围和环境特异性对核糖体募集和翻译效率的影响。最后，第四个目标是通过开发一个关于极端环境的适应和进化的课程模块，将这个项目的发现转化为高中课堂。这些目标的成功实现可以阐明翻译系统中异质性是如何产生的，以及不同核糖体群体如何介导与环境相关的细胞表型和生理状态转变。该奖项反映了美国国家科学基金会的法定使命，并通过使用基金会的知识价值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.