RNA structures regulating ribosomal protein synthesis in gram-positive bacteria

该项目的目的是研究细菌如何协调核糖体的生产，这对它们的生长至关重要。核糖体是负责制造蛋白质的生物机器，在活跃生长的细菌中，它们占细胞内容物的1/3以上。 因此，细胞将其资源的很大一部分用于核糖体的生产。核糖体需要大约60种不同的成分，必须以正确的比例生产。为了最有效地利用资源，细菌会及时生产它们的核糖体部分。这项研究将深入了解在土壤生物修复，农业和食品工业中发挥重要作用的细菌菌株的这一过程，从而提高设计这些菌株的生长速率和代谢的能力。通过了解不同菌株的细菌如何以不同的方式解决这个生物学问题，我们将更好地了解这种协调是如何进化的，以及重要的性能参数可能是什么。这项研究还为研究生、本科生和高中阶段的年轻科学家受训人员提供了重要机会，因为它可以分为许多范围有限的单独项目和新手科学家可以接触到的具体可检验假设。该项目旨在确定革兰氏阳性菌中RNA调节核糖体蛋白质合成的作用。虽然在革兰氏阴性细菌大肠杆菌模型中对该过程的调节已经很好地理解，但在革兰氏阳性细菌中几乎没有进行过研究。通过鉴定和表征在革兰氏阳性菌枯草芽孢杆菌模型中完成这一任务的RNA结构，我们将发现许多未表征的RNA调控结构，这些结构是相同生物学问题的替代解决方案，并提供了这一复杂过程如何发生的另一幅图景。这项研究还将为不断增长的RNA结构数据库和RNA-蛋白质相互作用的生物物理分析提供新的素材，并为影响此类系统如何进化的因素提供深入了解。为了实现这些目标，计算预测的RNA结构与核糖体蛋白将计算策划，以确定它们是否被转录，类似于核糖体RNA结合位点，或与通常具有调节作用的功能。这些RNA的生物学功能将通过体外RNA-蛋白质结合试验和体内遗传调控试验进行实验验证。

The objective of this project is to examine how bacteria coordinate production of ribosomes, which are crucial for their growth. Ribosomes are the biological machines responsible for making proteins, and in actively growing bacteria they constitute over 1/3 of the cell's contents. Thus, cells devote a large proportion of their resources to the production of ribosomes. Ribosomes require approximately 60 different components that must be produced in the correct proportions. In order to use resources most efficiently, bacteria practice just-in-time production of their ribosomal parts. This research will provide insight into this process in bacterial strains with important roles in soil bioremediation, agriculture, and the food industry, leading to increased ability to engineer the growth rate and metabolism of these strains. By understanding how this biological problem is solved in different ways by different strains of bacteria, we will better understand how such coordination can evolve and what the important performance parameters may be. This research also provides significant opportunities to young scientist trainees at the graduate, undergraduate and high school levels because it may be broken into many individual projects with limited scope and specific testable hypotheses that are accessible to novice scientists. This project seeks to determine the role of RNA regulation on ribosomal protein synthesis in gram-positive bacteria. While the regulation of this process is well understood in the model gram-negative bacterium Escherichia coli, it remains virtually unexamined in gram-positive bacteria. By identifying and characterizing RNA structures that accomplish this task in the model gram-positive bacterium Bacillus subtilis, we will uncover numerous uncharacterized RNA regulatory structures that are alternative solutions to the same biological problem, and provide another picture of how this complex process occurs. This research will also contribute new fodder for growing RNA structural databases and biophysical analysis of RNA-protein interactions, and provide insight into the factors influencing how such systems may evolve. To accomplish these goals computationally predicted RNA structures associated with ribosomal proteins will be computationally curated to determine whether they are transcribed, resemble ribosomal RNA binding sites, or are associated with features that commonly have regulatory roles. The biological function of these RNAs will then be experimentally validated using both in vitro RNA-protein binding assays and in vivo genetic regulatory assays.