IDENTIFICATION OF SMALL, NON-CODING RNA GENES IN THE BACTERIUM SHEWANELLA ONEIDE

这个子项目是许多研究子项目中利用 资源由NIH/NCRR资助的中心拨款提供。子项目和 调查员(PI)可能从NIH的另一个来源获得了主要资金， 并因此可以在其他清晰的条目中表示。列出的机构是 该中心不一定是调查人员的机构。 小的非编码RNA(SRNAs)是最近发现的一类基因，细菌用来调节其他基因的表达，以应对不断变化的环境条件。SRNAs通过碱基配对与其信使核糖核酸靶标结合，调节积极或消极的调控结果而发挥作用。然而，细菌中的sRNA基因很难识别，因为它们是相对较小的基因，并且它们不包含划分蛋白质编码基因的蛋白质编码信号。 我们正在使用一种整合了多个指数的计算方法来预测坚尼希瓦氏菌中的sRNA基因。单胞菌是一种被称为金属还原细菌的细菌。当在厌氧条件下生长时，沙门氏菌能将可溶的、有毒的重金属代谢成不溶的形式。因此，探索控制这一潜在的生物修复功能的机制是有意义的。我们的初步数据表明，我们的预测将在识别sRNA方面非常有用，包括无氧金属还原代谢的潜在调节因子。 这项建议描述了设计用来鉴定和鉴定圆顶螺旋藻中sRNA基因的实验，特别是那些可能参与调节重金属代谢的sRNA。我们正在使用sRNA功能获得和功能丧失试剂来确定sRNA如何调节下游代谢功能，并确定sRNA的mRNA靶标。我们的分析应该为sRNA基因是如何定义的，sRNAs如何与其靶标相互作用，以及S.onedensis重金属代谢是如何控制的提供新的见解。

This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. Small, non-coding RNAs (sRNAs) are a relatively recently discovered class of genes that bacteria use to regulate the expression of other genes in response to changing environmental conditions. sRNAs function by base pairing to their mRNA targets and mediating either positive or negative regulatory outcomes. However, sRNA genes in bacteria are difficult to identify, since they are relatively small genes and they do not contain the protein-coding signals that demarcate protein-coding genes. We are using a computational approach that integrates multiple indices to predict sRNA genes in the bacterium Shewanella oneidensis. S. oneidensis is a member of a class of bacteria known as the metal-reducing bacteria. When grown under anaerobic conditions, S. oneidensis can metabolize soluble, toxic heavy metals into insoluble forms. Thus, it is of interest to explore the mechanisms that control this potentially bioremediative function. Our preliminary data suggest that our predictions will be very useful in identifying sRNAs, including potential regulators of anaerobic metal-reducing metabolism. This proposal describes experiments designed to identify and characterize sRNA genes in S. oneidensis, particularly those sRNAs that may be involved in regulating heavy metal metabolism. We are using sRNA gain-of-function and loss-of-function reagents to determine how sRNAs regulate downstream metabolic functions and to identify the mRNA targets of sRNAs. Our analyses should provide novel insights into how sRNA genes are defined, how sRNAs interact with their targets, and how S. oneidensis heavy metal metabolism is controlled.