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的一个 由NIH/NCRR资助的中心赠款提供的资源。子项目和 研究者（PI）可能从另一个NIH来源获得了主要资金， 因此可以在其他CRISP条目中表示。所列机构为 研究中心，而研究中心不一定是研究者所在的机构。 小的非编码RNA（sRNA）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。sRNA通过与其mRNA靶点碱基配对并介导正或负调节结果来发挥功能。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，并且它们不包含区分蛋白质编码基因的蛋白质编码信号。 我们正在使用一种计算方法，该方法集成了多个指标来预测细菌希瓦氏菌oneidensis中的sRNA基因。S. oneidensis是一类被称为金属还原菌的细菌的成员。在厌氧条件下生长时，S. oneidensis可以将可溶性有毒重金属代谢成不溶性形式。因此，探索控制这种潜在生物修复功能的机制是有意义的。我们的初步数据表明，我们的预测将是非常有用的，在确定sRNAs，包括厌氧金属还原代谢的潜在监管机构。 该提案描述了旨在鉴定和表征S. oneidensis，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靶点。我们的分析应该提供新的见解如何sRNA基因的定义，sRNA如何与他们的目标相互作用，以及如何S。控制重金属代谢。

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.