Coordination Funds

协调基金

• 批准号: 378660098
• 负责人: Professorin Dr. Ruth Anne Schmitz-Streit
• 金额: --
• 依托单位: Institut für Allgemeine Mikrobiologie
• 依托单位国家: 德国
• 项目类别: Priority Programmes
• 资助国家: 德国
• 项目状态: 未结题
• 来源: https://gepris.dfg.de/gepris/projekt/378660098?language=en
• 关键词: Coordination; Funds

Modern genomics and transcriptomics technologies combined with systematic genome-wide approaches have uncovered an unexpected genome complexity in prokaryotes. Besides genes encoding larger proteins and non-coding RNAs, global approaches have over the past decade discovered a wealth of hidden small genes containing short open reading frames (sORFs) in many prokaryotic genomes. These sORFs often encode proteins smaller than 50 amino acids in length and have been typically missed in genome annotations by automated gene predictions due to too strict assumptions in the automated gene annotation tools. Besides, those small proteins have been difficult to detect due to technical limitations. Only few small proteins have been characterized concerning their cellular function, however demonstrating that they can play important roles in different functional scenarios and have a broad range of function. New technologies, which enable the global profiling of small proteins in genome-wide approaches - sophisticated bioinformatics predictions, peptidomics and ribosome profiling - have been implemented and established as platforms within the first funding phase of this SPP and applied to several microorganisms studied in the SPP. Results of the individual projects included predominantly the identification and verification of small proteins in several model organisms mainly by genome-wide screens followed by first functional analyses. The overall aim of this second funding phase focuses more on elucidating the detailed functional characterization of the identified small proteins and their interaction partners as well as studying the underlying molecular mechanisms of regulation and action. We envisage to uncover previously overlooked prokaryotic principles in regulation of gene expression and assembly/disassembly of large complexes. Thus, we will lay particular emphasis on the molecular mechanisms of action of small proteins combined with continuous further development of the central methods within the Z-projects to support the projects also in detailed functional analysis (e.g. complex composition analysis by size exclusion chromatography followed by LC-MS/MS, include specific start/stop information in the Ribo-seq analysis), besides expertise in NMR-, FRET- and HDX-analysis, and high end imaging tools will be available for the SPP through individual projects. We will also include comparative evaluation of the genome-wide approaches. Newly implemented tools for genome-wide identification are cross-link proteomics and discovery and functional annotation of small proteins in the cellular context. Overall, we are confident that by demonstrating representative new functions and mechanisms for small proteins, we will uncover currently unknown unique and universal principles in prokaryotic gene regulation and assembly/disassembly of large complexes.

现代基因组学和转录组学技术与系统的全基因组方法相结合，揭示了原核生物意想不到的基因组复杂性。除了编码较大蛋白质和非编码RNA的基因外，在过去的十年里，全球方法在许多原核生物基因组中发现了大量隐藏的含有短开放阅读框架(SORF)的小基因。这些sORF通常编码长度小于50个氨基酸的蛋白质，由于自动化基因注释工具中过于严格的假设，自动化基因预测通常会在基因组注释中遗漏这些sORF。此外，由于技术限制，这些小蛋白一直很难检测到。关于它们的细胞功能，只有少数几个小蛋白被表征，然而，证明它们可以在不同的功能场景中发挥重要作用，并具有广泛的功能。能够以全基因组方法--复杂的生物信息学预测、多肽组学和核糖体图谱--对小蛋白质进行全球图谱分析的新技术，已经作为该战略规划第一个供资阶段的平台得到实施和确立，并应用于该战略规划所研究的几个微生物。个别项目的结果主要包括主要通过全基因组筛选确定和核实几个模式生物中的小蛋白，然后进行第一次功能分析。第二个供资阶段的总体目标更侧重于阐明已确定的小蛋白及其相互作用伙伴的详细功能特征，以及研究调节和作用的基本分子机制。我们设想在基因表达的调控和大复合体的组装/拆解中揭示以前被忽视的原核原则。因此，我们将特别强调小蛋白质的分子作用机制，并在Z-项目中不断发展中心方法，以支持项目的详细功能分析(例如，通过尺寸排除层析进行复杂成分分析，然后进行LC-MS/MS，在RIBO-SEQ分析中包括特定的起始/停止信息)，除了在核磁共振、FRET和HDX-分析方面的专业知识外，还将通过各个项目为SPP提供高端成像工具。我们还将包括对全基因组方法的比较评估。新实施的全基因组鉴定工具是交叉连接蛋白质组学和发现，以及在细胞范围内对小蛋白进行功能注释。总体而言，我们相信，通过展示具有代表性的小蛋白的新功能和机制，我们将揭示目前未知的独特和普遍的原核基因调控原理和大分子复合体的组装/拆解。