Coordination Funds

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，揭示了原核生物中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，在过去的十年中，全球方法已经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（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，并且由于自动化基因注释工具中的假设过于严格，在基因组注释中通常被自动基因预测遗漏。此外，由于技术限制，这些小蛋白质很难检测到。只有少数小蛋白被描述为它们的细胞功能，然而，表明它们可以在不同的功能场景中发挥重要作用，具有广泛的功能。新技术使小蛋白质的全基因组分析成为可能——复杂的生物信息学预测，肽组学和核糖体分析——已经在SPP的第一个资助阶段实施并建立了平台，并应用于SPP研究的几种微生物。单个项目的结果主要包括通过全基因组筛选和首次功能分析来鉴定和验证几种模式生物中的小蛋白质。第二个资助阶段的总体目标更侧重于阐明已鉴定的小蛋白及其相互作用伙伴的详细功能特征，以及研究调控和作用的潜在分子机制。我们设想揭示以前被忽视的原核原理在基因表达和组装/拆卸大复合体的调节。因此，我们将特别强调小蛋白的分子作用机制，并结合z项目中中心方法的持续进一步发展，以支持项目的详细功能分析（例如，通过尺寸排除色谱法进行复杂成分分析，然后是LC-MS/MS，在riboseq分析中包括特定的开始/停止信息），除了NMR-， FRET-和hdx分析方面的专业知识，高端成像工具将通过个别项目提供给SPP。我们还将包括全基因组方法的比较评估。新实现的全基因组鉴定工具是交联蛋白质组学和细胞背景下小蛋白的发现和功能注释。总的来说，我们有信心通过展示小蛋白的代表性新功能和机制，我们将揭示目前未知的原核基因调控和大复合物组装/拆卸的独特和普遍原理。

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.