SPP 2002: Kleine Proteine in Prokaryoten, eine unbekannte Welt

Grunddaten zu diesem Projekt

Beschreibung

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.