Title: Systems Biology and engineering of M. pneumonia: simple can be quite complicated
Authors: Luis Serrano.
Abstract:To understand basic principles of bacterial metabolism organization and regulation, but also the impact of genome-size thereon, we systematically studied one of the smallest bacteria, Mycoplasma pneumoniae. A manually curated metabolic network of 189 reactions catalyzed by 129 enzymes allowed the design of a defined, minimal medium with 19 essential nutrients. More than 1,300 growth curves were recorded in the presence of various nutrient concentrations. Measurements of biomass indicators, metabolites and 13C-glucose provided information on directionality, fluxes and energetics; integration with transcription profiling enabled global analysis of metabolic regulation. Compared to more complex bacteria, the M. pneumoniae metabolic network has a more linear topology and contains a higher fraction of multifunctional enzymes; general features such as metabolite concentrations, cellular energetics, adaptability and global gene expression responses are similar though. In parallel we have combined strand-specific tiling arrays, complemented by transcriptome sequencing, with more than 252 spotted arrays. We detected 117 previously non described, mostly non-coding transcripts, 89 of them in antisense configuration to known genes. We identified 340 operons, of which 140 are polycistronic; almost half of the latter show decaying expression in a staircase-like manner. Under various conditions, operons could be divided into 447 smaller transcriptional units, resulting in many alternative transcripts. Frequent antisense transcripts, alternative transcripts, and multiple regulators per gene imply a highly dynamic transcriptome, more similar to that of eukaryotes than previously thought. Finally we used Tandem Affinity Purification-Mass Spectrometry (TAP-MS) in a proteome-wide screen. The analysis revealed 62 homomultimeric and 116 heteromultimeric soluble protein complexes, of which the majority are novel. About a third of the heteromultimeric complexes show higher levels of proteome organization, including assembly into larger, multi-protein complex entities, suggesting sequential steps in biological processes, and extensive sharing of components implying protein multi-functionality. Incorporation of structural models for 484 proteins, single particle EM and cellular electron tomograms provided supporting structural details for this proteome organization. The dataset provides a blueprint of the minimal cellular machinery required for life.
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