Survey of large protein complexes in D. vulgaris reveals great structural diversity

Abstract

An unbiased survey has been made of the stable, most abundant multi-protein complexes in Desulfovibrio vulgaris Hildenborough (DvH) that are larger than Mr Ϸ 400 k. The quaternary structures for 8 of the 16 complexes purified during this work were determined by single-particle reconstruction of negatively stained specimens, a success rate Ϸ10 times greater than that of previous ''proteomic'' screens. In addition, the subunit compositions and stoichiometries of the remaining complexes were determined by biochemical methods. Our data show that the structures of only two of these large complexes, out of the 13 in this set that have recognizable functions, can be modeled with confidence based on the structures of known homologs. These results indicate that there is significantly greater variability in the way that homologous prokaryotic macromolecular complexes are assembled than has generally been appreciated. As a consequence, we suggest that relying solely on previously determined quaternary structures for homologous proteins may not be sufficient to properly understand their role in another cell of interest.comparative evolutionary analysis ͉ single-particle electron microscopy ͉ structural homology

How sulphate-reducing microorganisms cope with stress: lessons from systems biology

“…A variety of 'omics' tools, targeting biological systems at various scales, are used in combination with conventional genetic and biochemical approaches to obtain system-level measurements for subsequent modelling and simulation of the system under study (see the figure). For instance, microbial populations can be phenotypically characterized in terms of their biochemistry, physiology and ecology and then analysed using high-throughput 'omics' tools, such as those provided by transcriptomics (for example, microarrays, RNA-sequencing (RNA-seq) or whole-transcriptome shotgun sequencing), proteomics (for example, mass spectrometry to identify proteins, protein complexes and post-translational modifications) 37,48,51,147,148 and metabolomics (for example, metabolite profiling and analysis of metabolite fluxes) 37,38,55,149 . At the community scale, high-throughput metagenomic technologies, such as large-scale genome sequencing 97 , GeoChip 15,109 and PhyloChip…”

Bacterial Interactomes: Interacting Protein Partners Share Similar Function and Are Validated in Independent Assays More Frequently Than Previously Reported

“…D. vulgaris has been extensively characterized by functional genomic studies of its response to environmentally relevant conditions (23,24), but relatively few protein complexes have been analyzed to date (25)(26)(27). Therefore, we have performed a global AP-MS screen to characterize its interactome and have also critically reexamined nine published AP-MS and Y2H screens.…”

Metabolic Networking through Enzymatic Sensing, Signaling and Response to Homeostatic Fluctuations

“…For instance, up to 16 stable and most abundant large multiprotein complexes with the mass more than 400 000 Da were characterized in a soil bacterium Desulfovibrio vulgaris (Han et al, 2009). Remarkably, the authors of this work conclude that the subunit composition and quaternary structure of these complexes vary to a great extent between different organisms.…”