Deep proteomics reveals incorporation of unedited proteins into mitochondrial protein complexes in Arabidopsis.

The mitochondrial proteome consists of numerous types of proteins which either are encoded and synthesized in the mitochondria, or encoded in the cell nucleus, synthesized in the cytoplasm and imported into the mitochondria. Their synthesis in the mitochondria, but not in the nucleus, relies on the editing of the primary transcripts of their genes at defined sites. Here, we present an in-depth investigation of the mitochondrial proteome of Arabidopsis (Arabidopsis thaliana) and a public online platform for the exploration of the data.

The Gene Space database.

The hemiparasitic flowering plant (European mistletoe) is known for its very special life cycle, extraordinary biochemical properties, and extremely large genome. The size of its genome is estimated to be 30 times larger than the human genome and 600 times larger than the genome of the model plant . To achieve insights into the Gene Space of the genome, which is defined as the space including and surrounding protein-coding regions, a transcriptome project based on PacBio sequencing has recently been conducted.

The gene space of European mistletoe (Viscum album).

European mistletoe (Viscum album) is a hemiparasitic flowering plant that is known for its very special life cycle and extraordinary biochemical properties. Particularly, V. album has an unusual mode of cellular respiration that takes place in the absence of mitochondrial complex I.

Structure and function of complex I in animals and plants - a comparative view.

The mitochondrial NADH dehydrogenase complex (complex I) has a molecular mass of about 1000 kDa and includes 40-50 subunits in animals, fungi and plants. It is composed of a membrane arm and a peripheral arm and has a conserved L-like shape in all species investigated. However, in plants and possibly some protists it has a second peripheral domain which is attached to the membrane arm on its matrix exposed side at a central position.

The mitochondrial complexome of Arabidopsis thaliana.

Mitochondria are central to cellular metabolism and energy conversion. In plants they also enable photosynthesis through additional components and functional flexibility. A majority of those processes relies on the assembly of individual proteins to larger protein complexes, some of which operate as large molecular machines.

The 'protein complex proteome' of chloroplasts in Arabidopsis thaliana.

Unlabelled: Here, a first GelMap of the chloroplast "protein complex proteome" of Arabidopsis thaliana is presented. The GelMap software tool allows assigning multiple proteins to gel spots, thereby taking advantage of the high sensitivity of state-of-the-art mass spectrometry systems. Furthermore, the software allows functional annotation of all identified proteins.

Functional Annotation of 2D Protein Maps: The GelMap Portal.

In classical proteome analyses, final experimental data are (a) images of 2D protein separations obtained by gel electrophoresis and (b) corresponding lists of proteins which were identified by mass spectrometry (MS). For data annotation, software tools were developed which allow the linking of protein identity data directly to 2D gels ("clickable gels"). GelMap is a new online software tool to annotate 2D protein maps.

Defining the protein complex proteome of plant mitochondria.

A classical approach, protein separation by two-dimensional blue native/sodium dodecyl sulfate-polyacrylamide gel electrophoresis, was combined with tandem mass spectrometry and up-to-date computer technology to characterize the mitochondrial "protein complex proteome" of Arabidopsis (Arabidopsis thaliana) in so far unrivaled depth. We further developed the novel GelMap software package to annotate and evaluate two-dimensional blue native/sodium dodecyl sulfate gels. The software allows (1) annotation of proteins according to functional and structural correlations (e.

GelMap-a novel software tool for building and presenting proteome reference maps.

Protein separation by two-dimensional gel electrophoresis is of central importance for proteomics. Upon combination with systematic protein identifications by mass spectrometry, large data sets are routinely generated in several proteome laboratories which can be used as "reference maps" for future analyses of analogous biochemical fractions. Here we present GelMap, a novel software tool for the building presentation and evaluation of proteomic reference maps.