The plant mitochondrial proteome

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The plant mitochondrial proteome might contain as many as 2000–3000 different gene products, each of which might undergo post-translational modification. Recent studies using analytical methods, such as one-, two- and three-dimensional gel electrophoresis and one- and two-dimensional liquid chromatography linked on-line with tandem mass spectrometry, have identified >400 mitochondrial proteins, including subunits of mitochondrial respiratory complexes, supercomplexes, phosphorylated proteins and oxidized proteins. The results also highlight a range of new mitochondrial proteins, new mitochondrial functions and possible new mechanisms for regulating mitochondrial metabolism. More than 70 identified proteins in Arabidopsis mitochondrial samples lack similarity to any protein of known function. In some cases, unknown proteins were found to form part of protein complexes, which allows a functional context to be defined for them. There are indications that some of these proteins add novel activities to mitochondrial protein complexes in plants.

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The function and biogenesis of mitochondria in plants

The primary role of plant mitochondria is in respiratory oxidation of organic acids and the transfer of electrons to O2 via the respiratory electron transport chain coupled to the synthesis of ATP. But mitochondria also perform many important secondary functions such as synthesis of nucleotides, metabolism of amino acids and lipids, synthesis of vitamins and cofactors, participation in the photorespiratory pathway, and export of organic acid intermediates for wider cellular biosynthesis. To

Advances in prediction of plant mitochondrial proteomes

A range of algorithms using both defined characteristics and machine-learning techniques have been developed to predict subcellular localization specifically on the basis of the N-terminal region of proteins that can contain presequence targeting information (reviewed in Ref. [10]). This has led to several publicly available programs that can be used generally to predict protein subcellular localization and, most notably, mitochondrial localization. MitoProt II [11], PSORT [12] and iPSORT [13]

New insights into mitochondrial protein composition using proteomics

Based on results of the first experimental proteome projects, a set of 416 mitochondrial proteins could be defined for Arabidopsis [2]. The molecular mass, isoelectric point and hydrophobicity distribution of the identified proteins were found to depend on the technology used for proteome analyses: gel-free strategies were more successful in identifying large, small and basic proteins as well as proteins of low abundance (Figure 3). Based on sequence comparison, nearly 80% of the identified

Developmental, genetic and environmental stress modification of mitochondrial proteome composition

The mitochondrial proteome is not static: it has a changing composition, reflecting the specialized roles of this organelle in different plant organs and cell types. Even in a given cell type, the proteome of mitochondria can change in response to genetic factors, environmental influences and programed developmental cues. The differences between mitochondria from different plant organs were highlighted in the work by Catherine Colas des Francs-Small et al. 38, 39 looking at potato mitochondria.

New insights into post-translational modification and regulation of the proteome

Although our knowledge of the sets of proteins that make up the plant mitochondrial proteomes in different scenarios continues to grow, a whole array of post-translational regulation and covalent and non-covalent modification within the proteome still awaits discovery. These modifications have the potential to dramatically modify mitochondrial proteome function. Modifications that alter molecular mass and the isoelectric point of proteins can theoretically be identified simply by 2D gel

Perspectives

Further development of localization prediction programs and more-extensive proteomics studies is likely to enable us to identify more than 90% of all mitochondrial proteins within the next ten years. Protein and cDNA microarrays will then allow us to determine the accumulation and expression pattern of these proteins as affected by tissue or cell type or by environmental factors. The next challenge, which could be called post-proteomics or functional proteomics, lies in understanding the

Acknowledgements

We thank the following agencies for financial support – The Danish Agricultural and Veterinary Research Council and the Danish Natural Science Research Council (I.M.M.), the Australian Research Council Discovery Programme (A.H.M.), The University of Western Australia (A.H.M. and J.L.H.) and the Deutsche Forschungsgemeinschaft (H-P.B.).

Glossary

BN-PAGE:
Blue Native-polyacrylamide gel electrophoresis.
CI–CV:
respiratory complexes I–V.
DAG:
Differentiation and Greening.
Homolog:
proteins derived from a common ancestor. By definition, these are structurally related.
HSP:
heat shock protein.
IEF:
isoelectric focusing.
LC-MS/MS:
liquid chromatography–tandem mass spectrometry.
ORF:
open reading frame.
Ortholog:
homolog in different species that catalyzes the same reaction.
PDI:
protein disulfide isomerase.
Proteome:
the complete profile of proteins expressed in

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