Phylogenetic transfer of organelle genes to the nucleus can lead to new mechanisms of protein integration into membranes

Photosynthetic complex stoichiometry dynamics in higher plants: biogenesis, function, and turnover of ATP synthase and the cytochrome b6f complex

During plant development and in response to fluctuating environmental conditions, large changes in leaf assimilation capacity and in the metabolic consumption of ATP and NADPH produced by the photosynthetic apparatus can occur. To minimize cytotoxic side reactions, such as the production of reactive oxygen species, photosynthetic electron transport needs to be adjusted to the metabolic demand. The cytochrome b6f complex and chloroplast ATP synthase form the predominant sites of photosynthetic flux control. Accordingly, both respond strongly to changing environmental conditions and metabolic states. Usually, their contents are strictly co-regulated. Thereby, the capacity for proton influx into the lumen, which is controlled by electron flux through the cytochrome b6f complex, is balanced with proton efflux through ATP synthase, which drives ATP synthesis. We discuss the environmental, systemic, and metabolic signals triggering the stoichiometry adjustments of ATP synthase and the cytochrome b6f complex. The contribution of transcriptional and post-transcriptional regulation of subunit synthesis, and the importance of auxiliary proteins required for complex assembly in achieving the stoichiometry adjustments is described. Finally, current knowledge on the stability and turnover of both complexes is summarized.

Assembly of F1F0-ATP synthases

F1F0-ATP synthases are multimeric protein complexes and common prerequisites for their correct assembly are (i) provision of subunits in appropriate relative amounts, (ii) coordination of membrane insertion and (iii) avoidance of assembly intermediates that uncouple the proton gradient or wastefully hydrolyse ATP. Accessory factors facilitate these goals and assembly occurs in a modular fashion. Subcomplexes common to bacteria and mitochondria, but in part still elusive in chloroplasts, include a soluble F1 intermediate, a membrane-intrinsic, oligomeric c-ring, and a membrane-embedded subcomplex composed of stator subunits and subunit a. The final assembly step is thought to involve association of the preformed F1-c10-14 with the ab2 module (or the ab8-stator module in mitochondria)--mediated by binding of subunit δ in bacteria or OSCP in mitochondria, respectively. Despite the common evolutionary origin of F1F0-ATP synthases, the set of auxiliary factors required for their assembly in bacteria, mitochondria and chloroplasts shows clear signs of evolutionary divergence. This article is part of a Special Issue entitled: Chloroplast Biogenesis.

The role of the transmembrane domain in determining the targeting of membrane proteins to either the inner envelope or thylakoid membrane

Chloroplastic membrane proteins can be targeted to any of three distinct membrane systems, i.e., the outer envelope membrane (OEM), inner envelope membrane (IEM), and thylakoid membrane. This complex structure of chloroplasts adds significantly to the challenge of studying protein targeting to various membrane sub-compartments within a chloroplast. In this investigation, we examined the role played by the transmembrane domain (TMD) in directing membrane proteins to either the IEM or thylakoid membrane. Using the IEM protein, Arc6 (Accumulation and Replication of Chloroplasts 6), we exchanged the stop-transfer TMD of Arc6 with various TMDs derived from different IEM and thylakoid membrane proteins and monitored the subcellular localization of these Arc6-hybrid proteins. We showed that when the Arc6 TMD was replaced with a TMD derived from various thylakoid membrane proteins, these Arc6(thylTMD) hybrid proteins could be directed to the thylakoid membrane rather than to the IEM. Conversely, when the TMD of the thylakoid membrane proteins, STN8 (State Transition protein kinase 8) or Plsp1 (Plastidic type I signal peptidase 1), was replaced with the stop-transfer TMD of Arc6, STN8 and Plsp1 were halted at the IEM. From our investigation, we conclude that the TMD plays a critical role in targeting integral membrane proteins to either the IEM or thylakoid membrane.

Protein translocation into and within cyanelles (Review)

The cyanelles of the glaucocystophyte alga Cyanophora paradoxa resemble endosymbiotic cyanobacteria in morphology, pigmentation and, especially, in the presence of a peptidoglycan wall situated between the inner and outer envelope membranes. However, it is now clear that cyanelles in fact are primitive plastids. Phylogenetic analyses of plastid, nuclear and mitochondrial genes support a single primary endosymbiotic event. In this scenario cyanelles and all other plastid types are derived from an ancestral photosynthetic organelle combining the high plastid gene content of the Porphyra purpurea rhodoplast and the peptidoglycan wall of glaucocystophyte cyanelles. This means that the import apparatus of all primary plastids should be homologous. Indeed, heterologous in vitro import can now be shown in both directions, provided a phenylalanine residue essential for cyanelle import is engineered into the N-terminal part of chloroplast transit peptides. The cyanelle and likely also the rhodoplast import apparatus can be envisaged as prototypes with a single receptor showing this requirement for N-terminal phenylalanine. In chloroplasts, multiple receptors with overlapping and less stringent specificities have evolved explaining the efficient heterologous import of native precursors from C. paradoxa. With respect to conservative sorting in cyanelles, both the Sec and Tat pathways could be demonstrated. Another cyanobacterial feature, the dual location of the Sec translocase in thylakoid and inner envelope membranes, is also unique to cyanelles. For the first time, protease protection of internalized lumenal proteins could be shown for cyanobacteria-like, phycobilisome-bearing thylakoid membranes after import into isolated cyanelles.

Prediction of dual protein targeting to plant organelles

* Dual targeting of proteins to more than one subcellular localization has been found in animals, in fungi and in plants. In the latter, ambiguous N-terminal targeting signals have been described that result in the protein being located in both mitochondria and plastids. We have developed ambiguous targeting predictor (ATP), a machine-learning implementation that classifies such ambiguous targeting signals. * Ambiguous targeting predictor is based on a support vector machine implementation that makes use of 12 different amino acid features. Prediction results were validated using fluorescent protein fusion. * Both in silico and in vivo evaluations demonstrate that ambiguous targeting predictor is useful for predicting dual targeting to mitochondria and plastids. Proteins that are targeted to both organelles by tandemly arrayed signals (so-called twin targeting) can be predicted by both ambiguous targeting predictor and a combination of single targeting prediction tools. Comparison of ambiguous targeting predictor with previous experimental approaches, as well as in silico approaches, shows good congruence. * Based on the prediction results, land plant genomes are expected to encode, on average, > 400 proteins that are located in mitochondria and plastids. Ambiguous targeting predictor is helpful for functional genome annotation and can be used as a tool to further our understanding about dual protein targeting and its evolution.

Toc, Tic, Tat et al.: structure and function of protein transport machineries in chloroplasts

The chloroplast is an organelle of prokaryotic origin that is situated in an eukaryotic cellular environment. As a result of this formerly endosymbiotic situation, the chloroplast houses a unique set of protein transport machineries. Among those are evolutionarily young transport pathways which are responsible for the import of the nuclear-encoded proteins into the organelle as well as ancient pathways operating in the 'export' of proteins from the stroma (the former cyanobacterial cytosol) across the thylakoid membrane into the thylakoid lumen. In this review, we have tried to address the main features of these various transport pathways.

Unique structural determinants in the signal peptides of "spontaneously" inserting thylakoid membrane proteins

A series of thylakoid membrane proteins, including PsbX, PsbY and PsbW, are synthesized with cleavable signal peptides yet inserted using none of the known Sec/SRP/Tat/Oxa1-type insertion machineries. Here, we show that, although superficially similar to Sec-type signal peptides, these thylakoidal signal peptides contain very different determinants. First, we show that basic residues in the N-terminal domain are not important, ruling out electrostatic interactions as an essential element of the insertion mechanism, and implying a fundamentally different targeting mechanism when compared with the structurally similar M13 procoat. Second, we show that acidic residues in the C-domain are essential for the efficient maturation of the PsbX and PsbY-A1 peptides, and that even a single substitution of the -5 Glu by Val in the PsbX signal peptide abolishes maturation in the thylakoid. Processing efficiency is restored to an extent, but not completely, by the highly hydrophilic Asn, implying that this domain is required to be hydrophilic, but preferably negatively charged, in order to present the cleavage site in an optimal manner. We show that substitution of the PsbX C-domain Glu residues by Val leads to a burial of the cleavage site within the bilayer although insertion is unaffected. Finally, we show that substitution of the Glu residues in the lumenal A2 loop of the PsbY polyprotein leads to a block in cleavage on the stromal side of the membrane, and present evidence that the PsbY-A2 signal peptide is required to be relatively hydrophilic and unable to adopt a transmembrane conformation on its own. These data indicate that, rather than being merely additional hydrophobic regions to promote insertion, the signal peptides of these thylakoid proteins are complex domains with uniquely stringent requirements in the C-domain and/or translocated loop regions.

Gene transfer from mitochondrion to nucleus: novel mechanisms for gene activation from Cox2

The evolutionarily recent transfer of the gene for cytochrome c oxidase subunit 2 (cox2) from the mitochondrion to the nucleus in legumes is shown to have involved novel gene-activation steps. The acquired mitochondrial targeting presequence is bordered by two introns. Characterization of the import of soybean Cox2 indicates that the presequence is cleaved in a three-step process which is independent of assembly. The final processing step takes place only in the mitochondria of legume species, and not in several non-legume plants. The unusually long presequence of 136 amino acids consists of three regions: the first 20 amino acids are required for mitochondrial targeting and can be replaced by another presequence; the central portion of the presequence is required for efficient import of the Cox2 protein into mitochondria; and the last 12 amino acids, derived from the mitochondrially encoded protein, are required for correct maturation of the imported protein. The acquisition of a unique presequence, and the capacity for legume mitochondria to remove this presequence post-import, are considered to be essential adaptations for targeting of Cox2 to the mitochondrion and therefore activation of the transferred gene in the nucleus.

Without a little help from 'my' friends: direct insertion of proteins into chloroplast membranes?

The chloroplast membranes are highly regulated and biological active regions of the living plant cell, which carry numerous essential proteinaceous components. For example, in the thylakoid membrane the photosynthesis apparatus, one of the most life-relevant biological machineries, is located. How these membrane proteins are targeted to and inserted into their target membranes was one of the questions we aimed to understand in the last few years. Fifteen years ago little to nothing was known about the targeting and translocation of outer envelope proteins (G.W. Schmidt and L.M. Mishkind, Annu. Rev. Biochem. 55 (1986)). Although several protein assisted pathways for translocation of proteins across the membranes have been characterised, only recent results gave insight into how membrane proteins are inserted into the chloroplast membranes. Here we will focus on the mode of insertion of a class of proteins into the outer envelope and the thylakoid membranes, which share a unique feature: they insert apparently directly into the lipid bilayer, i.e. without the help of a proteinaceous translocation pore.

Evolutionarily related insertion pathways of bacterial, mitochondrial, and thylakoid membrane proteins

The inner membranes of eubacteria and mitochondria, as well as the chloroplast thylakoid membrane, contain essential proteins that function in oxidative phosphorylation and electron transport processes or in photosynthesis. Because most of the organellar proteins are nuclear encoded, they are synthesized in the cytoplasm and subsequently imported into the organelle before they are inserted into the membrane. This review focuses on the pathways of protein insertion into the inner membrane of eubacteria and mitochondria and into the chloroplast thylakoid membrane. In many respects, insertion of proteins into the inner membrane of bacteria is a process similar to that used by proteins of the thylakoid membrane. In both of these systems a signal recognition particle (SRP) and a SecYE-translocase are involved, as in translocation into the endoplasmic reticulum. The pathway of proteins into the mitochondrial membranes appears to be different in that it involves no SecYE-like components. A conservative pathway, recently identified in mitochondria, involves the Oxa1 protein for the insertion of proteins from the matrix. The presence of Oxa1 homologues in eubacteria and chloroplasts suggests that this pathway is evolutionarily conserved.