Comparison of the peroxisomal matrix protein import system of different organisms. Exploration of possibilities for developing inhibitors of the import system of trypanosomatids for anti-parasite chemotherapy

Galland, Nathalie; Michels, Paul A.M.

doi:10.1016/j.ejcb.2010.04.001

Cited by 35 publications

(36 citation statements)

References 128 publications

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“…Peroxisomes display significant diversity among organisms (63), and the peroxisomes of plants, although less studied than their animal and yeast counterparts, have divergent features in their matrix protein import machinery (64). An example is the GreenCut2 peroxisomal protein AtPEX13 (At3g07560) (65).…”

Section: Functional Meta-analysis Of Localizationmentioning

confidence: 99%

The GreenCut2 Resource, a Phylogenomically Derived Inventory of Proteins Specific to the Plant Lineage

Karpowicz

Prochnik

Grossman

et al. 2011

Journal of Biological Chemistry

120

152

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The plastid is a defining structure of photosynthetic eukaryotes and houses many plant-specific processes, including the light reactions, carbon fixation, pigment synthesis, and other primary metabolic processes. Identifying proteins associated with catalytic, structural, and regulatory functions that are unique to plastid-containing organisms is necessary to fully define the scope of plant biochemistry. Here, we performed phylogenomics on 20 genomes to compile a new inventory of 597 nucleus-encoded proteins conserved in plants and green algae but not in non-photosynthetic organisms. 286 of these proteins are of known function, whereas 311 are not characterized. This inventory was validated as applicable and relevant to diverse photosynthetic eukaryotes using an additional eight genomes from distantly related plants (including Micromonas, Selaginella, and soybean). Manual curation of the known proteins in the inventory established its importance to plastid biochemistry. To predict functions for the 52% of proteins of unknown function, we used sequence motifs, subcellular localization, co-expression analysis, and RNA abundance data. We demonstrate that 18% of the proteins in the inventory have functions outside the plastid and/or beyond green tissues. Although 32% of proteins in the inventory have homologs in all cyanobacteria, unexpectedly, 30% are eukaryote-specific. Finally, 8% of the proteins of unknown function share no similarity to any characterized protein and are plant lineage-specific. We present this annotated inventory of 597 proteins as a resource for functional analyses of plant-specific biochemistry.The plastid is an organelle in plants and algae that evolved from a photosynthetic cyanobacterium after it was engulfed by an ancestral eukaryotic cell over 1.5 billion years ago (1, 2). How the endosymbiont became integral to host cell functions and evolved into a plastid is still under debate (3), but functions localized to the present day plastid depend on both plastid-and nucleus-encoded proteins. The latter are synthesized in the cytoplasm and imported into the organelle by a specific multiprotein complex composed of the translocon of the outer and inner chloroplast envelope membrane (TOC 4 and TIC, respectively) proteins (4, 5). Over 2000 proteins are estimated to be located in the plastid with the vast majority (Ͼ90%) encoded by genes in the nucleus (6 -9). Many of the nucleus-encoded proteins that function within plastids are conserved among photosynthetic organisms. These conserved proteins function in processes such as the capture and utilization of excitation energy, carbohydrate metabolism, and the synthesis of key cellular metabolites (such as lipids, isoprenoids, pigments, and amino acids). Interestingly, however, many plastid-localized proteins have not yet been assigned a specific biochemical function.The increasing availability of sequence information from diverse organisms has allowed the application of comparative genomics, or phylogenomics, to discover proteins specific to bacteria (...

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Section: Functional Meta-analysis Of Localizationmentioning

confidence: 99%

The GreenCut2 Resource, a Phylogenomically Derived Inventory of Proteins Specific to the Plant Lineage

Karpowicz

Prochnik

Grossman

et al. 2011

Journal of Biological Chemistry

120

152

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“…In trypanosomes, a number of proteins involved in import have been characterized, and recent studies have begun to identify processes involved in glycosome turnover and remodeling (5)(6)(7). However, very little is known about organelle biogenesis.…”

mentioning

confidence: 99%

Environmentally Regulated Glycosome Protein Composition in the African Trypanosome

Bauer

Morris

2013

Eukaryot Cell

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Trypanosomes compartmentalize many metabolic enzymes in glycosomes, peroxisome-related microbodies that are essential to parasite survival. While it is understood that these dynamic organelles undergo profound changes in protein composition throughout life cycle differentiation, the adaptations that occur in response to changes in environmental conditions are less appreciated. We have adopted a fluorescent-organelle reporter system in procyclic Trypanosoma brucei by expressing a fluorescent protein (FP) fused to a glycosomal targeting sequence (peroxisome-targeting sequence 2 [PTS2]). In these cell lines, PTS2-FP is localized within import-competent glycosomes, and organelle composition can be analyzed by microscopy and flow cytometry. Using this reporter system, we have characterized parasite populations that differ in their glycosome composition. In glucoserich medium, two parasite populations are observed; one population harbors glycosomes bearing the full repertoire of glycosome proteins, while the other parasite population contains glycosomes that lack the usual glycosome-resident proteins but do contain the glycosome membrane protein TbPEX11. Interestingly, these cells lack TbPEX13, a protein essential for the import of proteins into the glycosome. This bimodal distribution is lost in low-glucose medium. Furthermore, we have demonstrated that changes in environmental conditions trigger changes in glycosome protein composition. These findings demonstrate a level of procyclic glycosome diversity heretofore unappreciated and offer a system by which glycosome dynamics can be studied in live cells. This work adds to our growing understanding of how the regulation of glycosome composition relates to environmental sensing.T rypanosoma brucei, the causative agent of human African trypanosomiasis, has a complex life cycle, with developmental stages in the bloodstream of the mammalian host and the tsetse fly vector. Each host provides a distinct environment in which the parasites must survive. Bloodstream-form (BSF) parasites are bathed in glucose and generate ATP exclusively by glycolysis. While in the tsetse fly, the procyclic-form (PF) parasites experience a drop in glucose levels with a concomitant increase in the availability of amino acids (namely, proline). Under these conditions, the parasite adapts its metabolism, generating ATP from both glycolysis and amino acid metabolism (1).In trypanosomes, many of the enzymes involved in glycolysis are contained within membrane-bounded organelles called glycosomes (reviewed in references 2, 3, and 4). Similarities between the metabolic activities and the matrix protein import machineries of glycosomes and peroxisomes indicate an evolutionary relationship between the two organelles. In contrast to peroxisomes, however, glycosomes are essential, making mechanisms of glycosome biogenesis and maintenance attractive drug targets.Glycosome dynamics are governed by a number of processes, including organelle biogenesis, protein import, and changes in protein composition. In t...

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“…Peroxisomal import of both PTS1-and PTS2-containing proteins requires a family of proteins, peroxins (PEX), that recognize PTS1 or PTS2 and allow import (46). Several homologues of the PEX proteins have now been identified in trypanosomes and have been shown to be necessary for protein import into the glycosome (47)(48)(49)(50).…”

Section: Discussionmentioning

confidence: 99%

The Krebs Cycle Enzyme α-Ketoglutarate Decarboxylase Is an Essential Glycosomal Protein in Bloodstream African Trypanosomes

2015

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␣-Ketoglutarate decarboxylase (␣-KDE1) is a Krebs cycle enzyme found in the mitochondrion of the procyclic form (PF) of Trypanosoma brucei. The bloodstream form (BF) of T. brucei lacks a functional Krebs cycle and relies exclusively on glycolysis for ATP production. Despite the lack of a functional Krebs cycle, ␣-KDE1 was expressed in BF T. brucei and RNA interference knockdown of ␣-KDE1 mRNA resulted in rapid growth arrest and killing. Cell death was preceded by progressive swelling of the flagellar pocket as a consequence of recruitment of both flagellar and plasma membranes into the pocket. BF T. brucei expressing an epitope-tagged copy of ␣-KDE1 showed localization to glycosomes and not the mitochondrion. We used a cell line transfected with a reporter construct containing the N-terminal sequence of ␣-KDE1 fused to green fluorescent protein to examine the requirements for glycosome targeting. We found that the N-terminal 18 amino acids of ␣-KDE1 contain overlapping mitochondrion-and peroxisome-targeting sequences and are sufficient to direct localization to the glycosome in BF T. brucei. These results suggest that ␣-KDE1 has a novel moonlighting function outside the mitochondrion in BF T. brucei.

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Comparison of the peroxisomal matrix protein import system of different organisms. Exploration of possibilities for developing inhibitors of the import system of trypanosomatids for anti-parasite chemotherapy

Cited by 35 publications

References 128 publications

The GreenCut2 Resource, a Phylogenomically Derived Inventory of Proteins Specific to the Plant Lineage

The GreenCut2 Resource, a Phylogenomically Derived Inventory of Proteins Specific to the Plant Lineage

Environmentally Regulated Glycosome Protein Composition in the African Trypanosome

The Krebs Cycle Enzyme α-Ketoglutarate Decarboxylase Is an Essential Glycosomal Protein in Bloodstream African Trypanosomes

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