Organellar proteomics reveals hundreds of novel nuclear proteins in the malaria parasite Plasmodium falciparum

Genome Biology, Nov 2012

Background The post-genomic era of malaria research provided unprecedented insights into the biology of Plasmodium parasites. Due to the large evolutionary distance to model eukaryotes, however, we lack a profound understanding of many processes in Plasmodium biology. One example is the cell nucleus, which controls the parasite genome in a development- and cell cycle-specific manner through mostly unknown mechanisms. To study this important organelle in detail, we conducted an integrative analysis of the P. falciparum nuclear proteome. Results We combined high accuracy mass spectrometry and bioinformatic approaches to present for the first time an experimentally determined core nuclear proteome for P. falciparum. Besides a large number of factors implicated in known nuclear processes, one-third of all detected proteins carry no functional annotation, including many phylum- or genus-specific factors. Importantly, extensive experimental validation using 30 transgenic cell lines confirmed the high specificity of this inventory, and revealed distinct nuclear localization patterns of hitherto uncharacterized proteins. Further, our detailed analysis identified novel protein domains potentially implicated in gene transcription pathways, and sheds important new light on nuclear compartments and processes including regulatory complexes, the nucleolus, nuclear pores, and nuclear import pathways. Conclusion Our study provides comprehensive new insight into the biology of the Plasmodium nucleus and will serve as an important platform for dissecting general and parasite-specific nuclear processes in malaria parasites. Moreover, as the first nuclear proteome characterized in any protist organism, it will provide an important resource for studying evolutionary aspects of nuclear biology.

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Organellar proteomics reveals hundreds of novel nuclear proteins in the malaria parasite Plasmodium falciparum

Oehring et al. Genome Biology Organellar proteomics reveals hundreds of novel nuclear proteins in the malaria parasite Plasmodium falciparum Sophie C Oehring 0 2 Ben J Woodcroft 1 Suzette Moes 3 Johanna Wetzel 0 2 Olivier Dietz 0 2 Andreas Pulfer 0 2 Chaitali Dekiwadia 1 Pascal Maeser 0 2 Christian Flueck 0 2 Kathrin Witmer 0 2 Nicolas MB Brancucci 0 2 Igor Niederwieser 0 2 Paul Jenoe 3 Stuart A Ralph 1 Till S Voss 0 2 0 Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute , Socinstrasse 57, Basel 4051 , Switzerland 1 Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne , 30 Flemington Road, Parkville 3010 , Australia 2 University of Basel , Petersplatz 1, Basel 4003 , Switzerland 3 Biozentrum, University of Basel , Klingelbergstrasse 50/70, Basel 4056 , Switzerland Background: The post-genomic era of malaria research provided unprecedented insights into the biology of Plasmodium parasites. Due to the large evolutionary distance to model eukaryotes, however, we lack a profound understanding of many processes in Plasmodium biology. One example is the cell nucleus, which controls the parasite genome in a development- and cell cycle-specific manner through mostly unknown mechanisms. To study this important organelle in detail, we conducted an integrative analysis of the P. falciparum nuclear proteome. Results: We combined high accuracy mass spectrometry and bioinformatic approaches to present for the first time an experimentally determined core nuclear proteome for P. falciparum. Besides a large number of factors implicated in known nuclear processes, one-third of all detected proteins carry no functional annotation, including many phylum- or genus-specific factors. Importantly, extensive experimental validation using 30 transgenic cell lines confirmed the high specificity of this inventory, and revealed distinct nuclear localization patterns of hitherto uncharacterized proteins. Further, our detailed analysis identified novel protein domains potentially implicated in gene transcription pathways, and sheds important new light on nuclear compartments and processes including regulatory complexes, the nucleolus, nuclear pores, and nuclear import pathways. Conclusion: Our study provides comprehensive new insight into the biology of the Plasmodium nucleus and will serve as an important platform for dissecting general and parasite-specific nuclear processes in malaria parasites. Moreover, as the first nuclear proteome characterized in any protist organism, it will provide an important resource for studying evolutionary aspects of nuclear biology. Malaria; Plasmodium falciparum; Nucleus; Proteomics; Bioinformatics; IFA; Transcription; Nucleolus; Nuclear pore; Transfection - Background As one of the most deadly infectious diseases in the world, malaria causes close to 500 million clinical cases and 1 million deaths every year [1,2]. Most of this burden is due to infections with Plasmodium falciparum, one of six Plasmodium species known to elicit malaria in humans [3,4]. Malaria-related morbidity and mortality is exclusively associated with the erythrocytic stage of infection where repeated rounds of intracellular parasite development and re-invasion into red blood cells (RBCs) lead to exponential parasite proliferation. The entire parasite life cycle is much more complex involving several morphologically and functionally distinct extra- and intracellular stages, and obligate transmission between two hosts, female Anopheles spp. and humans. The key to this amazing biological complexity lies within the parasite nucleus that, in the case of P. falciparum, encloses and regulates a 23Mb genome encoding 5,400 genes on 14 linear chromosomes [5]. However, albeit many nuclear processes such as transcription, splicing, DNA replication/repair, mitosis, and the temporal and spatial organization of the nucleus have been studied in detail in model eukaryotes our understanding of nuclear biology in P. falciparum is very limited. This is not surprising given that >50% of all genes code for proteins with no known or even inferred function [5-7]. While many seminal studies in the post-genomic era of malaria research provided unprecedented insights into the biology of P. falciparum, they also highlighted our profound lack of understanding of basic biological processes in this parasite. In light of spreading drug resistance and the eager expectation for an effective vaccine, acquisition of such knowledge is urgently needed. During the pre-replicative phase of the intra-erythrocytic developmental cycle (IDC), parasites develop into morphologically distinct ring and trophozoite stages. Schizogony is characterized by multiple rounds of genome replication and closed mitosis before cytokinesis produces new daughter merozoites from multinucleated schizonts [8,9]. At the ultrastructural level, the parasite nucle (...truncated)


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Sophie C Oehring, Ben J Woodcroft, Suzette Moes, Johanna Wetzel, Olivier Dietz, Andreas Pulfer, Chaitali Dekiwadia, Pascal Maeser, Christian Flueck, Kathrin Witmer, Nicolas MB Brancucci, Igor Niederwieser, Paul Jenoe, Stuart A Ralph, Till S Voss. Organellar proteomics reveals hundreds of novel nuclear proteins in the malaria parasite Plasmodium falciparum, Genome Biology, 2012, pp. R108, 13, DOI: 10.1186/gb-2012-13-11-r108