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
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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)