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      Identification by functional proteomics of a deubiquitinating/deNeddylating enzyme in Plasmodium falciparum

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          Summary

          Ubiquitination is a post‐translational modification implicated in a variety of cellular functions, including transcriptional regulation, protein degradation and membrane protein trafficking. Ubiquitin and the enzymes that act on it, although conserved and essential in eukaryotes, have not been well studied in parasites, despite sequencing of several parasite genomes. Several putative ubiquitin hydrolases have been identified in Plasmodium falciparum based on sequence homology alone, with no evidence of expression or function. Here we identify the first deubiquitinating enzyme in P. falciparum, PfUCH54, by its activity. We show that PfUCH54 also has deNeddylating activity, as assayed by a mammalian Nedd8‐based probe. This activity is absent from mammalian homologues of PfUCH54. Given the importance of parasitic membrane protein trafficking as well as protein degradation in the virulence of this parasite, this family of enzymes may represent a target for pharmacological intervention with this disease.

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          Most cited references23

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          Human malaria parasites in continuous culture.

          Plasmodium falciparum can now be maintained in continuous culture in human erythrocytes incubated at 38 degrees C in RPMI 1640 medium with human serum under an atmosphere with 7 percent carbon dioxide and low oxygen (1 or 5 percent). The original parasite material, derived from an infected Aotus trivirgatus monkey, was diluted more than 100 million times by the addition of human erythrocytes at 3- or 4-day intervals. The parasites continued to reproduce in their normal asexual cycle of approximately 48 hours but were no longer highly synchronous. The have remained infective to Aotus.
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            The global distribution of clinical episodes of Plasmodium falciparum malaria.

            Interest in mapping the global distribution of malaria is motivated by a need to define populations at risk for appropriate resource allocation and to provide a robust framework for evaluating its global economic impact. Comparison of older and more recent malaria maps shows how the disease has been geographically restricted, but it remains entrenched in poor areas of the world with climates suitable for transmission. Here we provide an empirical approach to estimating the number of clinical events caused by Plasmodium falciparum worldwide, by using a combination of epidemiological, geographical and demographic data. We estimate that there were 515 (range 300-660) million episodes of clinical P. falciparum malaria in 2002. These global estimates are up to 50% higher than those reported by the World Health Organization (WHO) and 200% higher for areas outside Africa, reflecting the WHO's reliance upon passive national reporting for these countries. Without an informed understanding of the cartography of malaria risk, the global extent of clinical disease caused by P. falciparum will continue to be underestimated.
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              Enhanced genome annotation using structural profiles in the program 3D-PSSM.

              A method (three-dimensional position-specific scoring matrix, 3D-PSSM) to recognise remote protein sequence homologues is described. The method combines the power of multiple sequence profiles with knowledge of protein structure to provide enhanced recognition and thus functional assignment of newly sequenced genomes. The method uses structural alignments of homologous proteins of similar three-dimensional structure in the structural classification of proteins (SCOP) database to obtain a structural equivalence of residues. These equivalences are used to extend multiply aligned sequences obtained by standard sequence searches. The resulting large superfamily-based multiple alignment is converted into a PSSM. Combined with secondary structure matching and solvation potentials, 3D-PSSM can recognise structural and functional relationships beyond state-of-the-art sequence methods. In a cross-validated benchmark on 136 homologous relationships unambiguously undetectable by position-specific iterated basic local alignment search tool (PSI-Blast), 3D-PSSM can confidently assign 18 %. The method was applied to the remaining unassigned regions of the Mycoplasma genitalium genome and an additional 13 regions were assigned with 95 % confidence. 3D-PSSM is available to the community as a web server: http://www.bmm.icnet.uk/servers/3dpssm Copyright 2000 Academic Press.
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                Author and article information

                Journal
                Mol Microbiol
                Mol. Microbiol
                10.1111/(ISSN)1365-2958
                MMI
                Molecular Microbiology
                Blackwell Publishing Ltd (Oxford, UK )
                0950-382X
                1365-2958
                02 August 2006
                September 2006
                : 61
                : 5 ( doiID: 10.1111/mmi.2006.61.issue-5 )
                : 1187-1195
                Affiliations
                [ 1 ]Whitehead Institute for Biomedical Research, Nine Cambridge Center, Cambridge, MA 02142, USA.
                [ 2 ]Harvard School of Public Health, Building I, 665 Huntington Avenue, Boston, MA 02115, USA.
                Author notes
                [*] [* ] *E‐mail ploegh@ 123456wi.mit.edu ; Tel. (+1) 617 324 1878; Fax (+1) 617 452 3566.
                [†]

                Present address: Genentech, Inc. 1 DNA Way, South San Francisco, CA 94080, USA.

                Article
                MMI5307
                10.1111/j.1365-2958.2006.05307.x
                7168409
                16925553
                7eb08dad-a1fc-45b2-8346-fb90090ba1b9

                This article is being made freely available through PubMed Central as part of the COVID-19 public health emergency response. It can be used for unrestricted research re-use and analysis in any form or by any means with acknowledgement of the original source, for the duration of the public health emergency.

                History
                : 26 June 2006
                Page count
                links-crossref: 0, links-pubmed: 0, Figures: 5, Tables: 1, Equations: 0, References: 32, Pages: 9, Words: 5708
                Categories
                Research Articles
                Custom metadata
                2.0
                September 2006
                Converter:WILEY_ML3GV2_TO_JATSPMC version:5.8.0 mode:remove_FC converted:15.04.2020

                Microbiology & Virology
                Microbiology & Virology

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