Targeting and function of proteins mediating translation initiation in organelles of Plasmodium falciparum

The malaria parasite Plasmodium falciparum has two translationally active organelles – the apicoplast and mitochondrion, which import nuclear‐encoded translation factors to mediate protein synthesis. Initiation of translation is a complex step wherein initiation factors (IFs) act in a regulated manner to form an initiation complex. We identified putative organellar IFs and investigated the targeting, structure and function of IF1, IF2 and IF3 homologues encoded by the parasite nuclear genome. A single PfIF1 is targeted to the apicoplast. Apart from its critical ribosomal interactions, PfIF1 also exhibited nucleic‐acid binding and melting activities and mediated transcription anti‐termination. This suggests a prominent ancillary function for PfIF1 in destabilisation of DNA and RNA hairpin loops encountered during transcription and translation of the A+T rich apicoplast genome. Of the three putative IF2 homologues, only one (PfIF2a) was an organellar protein with mitochondrial localisation. We additionally identified an IF3 (PfIF3a) that localised exclusively to the mitochondrion and another protein, PfIF3b, that was apicoplast targeted. PfIF3a exhibited ribosome anti‐association activity, and monosome splitting by PfIF3a was enhanced by ribosome recycling factor (PfRRF2) and PfEF‐GMit. These results fill a gap in our understanding of organellar translation in Plasmodium, which is the site of action of several anti‐malarial compounds.

[1]  S. Ralph,et al.  Reduced ribosomes of the apicoplast and mitochondrion of Plasmodium spp. and predicted interactions with antibiotics , 2014, Open Biology.

[2]  K. Srivastava,et al.  The effect of fusidic acid on Plasmodium falciparum elongation factor G (EF-G). , 2013, Molecular and biochemical parasitology.

[3]  S. Ralph,et al.  Recycling factors for ribosome disassembly in the apicoplast and mitochondrion of Plasmodium falciparum , 2013, Molecular microbiology.

[4]  L. Ribas de Pouplana,et al.  Structural analysis of malaria-parasite lysyl-tRNA synthetase provides a platform for drug development. , 2013, Acta crystallographica. Section D, Biological crystallography.

[5]  R. Gutell,et al.  The Fragmented Mitochondrial Ribosomal RNAs of Plasmodium falciparum , 2012, PloS one.

[6]  Tanel Tenson,et al.  Evolutionary and genetic analyses of mitochondrial translation initiation factors identify the missing mitochondrial IF3 in S. cerevisiae , 2012, Nucleic acids research.

[7]  G. McFadden,et al.  Plasmodium falciparum apicoplast drugs: targets or off-targets? , 2012, Chemical reviews.

[8]  S. Ralph,et al.  Protein translation in Plasmodium parasites. , 2011, Trends in parasitology.

[9]  R. Agrawal,et al.  Computational Exploration of Structural Hypotheses for an Additional Sequence in a Mammalian Mitochondrial Protein , 2011, PloS one.

[10]  M. Valle,et al.  The Cryo-EM Structure of a Complete 30S Translation Initiation Complex from Escherichia coli , 2011, PLoS biology.

[11]  G. McFadden,et al.  Characterization of Two Malaria Parasite Organelle Translation Elongation Factor G Proteins: The Likely Targets of the Anti-Malarial Fusidic Acid , 2011, PloS one.

[12]  S. Ralph,et al.  Interaction of apicoplast-encoded elongation factor (EF) EF-Tu with nuclear-encoded EF-Ts mediates translation in the Plasmodiumfalciparum plastid. , 2011, International journal for parasitology.

[13]  M. Haque,et al.  Insertion domain within mammalian mitochondrial translation initiation factor 2 serves the role of eubacterial initiation factor 1 , 2011, Proceedings of the National Academy of Sciences.

[14]  B. Foth,et al.  Mitochondrial translation in absence of local tRNA aminoacylation and methionyl tRNAMet formylation in Apicomplexa , 2010, Molecular microbiology.

[15]  G. McFadden,et al.  The evolution, metabolism and functions of the apicoplast , 2010, Philosophical Transactions of the Royal Society B: Biological Sciences.

[16]  G. Hatzopoulos,et al.  Structure of translation initiation factor 1 from Mycobacterium tuberculosis and inferred binding to the 30S ribosomal subunit , 2010, FEBS letters.

[17]  C. Florentz,et al.  Diversity and similarity in the tRNA world: Overall view and case study on malaria‐related tRNAs , 2010, FEBS letters.

[18]  A. Schneider,et al.  A mechanism for functional segregation of mitochondrial and cytosolic genetic codes , 2009, Proceedings of the National Academy of Sciences.

[19]  K. Severinov,et al.  Comparative analysis of changes in gene expression due to RNA melting activities of translation initiation factor IF1 and a cold shock protein of the CspA family , 2009, Genes to cells : devoted to molecular & cellular mechanisms.

[20]  M. Mather,et al.  Mitochondrial evolution and functions in malaria parasites. , 2009, Annual review of microbiology.

[21]  T. Triglia,et al.  Reticulocyte binding protein homologues are key adhesins during erythrocyte invasion by Plasmodium falciparum , 2009, Cellular microbiology.

[22]  L. Spremulli,et al.  Evidence for an active role of IF3mt in the initiation of translation in mammalian mitochondria. , 2009, Biochemistry.

[23]  Robert L Moritz,et al.  Role of the Plasmodium Export Element in Trafficking Parasite Proteins to the Infected Erythrocyte , 2009, Traffic.

[24]  Rangeetha J Naik,et al.  DNA organization by the apicoplast-targeted bacterial histone-like protein of Plasmodium falciparum , 2008, Nucleic acids research.

[25]  M. Ehrenberg,et al.  Complementary roles of initiation factor 1 and ribosome recycling factor in 70S ribosome splitting , 2008, The EMBO journal.

[26]  P. Rosenthal,et al.  Apicoplast translation, transcription and genome replication: targets for antimalarial antibiotics. , 2008, Trends in parasitology.

[27]  Christian Cole,et al.  The Jpred 3 secondary structure prediction server , 2008, Nucleic Acids Res..

[28]  R. Agrawal,et al.  A single mammalian mitochondrial translation initiation factor functionally replaces two bacterial factors. , 2008, Molecular cell.

[29]  M. Haque,et al.  The interaction of mammalian mitochondrial translational initiation factor 3 with ribosomes: evolution of terminal extensions in IF3mt , 2007, Nucleic acids research.

[30]  A. Manuell,et al.  Chloroplast translation regulation , 2007, Photosynthesis Research.

[31]  C. Howe,et al.  The little genome of apicomplexan plastids: its raison d'etre and a possible explanation for the 'delayed death' phenomenon. , 2007, Protist.

[32]  G. McFadden,et al.  The effects of anti-bacterials on the malaria parasite Plasmodium falciparum. , 2007, Molecular and biochemical parasitology.

[33]  S. Brunak,et al.  Locating proteins in the cell using TargetP, SignalP and related tools , 2007, Nature Protocols.

[34]  D. Court,et al.  Transcription Antitermination by Translation Initiation Factor IF1 , 2007, Journal of bacteriology.

[35]  L. Isaksson,et al.  RNA chaperone activity of translation initiation factor IF1. , 2006, Biochimie.

[36]  Joseph L. DeRisi,et al.  Tetracyclines Specifically Target the Apicoplast of the Malaria Parasite Plasmodium falciparum , 2006, Antimicrobial Agents and Chemotherapy.

[37]  N. S. Singh,et al.  Evidence for a role of initiation factor 3 in recycling of ribosomal complexes stalled on mRNAs in Escherichia coli , 2005, Nucleic acids research.

[38]  L. Spremulli,et al.  The interaction of mitochondrial translational initiation factor 2 with the small ribosomal subunit. , 2005, Biochimica et biophysica acta.

[39]  Sushma Chaubey,et al.  The apicoplast of Plasmodium falciparum is translationally active , 2005, Molecular microbiology.

[40]  B. S. Laursen,et al.  Initiation of Protein Synthesis in Bacteria , 2005, Microbiology and Molecular Biology Reviews.

[41]  Christopher J. Tonkin,et al.  Localization of organellar proteins in Plasmodium falciparum using a novel set of transfection vectors and a new immunofluorescence fixation method. , 2004, Molecular and biochemical parasitology.

[42]  A. Kaji,et al.  Release of Ribosome-bound Ribosome Recycling Factor by Elongation Factor G* , 2003, Journal of Biological Chemistry.

[43]  M. Ehrenberg,et al.  The roles of initiation factor 2 and guanosine triphosphate in initiation of protein synthesis , 2003, The EMBO journal.

[44]  C. Gualerzi,et al.  Mapping the active sites of bacterial translation initiation factor IF3. , 2003, Journal of molecular biology.

[45]  G. Kramer,et al.  Purification and characterization of yeast mitochondrial initiation factor 2. , 2003, Archives of biochemistry and biophysics.

[46]  Christopher J. Tonkin,et al.  Dissecting Apicoplast Targeting in the Malaria Parasite Plasmodium falciparum , 2003, Science.

[47]  C. Gualerzi,et al.  Structure and function of bacterial initiation factors. , 2002, Current protein & peptide science.

[48]  J Zuegge,et al.  Deciphering apicoplast targeting signals--feature extraction from nuclear-encoded precursors of Plasmodium falciparum apicoplast proteins. , 2001, Gene.

[49]  C. Gualerzi,et al.  Translation initiation factor IF3: two domains, five functions, one mechanism? , 2001, The EMBO journal.

[50]  A. James,et al.  Stage-dependent Localization of a Novel Gene Product of the Malaria Parasite, Plasmodium falciparum * , 2001, The Journal of Biological Chemistry.

[51]  M. Inouye,et al.  Acquirement of cold sensitivity by quadruple deletion of the cspA family and its suppression by PNPase S1 domain in Escherichia coli , 2001, Molecular microbiology.

[52]  V. Ramakrishnan,et al.  Crystal structure of an initiation factor bound to the 30S ribosomal subunit. , 2001, Science.

[53]  J. Puglisi,et al.  Interaction of translation initiation factor IF1 with the E. coli ribosomal A site. , 2000, Journal of molecular biology.

[54]  J Frank,et al.  Location of translational initiation factor IF3 on the small ribosomal subunit. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[55]  U. RajBhandary,et al.  Suppressor mutations in Escherichia coli methionyl-tRNA formyltransferase: role of a 16-amino acid insertion module in initiator tRNA recognition. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[56]  C. Gualerzi,et al.  The structure of the translational initiation factor IF1 from E.coli contains an oligomer‐binding motif , 1997, The EMBO journal.

[57]  R. Wilson,et al.  Extrachromosomal DNA in the Apicomplexa. , 1997, Microbiology and molecular biology reviews : MMBR.

[58]  T. Fox.  Translational control of endogenous and recoded nuclear genes in yeast mitochondria: Regulation and membrane targeting , 1996, Experientia.

[59]  P Vincens,et al.  Computational method to predict mitochondrially imported proteins and their targeting sequences. , 1996, European journal of biochemistry.

[60]  S. Blanquet,et al.  Solution structure of the ribosome-binding domain of E. coli translation initiation factor IF3. Homology with the U1A protein of the eukaryotic spliceosome. , 1995, Journal of molecular biology.

[61]  V. Ramakrishnan,et al.  X‐ray crystallography shows that translational initiation factor IF3 consists of two compact alpha/beta domains linked by an alpha‐helix. , 1995, The EMBO journal.

[62]  S. Blanquet,et al.  1H and 15N resonance assignments and structure of the N-terminal domain of Escherichia coli initiation factor 3. , 1995, European journal of biochemistry.

[63]  R. Landick,et al.  Termination-altering amino acid substitutions in the beta' subunit of Escherichia coli RNA polymerase identify regions involved in RNA chain elongation. , 1994, Genes & development.

[64]  T. Fox,et al.  COX3 mRNA-specific translational activator proteins are associated with the inner mitochondrial membrane in Saccharomyces cerevisiae. , 1993, The Journal of biological chemistry.

[65]  C. Gualerzi,et al.  Translation of mRNAs with degenerate initiation triplet AUU displays high initiation factor 2 dependence and is subject to initiation factor 3 repression. , 1993, Proceedings of the National Academy of Sciences of the United States of America.

[66]  J. Feagin.  The 6-kb element of Plasmodium falciparum encodes mitochondrial cytochrome genes. , 1992, Molecular and biochemical parasitology.

[67]  L. Gold,et al.  Domains of initiator tRNA and initiation codon crucial for initiator tRNA selection by Escherichia coli IF3. , 1990, Genes & development.

[68]  T. Schleich,et al.  A circular dichroism study of Escherichia coli Initiation Factor-1 binding to polynucleotides. , 1980, Biochimica et biophysica acta.

[69]  C. Gualerzi,et al.  Initial rate kinetic analysis of the mechanism of initiation complex formation and the role of initiation factor IF-3. , 1977, Biochemistry.

[70]  W. Trager,et al.  Human malaria parasites in continuous culture. , 1976, Science.

[71]  M Grunberg-Manago,et al.  Light-scattering studies showing the effect of initiation factors on the reversible dissociation of Escherichia coli ribosomes. , 1975, Journal of molecular biology.

[72]  R. Agrawal,et al.  Insights into Structural Basis of Mammalian Mitochondrial Translation , 2013 .

[73]  A. Duchêne.  Translation in Mitochondria and Other Organelles , 2013, Springer Berlin Heidelberg.

[74]  Michael D. Abràmoff,et al.  Image processing with ImageJ , 2004 .

[75]  T. Triglia,et al.  Negative selection of Plasmodium falciparum reveals targeted gene deletion by double crossover recombination. , 2002, International journal for parasitology.

[76]  Roman A. Laskowski,et al.  PDBsum: summaries and analyses of PDB structures , 2001, Nucleic Acids Res..