Hostname: page-component-8448b6f56d-t5pn6 Total loading time: 0 Render date: 2024-04-24T05:08:25.363Z Has data issue: false hasContentIssue false

Characterization of mitochondrion-targeted GTPases in Plasmodium falciparum

Published online by Cambridge University Press:  12 April 2018

Kirti Gupta
Affiliation:
Division of Molecular and Structural Biology, CSIR-Central Drug Research Institute, Lucknow, India
Ankit Gupta
Affiliation:
Division of Molecular and Structural Biology, CSIR-Central Drug Research Institute, Lucknow, India
Afreen Haider
Affiliation:
Division of Molecular and Structural Biology, CSIR-Central Drug Research Institute, Lucknow, India
Saman Habib*
Affiliation:
Division of Molecular and Structural Biology, CSIR-Central Drug Research Institute, Lucknow, India
*
Author for correspondence: Saman Habib, E-mail: saman.habib@gmail.com, saman_habib@cdri.res.in

Abstract

Ribosome assembly is critical for translation and regulating the response to cellular events and requires a complex interplay of ribosomal RNA and proteins with assembly factors. We investigated putative participants in the biogenesis of the reduced organellar ribosomes of Plasmodium falciparum and identified homologues of two assembly GTPases – EngA and Obg that were found in mitochondria. Both are indispensable in bacteria and P. berghei EngA is among the ‘essential’ parasite blood stage proteins identified recently. PfEngA and PfObg1 interacted with parasite mitoribosomes in vivo. GTP stimulated PfEngA interaction with the 50S subunit of Escherichia coli surrogate ribosomes. Although PfObg1–ribosome interaction was independent of nucleotide binding, GTP hydrolysis by PfObg1 was enhanced upon ribosomal association. An additional function for PfObg1 in mitochondrial DNA transactions was suggested by its specific interaction with the parasite mitochondrial genome in vivo. Deletion analysis revealed that the positively-charged OBG (spoOB-associated GTP-binding protein) domain mediates DNA-binding. A role for PfEngA in mitochondrial genotoxic stress response was indicated by its over-expression upon methyl methanesulfonate-induced DNA damage. PfEngA had lower sensitivity to an E. coli EngA inhibitor suggesting differences with bacterial counterparts. Our results show the involvement of two important GTPases in P. falciparum mitochondrial function, with the first confirmed localization of an EngA homologue in eukaryotic mitochondria.

Type
Research Article
Copyright
Copyright © Cambridge University Press 2018 

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

References

Amunts, A, et al. (2015) The structure of the human mitochondrial ribosome. Science 348, 9598.Google Scholar
Atkinson, GC, Tenson, T and Hauryliuk, V (2011) The RelA/SpoT homolog (RSH) superfamily: distribution and functional evolution of ppGpp synthetases and hydrolases across the tree of life. PLoS ONE 6, e23479.Google Scholar
Baca, AM and Hol, WG (2000) Overcoming codon bias: a method for high-level overexpression of Plasmodium and other AT-rich parasite genes in Escherichia coli. International Journal for Parasitology 30, 113118.Google Scholar
Bharat, A, Blanchard, JE and Brown, ED (2013) A high-throughput screen of the GTPase activity of Escherichia coli EngA to find an inhibitor of bacterial ribosome biogenesis. Journal of Biomolecular Screening 18, 830836.Google Scholar
Bieri, P, et al. (2017) The complete structure of the chloroplast 70S ribosome in complex with translation factor pY. The EMBO Journal 36, 475486.Google Scholar
Bonventre, JA, et al. (2016) Targeting an essential GTPase Obg for the development of broad-spectrum antibiotics. PLoS ONE 11, e0148222.Google Scholar
Britton, RA (2009) Role of GTPases in bacterial ribosome assembly. Annual Review of Microbiology 63, 155176.Google Scholar
Buglino, J, et al. (2002) Structural and biochemical analysis of the Obg GTP binding protein. Structure 10, 15811592.Google Scholar
Bushell, E, et al. (2017) Functional profiling of a Plasmodium genome reveals an abundance of essential genes. Cell 170, 260272 e268.Google Scholar
Chatterjee, A and Datta, PP (2016) Intrinsic GTPase activity of a ribosomal maturation protein CgtA is associated with its inter-domain movement: insights from MD simulations and biochemical studies. Journal of Biomolecular Structure & Dynamics 35, 25782587.Google Scholar
Chen, SS and Williamson, JR (2013) Characterization of the ribosome biogenesis landscape in E. coli using quantitative mass spectrometry. Journal of Molecular Biology 425, 767779.Google Scholar
Desmond, E, et al. (2011) On the last common ancestor and early evolution of eukaryotes: reconstructing the history of mitochondrial ribosomes. Research in Microbiology 162, 5370.Google Scholar
Feagin, JE, et al. (2012) The fragmented mitochondrial ribosomal RNAs of Plasmodium falciparum. PLoS ONE 7, e38320.Google Scholar
Feng, B, et al. (2014) Structural and functional insights into the mode of action of a universally conserved Obg GTPase. PLoS Biology 12, e1001866.Google Scholar
Foth, BJ, et al. (2003) Dissecting apicoplast targeting in the malaria parasite Plasmodium falciparum. Science 299, 705708.Google Scholar
Greber, BJ and Ban, N (2016) Structure and function of the mitochondrial ribosome. Annual Review of Biochemistry 85, 103132.Google Scholar
Gupta, A, et al. (2014) Reduced ribosomes of the apicoplast and mitochondrion of Plasmodium spp. and predicted interactions with antibiotics. Open Biology 4, 140045.Google Scholar
Gupta, DK, et al. (2016) DNA damage regulation and its role in drug-related phenotypes in the malaria parasites. Scientific Reports 6, 23603.Google Scholar
Habib, S, Vaishya, S and Gupta, K (2016) Translation in organelles of apicomplexan parasites. Trends in Parasitology 32, 939952.Google Scholar
Haider, A, et al. (2015) Targeting and function of proteins mediating translation initiation in organelles of Plasmodium falciparum. Molecular Microbiology 96, 796814.Google Scholar
Hirano, Y, et al. (2006) Human small G proteins, ObgH1, and ObgH2, participate in the maintenance of mitochondria and nucleolar architectures. Genes to Cells 11, 12951304.Google Scholar
Hwang, J and Inouye, M (2006) The tandem GTPase, Der, is essential for the biogenesis of 50S ribosomal subunits in Escherichia coli. Molecular Microbiology 61, 16601672.Google Scholar
Hwang, J and Inouye, M (2008) Rela functionally suppresses the growth defect caused by a mutation in the G domain of the essential Der protein. Journal of Bacteriology 190, 32363243.Google Scholar
Hwang, J and Inouye, M (2010) Interaction of an essential Escherichia coli GTPase, Der, with the 50S ribosome via the KH-like domain. Journal of Bacteriology 192, 22772283.Google Scholar
Jeon, Y, et al. (2014) DER containing two consecutive GTP-binding domains plays an essential role in chloroplast ribosomal RNA processing and ribosome biogenesis in higher plants. Journal of Experimental Botany 65, 117130.Google Scholar
Jiang, M, et al. (2006) The Escherichia coli GTPase CgtAE is involved in late steps of large ribosome assembly. Journal of Bacteriology 188, 67576770.Google Scholar
Kaiser, A, et al. (2015) A putative non-canonical Ras-like GTPase from P. falciparum: chemical properties and characterization of the protein. PLoS ONE 10, e0140994.Google Scholar
Kint, C, et al. (2014) Bacterial Obg proteins: GTPases at the nexus of protein and DNA synthesis. Critical Reviews in Microbiology 40, 207224.Google Scholar
Kobayashi, G, Moriya, S and Wada, C (2001) Deficiency of essential GTP-binding protein ObgE in Escherichia coli inhibits chromosome partition. Molecular Microbiology 41, 10371051.Google Scholar
Kukimoto-Niino, M, et al. (2004) Crystal structure of the GTP-binding protein Obg from Thermus thermophilus HB8. Journal of Molecular Biology 337, 761770.Google Scholar
Lee, R, et al. (2011) Expression phenotypes suggest that Der participates in a specific, high affinity interaction with membranes. Protein Expression and Purification 78, 102112.Google Scholar
Majumdar, S, et al. (2017) Disrupting domain-domain interactions is indispensable for EngA-ribosome interactions. Biochimica et Biophysica Acta 1865, 289303.Google Scholar
Nierhaus, KH and Dohme, F (1974) Total reconstitution of functionally active 50S ribosomal subunits from Escherichia coli. Proceedings of the National Academy of Sciences of the United States of America 71, 47134717.Google Scholar
Ram, EV, et al. (2008) DNA organization by the apicoplast-targeted bacterial histone-like protein of Plasmodium falciparum. Nucleic Acids Research 36, 50615073.Google Scholar
Rao, AR and Varshney, U (2001) Specific interaction between the ribosome recycling factor and the elongation factor G from Mycobacterium tuberculosis mediates peptidyl-tRNA release and ribosome recycling in Escherichia coli. The EMBO Journal 20, 29772986.Google Scholar
Robinson, VL, et al. (2002) Domain arrangement of Der, a switch protein containing two GTPase domains. Structure 10, 16491658.Google Scholar
Sali, A and Blundell, TL (1993) Comparative protein modelling by satisfaction of spatial restraints. Journal of Molecular Biology 234, 779815.Google Scholar
Sasindran, SJ, et al. (2011) Biochemical and physiological characterization of the GTP-binding protein Obg of Mycobacterium tuberculosis. BMC Microbiology 11, 4354.Google Scholar
Sato, A, et al. (2005) The GTP binding protein Obg homolog ObgE is involved in ribosome maturation. Genes to Cells 10, 393408.Google Scholar
Shajani, Z, Sykes, MT and Williamson, JR (2011) Assembly of bacterial ribosomes. Annual Review of Biochemistry 80, 501526.Google Scholar
Smith, DE and Fisher, PA (1984) Identification, developmental regulation, and response to heat shock of two antigenically related forms of a major nuclear envelope protein in Drosophila embryos: application of an improved method for affinity purification of antibodies using polypeptides immobilized on nitrocellulose blots. The Journal of Cell Biology 99, 2028.Google Scholar
Strunk, BS and Karbstein, K (2009) Powering through ribosome assembly. RNA 15, 20832104.Google Scholar
Suwastika, IN, et al. (2014) Evidence for lateral gene transfer (LGT) in the evolution of eubacteria-derived small GTPases in plant organelles. Frontiers in Plant Science 5, 678693.Google Scholar
Tan, J, Jakob, U and Bardwell, JC (2002) Overexpression of two different GTPases rescues a null mutation in a heat-induced rRNA methyltransferase. Journal of Bacteriology 184, 26922698.Google Scholar
Tomar, SK, et al. (2009) Distinct GDP/GTP bound states of the tandem G-domains of EngA regulate ribosome binding. Nucleic Acids Research 37, 23592370.Google Scholar
Traub, P and Nomura, M (1968) Structure and function of E. coli ribosomes. V. Reconstitution of functionally active 30S ribosomal particles from RNA and proteins. Proceedings of the National Academy of Sciences of the United States of America 59, 777784.Google Scholar
Verstraeten, N, et al. (2011) The universally conserved prokaryotic GTPases. Microbiology and Molecular Biology Reviews 75, 507542.Google Scholar
Walter, JD, et al. (2012) Thiostrepton inhibits stable 70S ribosome binding and ribosome-dependent GTPase activation of elongation factor G and elongation factor 4. Nucleic Acids Research 40, 360370.Google Scholar
Wilson, DN and Nierhaus, KH (2007) The weird and wonderful world of bacterial ribosome regulation. Critical Reviews in Biochemistry and Molecular Biology 42, 187219.Google Scholar
Wout, P, et al. (2004) The Escherichia coli GTPase CgtAE cofractionates with the 50S ribosomal subunit and interacts with SpoT, a ppGpp synthetase/hydrolase. Journal of Bacteriology 186, 52495257.Google Scholar
Zhang, X, et al. (2014) Structural insights into the function of a unique tandem GTPase EngA in bacterial ribosome assembly. Nucleic Acids Research 42, 1343013439.Google Scholar
Zuegge, J, et al. (2001) Deciphering apicoplast targeting signals--feature extraction from nuclear-encoded precursors of Plasmodium falciparum apicoplast proteins. Gene 280, 1926.Google Scholar
Supplementary material: PDF

Gupta et al. supplementary material 1

Gupta et al. supplementary material

Download Gupta et al. supplementary material 1(PDF)
PDF 1.7 MB