1
|
Chatterjee T, Tiwari A, Gupta R, Shukla H, Varshney A, Mishra S, Habib S. A Plasmodium apicoplast-targeted unique exonuclease/FEN exhibits interspecies functional differences attributable to an insertion that alters DNA-binding. Nucleic Acids Res 2024; 52:7843-7862. [PMID: 38888125 PMCID: PMC11260460 DOI: 10.1093/nar/gkae512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 05/30/2024] [Accepted: 06/03/2024] [Indexed: 06/20/2024] Open
Abstract
The human malaria parasite Plasmodium falciparum genome is among the most A + T rich, with low complexity regions (LCRs) inserted in coding sequences including those for proteins targeted to its essential relict plastid (apicoplast). Replication of the apicoplast genome (plDNA), mediated by the atypical multifunctional DNA polymerase PfPrex, would require additional enzymatic functions for lagging strand processing. We identified an apicoplast-targeted, [4Fe-4S]-containing, FEN/Exo (PfExo) with a long LCR insertion and detected its interaction with PfPrex. Distinct from other known exonucleases across organisms, PfExo recognized a wide substrate range; it hydrolyzed 5'-flaps, processed dsDNA as a 5'-3' exonuclease, and was a bipolar nuclease on ssDNA and RNA-DNA hybrids. Comparison with the rodent P. berghei ortholog PbExo, which lacked the insertion and [4Fe-4S], revealed interspecies functional differences. The insertion-deleted PfExoΔins behaved like PbExo with a limited substrate repertoire because of compromised DNA binding. Introduction of the PfExo insertion into PbExo led to gain of activities that the latter initially lacked. Knockout of PbExo indicated essentiality of the enzyme for survival. Our results demonstrate the presence of a novel apicoplast exonuclease with a functional LCR that diversifies substrate recognition, and identify it as the candidate flap-endonuclease and RNaseH required for plDNA replication and maintenance.
Collapse
Affiliation(s)
- Tribeni Chatterjee
- Division of Biochemistry and Structural Biology, CSIR-Central Drug Research Institute, Lucknow, India
| | - Anupama Tiwari
- Division of Biochemistry and Structural Biology, CSIR-Central Drug Research Institute, Lucknow, India
| | - Ritika Gupta
- Division of Biochemistry and Structural Biology, CSIR-Central Drug Research Institute, Lucknow, India
| | - Himadri Shukla
- Division of Molecular Microbiology and Immunology, CSIR-Central Drug Research Institute, Lucknow, India
| | - Aastha Varshney
- Division of Molecular Microbiology and Immunology, CSIR-Central Drug Research Institute, Lucknow, India
| | - Satish Mishra
- Division of Molecular Microbiology and Immunology, CSIR-Central Drug Research Institute, Lucknow, India
| | - Saman Habib
- Division of Biochemistry and Structural Biology, CSIR-Central Drug Research Institute, Lucknow, India
| |
Collapse
|
2
|
Tiwari A, Verma N, Shukla H, Mishra S, Kennedy K, Chatterjee T, Kuldeep J, Parwez S, Siddiqi MI, Ralph SA, Mishra S, Habib S. DNA N-glycosylases Ogg1 and EndoIII as components of base excision repair in Plasmodium falciparum organelles. Int J Parasitol 2024:S0020-7519(24)00137-1. [PMID: 38964640 DOI: 10.1016/j.ijpara.2024.06.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 05/31/2024] [Accepted: 06/28/2024] [Indexed: 07/06/2024]
Abstract
The integrity of genomes of the two crucial organelles of the malaria parasite - an apicoplast and mitochondrion in each cell - must be maintained by DNA repair mediated by proteins targeted to these compartments. We explored the localisation and function of Plasmodium falciparum base excision repair (BER) DNA N-glycosylase homologs PfEndoIII and PfOgg1. These N-glycosylases would putatively recognise DNA lesions prior to the action of apurinic/apyrimidinic (AP)-endonucleases. Both Ape1 and Apn1 endonucleases have earlier been shown to function solely in the parasite mitochondrion. Immunofluorescence localisation showed that PfEndoIII was exclusively mitochondrial. PfOgg1 was not seen clearly in mitochondria when expressed as a PfOgg1leader-GFP fusion, although chromatin immunoprecipitation assays showed that it could interact with both mitochondrial and apicoplast DNA. Recombinant PfEndoIII functioned as a DNA N-glycosylase as well as an AP-lyase on thymine glycol (Tg) lesions. We further studied the importance of Ogg1 in the malaria life cycle using reverse genetic approaches in Plasmodium berghei. Targeted disruption of PbOgg1 resulted in loss of 8-oxo-G specific DNA glycosylase/lyase activity. PbOgg1 knockout did not affect blood, mosquito or liver stage development but caused reduced blood stage infection after inoculation of sporozoites in mice. A significant reduction in erythrocyte infectivity by PbOgg1 knockout hepatic merozoites was also observed, thus showing that PbOgg1 ensures smooth transition from liver to blood stage infection. Our results strengthen the view that the Plasmodium mitochondrial genome is an important site for DNA repair by the BER pathway.
Collapse
Affiliation(s)
- Anupama Tiwari
- Division of Biochemistry and Structural Biology, CSIR-Central Drug Research Institute, Lucknow 226031, India
| | - Neetu Verma
- Division of Biochemistry and Structural Biology, CSIR-Central Drug Research Institute, Lucknow 226031, India
| | - Himadri Shukla
- Division of Molecular Microbiology and Immunology, CSIR-Central Drug Research Institute, Lucknow 226031, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Shivani Mishra
- Division of Biochemistry and Structural Biology, CSIR-Central Drug Research Institute, Lucknow 226031, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Kit Kennedy
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Victoria 3010, Australia
| | - Tribeni Chatterjee
- Division of Biochemistry and Structural Biology, CSIR-Central Drug Research Institute, Lucknow 226031, India
| | - Jitendra Kuldeep
- Division of Biochemistry and Structural Biology, CSIR-Central Drug Research Institute, Lucknow 226031, India
| | - Shahid Parwez
- Division of Biochemistry and Structural Biology, CSIR-Central Drug Research Institute, Lucknow 226031, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - M I Siddiqi
- Division of Biochemistry and Structural Biology, CSIR-Central Drug Research Institute, Lucknow 226031, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Stuart A Ralph
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Victoria 3010, Australia
| | - Satish Mishra
- Division of Molecular Microbiology and Immunology, CSIR-Central Drug Research Institute, Lucknow 226031, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
| | - Saman Habib
- Division of Biochemistry and Structural Biology, CSIR-Central Drug Research Institute, Lucknow 226031, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
| |
Collapse
|
3
|
Shrivastava D, Jha A, Kabrambam R, Vishwakarma J, Mitra K, Ramachandran R, Habib S. Plasmodium falciparum ZIP1 Is a Zinc-Selective Transporter with Stage-Dependent Targeting to the Apicoplast and Plasma Membrane in Erythrocytic Parasites. ACS Infect Dis 2024; 10:155-169. [PMID: 38163252 DOI: 10.1021/acsinfecdis.3c00426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2024]
Abstract
Replication of the malarial parasite in human erythrocytes requires massive zinc fluxes, necessitating the action of zinc transporters across the parasite plasma and organellar membranes. Although genetic knockout studies have been conducted on a few "orphan" zinc transporters in Plasmodium spp., none of them have been functionally characterized. We used the recombinant Plasmodium falciparum Zrt-/Irt-like protein (PfZIP1) and specific antibodies generated against it to explore the subcellular localization, function, metal-ion selectivity, and response to cellular zinc levels. PfZIP1 expression was enhanced upon the depletion of cytosolic Zn2+. The protein transitioned from the processed to unprocessed form through blood stages, localizing to the apicoplast in trophozoites and to the parasite plasma membrane in schizonts and gametocytes, indicating stage-specific functional role. The PfZIP1 dimer mediated Zn2+ influx in proteoliposomes. It exhibited preferential binding to Zn2+ compared to Fe2+, with the selectivity for zinc being driven by a C-terminal histidine-rich region conserved only in primate-infecting Plasmodium species.
Collapse
Affiliation(s)
- Deepti Shrivastava
- Division of Biochemistry and Structural Biology, CSIR-Central Drug Research Institute, Lucknow 226031, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Akanksha Jha
- Division of Biochemistry and Structural Biology, CSIR-Central Drug Research Institute, Lucknow 226031, India
| | - Rajlakshmi Kabrambam
- Division of Biochemistry and Structural Biology, CSIR-Central Drug Research Institute, Lucknow 226031, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Jyoti Vishwakarma
- Division of Biochemistry and Structural Biology, CSIR-Central Drug Research Institute, Lucknow 226031, India
| | - Kalyan Mitra
- Sophisticated Analytical Instrument Facility and Research Division, CSIR-Central Drug Research Institute, Lucknow 226031, India
| | - Ravishankar Ramachandran
- Division of Biochemistry and Structural Biology, CSIR-Central Drug Research Institute, Lucknow 226031, India
| | - Saman Habib
- Division of Biochemistry and Structural Biology, CSIR-Central Drug Research Institute, Lucknow 226031, India
| |
Collapse
|
4
|
Mohammad Sadik, Mohammad Afsar, Ramachandran R, Habib S. [Fe-S] biogenesis and unusual assembly of the ISC scaffold complex in the Plasmodium falciparum mitochondrion. Mol Microbiol 2021; 116:606-623. [PMID: 34032321 DOI: 10.1111/mmi.14735] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 05/06/2021] [Accepted: 05/06/2021] [Indexed: 12/16/2022]
Abstract
The malaria parasite harbors two [Fe-S] biogenesis pathways of prokaryotic origin-the SUF and ISC systems in the apicoplast and mitochondrion, respectively. While the SUF machinery has been delineated, there is little experimental evidence on the ISC pathway. We confirmed mitochondrial targeting of Plasmodium falciparum ISC proteins followed by analyses of cysteine desulfurase, scaffold, and [Fe-S]-carrier components. PfIscU functioned as the scaffold in complex with the PfIscS-PfIsd11 cysteine desulfurase and could directly assemble [4Fe-4S] without prior [2Fe-2S] formation seen in other homologs. Small angle X-ray scattering and spectral studies showed that PfIscU, a trimer, bound one [4Fe-4S]. In a deviation from reported complexes from other organisms, the P. falciparum desulfurase-scaffold complex assembled around a PfIscS tetramer instead of a dimer, resulting in a symmetric hetero-hexamer [2× (2PfIscS-2PfIsd11-2PfIscU)]. PfIscU directly transferred [4Fe-4S] to the apo-protein aconitase B thus abrogating the requirement of intermediary proteins for conversion of [2Fe-2S] to [4Fe-4S] before transfer to [4Fe-4S]-recipients. Among the putative cluster-carriers, PfIscA2 was more efficient than PfNifU-like protein; PfIscA1 primarily bound iron, suggesting its potential role as a Fe2+ carrier/donor. Our results identify the core P. falciparum ISC machinery and reveal unique features compared with those in bacteria or yeast and human mitochondria.
Collapse
Affiliation(s)
- Mohammad Sadik
- Division of Molecular and Structural Biology, CSIR-Central Drug Research Institute, Lucknow, India
| | - Mohammad Afsar
- Division of Molecular and Structural Biology, CSIR-Central Drug Research Institute, Lucknow, India
| | - Ravishankar Ramachandran
- Division of Molecular and Structural Biology, CSIR-Central Drug Research Institute, Lucknow, India
| | - Saman Habib
- Division of Molecular and Structural Biology, CSIR-Central Drug Research Institute, Lucknow, India
| |
Collapse
|