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Saha D, Pramanik A, Freville A, Siddiqui AA, Pal U, Banerjee C, Nag S, Debsharma S, Pramanik S, Mazumder S, Maiti NC, Datta S, van Ooij C, Bandyopadhyay U. Structure-function analysis of nucleotide housekeeping protein HAM1 from human malaria parasite Plasmodium falciparum. FEBS J 2024. [PMID: 39003571 DOI: 10.1111/febs.17216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2024] [Revised: 03/29/2024] [Accepted: 06/20/2024] [Indexed: 07/15/2024]
Abstract
Non-canonical nucleotides, generated as oxidative metabolic by-products, significantly threaten the genome integrity of Plasmodium falciparum and thereby, their survival, owing to their mutagenic effects. PfHAM1, an evolutionarily conserved inosine/xanthosine triphosphate pyrophosphohydrolase, maintains nucleotide homeostasis in the malaria parasite by removing non-canonical nucleotides, although structure-function intricacies are hitherto poorly reported. Here, we report the X-ray crystal structure of PfHAM1, which revealed a homodimeric structure, additionally validated by size-exclusion chromatography-multi-angle light scattering analysis. The two monomeric units in the dimer were aligned in a parallel fashion, and critical residues associated with substrate and metal binding were identified, wherein a notable structural difference was observed in the β-sheet main frame compared to human inosine triphosphate pyrophosphatase. PfHAM1 exhibited Mg++-dependent pyrophosphohydrolase activity and the highest binding affinity to dITP compared to other non-canonical nucleotides as measured by isothermal titration calorimetry. Modifying the pfham1 genomic locus followed by live-cell imaging of expressed mNeonGreen-tagged PfHAM1 demonstrated its ubiquitous presence in the cytoplasm across erythrocytic stages with greater expression in trophozoites and schizonts. Interestingly, CRISPR-Cas9/DiCre recombinase-guided pfham1-null P. falciparum survived in culture under standard growth conditions, indicating its assistive role in non-canonical nucleotide clearance during intra-erythrocytic stages. This is the first comprehensive structural and functional report of PfHAM1, an atypical nucleotide-cleansing enzyme in P. falciparum.
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Affiliation(s)
- Debanjan Saha
- Division of Infectious Diseases and Immunology, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Atanu Pramanik
- Division of Structural Biology & Bioinformatics, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Aline Freville
- Department of Infection Biology, London School of Hygiene & Tropical Medicine, UK
| | - Asim Azhar Siddiqui
- Division of Infectious Diseases and Immunology, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Uttam Pal
- Division of Structural Biology & Bioinformatics, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Chinmoy Banerjee
- Division of Infectious Diseases and Immunology, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Shiladitya Nag
- Division of Infectious Diseases and Immunology, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Subhashis Debsharma
- Division of Infectious Diseases and Immunology, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Saikat Pramanik
- Division of Infectious Diseases and Immunology, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Somnath Mazumder
- Department of Zoology, Raja Peary Mohan College, Uttarpara, India
| | - Nakul C Maiti
- Division of Structural Biology & Bioinformatics, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Saumen Datta
- Division of Structural Biology & Bioinformatics, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Christiaan van Ooij
- Department of Infection Biology, London School of Hygiene & Tropical Medicine, UK
| | - Uday Bandyopadhyay
- Division of Infectious Diseases and Immunology, CSIR-Indian Institute of Chemical Biology, Kolkata, India
- Department of Biological Sciences, Bose Institute, Kolkata, India
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2
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Cissé OH, Ma L, Kovacs JA. Retracing the evolution of Pneumocystis species, with a focus on the human pathogen Pneumocystis jirovecii. Microbiol Mol Biol Rev 2024; 88:e0020222. [PMID: 38587383 PMCID: PMC11332345 DOI: 10.1128/mmbr.00202-22] [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: 04/09/2024] Open
Abstract
SUMMARYEvery human being is presumed to be infected by the fungus Pneumocystis jirovecii at least once in his or her lifetime. This fungus belongs to a large group of species that appear to exclusively infect mammals, with P. jirovecii being the only one known to cause disease in humans. The mystery of P. jirovecii origin and speciation is just beginning to unravel. Here, we provide a review of the major steps of P. jirovecii evolution. The Pneumocystis genus likely originated from soil or plant-associated organisms during the period of Cretaceous ~165 million years ago and successfully shifted to mammals. The transition coincided with a substantial loss of genes, many of which are related to the synthesis of nutrients that can be scavenged from hosts or cell wall components that could be targeted by the mammalian immune system. Following the transition, the Pneumocystis genus cospeciated with mammals. Each species specialized at infecting its own host. Host specialization is presumably built at least partially upon surface glycoproteins, whose protogene was acquired prior to the genus formation. P. jirovecii appeared at ~65 million years ago, overlapping with the emergence of the first primates. P. jirovecii and its sister species P. macacae, which infects macaques nowadays, may have had overlapping host ranges in the distant past. Clues from molecular clocks suggest that P. jirovecii did not cospeciate with humans. Molecular evidence suggests that Pneumocystis speciation involved chromosomal rearrangements and the mounting of genetic barriers that inhibit gene flow among species.
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Affiliation(s)
- Ousmane H. Cissé
- Critical Care Medicine Department, Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Liang Ma
- Critical Care Medicine Department, Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Joseph A. Kovacs
- Critical Care Medicine Department, Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
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Kalamuddin M, Shakri AR, Wang C, Min H, Li X, Cui L, Miao J. MYST regulates DNA repair and forms a NuA4-like complex in the malaria parasite Plasmodium falciparum. mSphere 2024; 9:e0014024. [PMID: 38564734 PMCID: PMC11036802 DOI: 10.1128/msphere.00140-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Accepted: 03/13/2024] [Indexed: 04/04/2024] Open
Abstract
Histone lysine acetyltransferase MYST-associated NuA4 complex is conserved from yeast to humans and plays key roles in cell cycle regulation, gene transcription, and DNA replication/repair. Here, we identified a Plasmodium falciparum MYST-associated complex, PfNuA4, which contains 11 of the 13 conserved NuA4 subunits. Reciprocal pulldowns using PfEAF2, a shared component between the NuA4 and SWR1 complexes, not only confirmed the PfNuA4 complex but also identified the PfSWR1 complex, a histone remodeling complex, although their identities are low compared to the homologs in yeast or humans. Notably, both H2A.Z/H2B.Z were associated with the PfSWR1 complex, indicating that this complex is involved in the deposition of H2A.Z/H2B.Z, the variant histone pair that is enriched in the activated promoters. Overexpression of PfMYST resulted in earlier expression of genes involved in cell cycle regulation, DNA replication, and merozoite invasion, and upregulation of the genes related to antigenic variation and DNA repair. Consistently, PfMYST overexpression led to high basal phosphorylated PfH2A (γ-PfH2A), the mark of DNA double-strand breaks, and conferred protection against genotoxic agent methyl methanesulfonate (MMS), X-rays, and artemisinin, the first-line antimalarial drug. In contrast, the knockdown of PfMYST caused a delayed parasite recovery upon MMS treatment. MMS induced the gradual disappearance of PfMYST in the cytoplasm and concomitant accumulation of PfMYST in the nucleus, suggesting cytoplasm-nucleus shuttling of PfMYST. Meanwhile, PfMYST colocalized with the γ-PfH2A, indicating PfMYST was recruited to the DNA damage sites. Collectively, PfMYST plays critical roles in cell cycle regulation, gene transcription, and DNA replication/DNA repair in this low-branching parasitic protist.IMPORTANCEUnderstanding gene regulation and DNA repair in malaria parasites is critical for identifying targets for antimalarials. This study found PfNuA4, a PfMYST-associated, histone modifier complex, and PfSWR1, a chromatin remodeling complex in malaria parasite Plasmodium falciparum. These complexes are divergent due to the low identities compared to their homologs from yeast and humans. Furthermore, overexpression of PfMYST resulted in substantial transcriptomic changes, indicating that PfMYST is involved in regulating the cell cycle, antigenic variation, and DNA replication/repair. Consistently, PfMYST was found to protect against DNA damage caused by the genotoxic agent methyl methanesulfonate, X-rays, and artemisinin, the first-line antimalarial drug. Additionally, DNA damage led to the relocation of cytoplasmic PfMYST to the nucleus and colocalization of PfMYST with γ-PfH2A, the mark of DNA damage. In summary, this study demonstrated that the PfMYST complex has critical functions in regulating cell cycle, antigenic variation, and DNA replication/DNA repair in P. falciparum.
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Affiliation(s)
- Mohammad Kalamuddin
- Department of Internal Medicine, University of South Florida, Morsani College of Medicine, Tampa, Florida, USA
| | - Ahmad Rushdi Shakri
- Department of Internal Medicine, University of South Florida, Morsani College of Medicine, Tampa, Florida, USA
| | - Chengqi Wang
- Center for Global Health and Infectious Diseases Research, College of Public Health, University of South Florida, Tampa, Florida, USA
| | - Hui Min
- Department of Internal Medicine, University of South Florida, Morsani College of Medicine, Tampa, Florida, USA
| | - Xiaolian Li
- Department of Internal Medicine, University of South Florida, Morsani College of Medicine, Tampa, Florida, USA
| | - Liwang Cui
- Department of Internal Medicine, University of South Florida, Morsani College of Medicine, Tampa, Florida, USA
- Center for Global Health and Infectious Diseases Research, College of Public Health, University of South Florida, Tampa, Florida, USA
| | - Jun Miao
- Department of Internal Medicine, University of South Florida, Morsani College of Medicine, Tampa, Florida, USA
- Center for Global Health and Infectious Diseases Research, College of Public Health, University of South Florida, Tampa, Florida, USA
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Nag S, Banerjee C, Goyal M, Siddiqui AA, Saha D, Mazumder S, Debsharma S, Pramanik S, Saha SJ, De R, Bandyopadhyay U. Plasmodium falciparum Alba6 exhibits DNase activity and participates in stress response. iScience 2024; 27:109467. [PMID: 38558939 PMCID: PMC10981135 DOI: 10.1016/j.isci.2024.109467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 12/12/2023] [Accepted: 03/07/2024] [Indexed: 04/04/2024] Open
Abstract
Alba domain proteins, owing to their functional plasticity, play a significant role in organisms. Here, we report an intrinsic DNase activity of PfAlba6 from Plasmodium falciparum, an etiological agent responsible for human malignant malaria. We identified that tyrosine28 plays a critical role in the Mg2+ driven 5'-3' DNase activity of PfAlba6. PfAlba6 cleaves both dsDNA as well as ssDNA. We also characterized PfAlba6-DNA interaction and observed concentration-dependent oligomerization in the presence of DNA, which is evident from size exclusion chromatography and single molecule AFM-imaging. PfAlba6 mRNA expression level is up-regulated several folds following heat stress and treatment with artemisinin, indicating a possible role in stress response. PfAlba6 has no human orthologs and is expressed in all intra-erythrocytic stages; thus, this protein can potentially be a new anti-malarial drug target.
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Affiliation(s)
- Shiladitya Nag
- Division of Infectious Diseases and Immunology, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, West Bengal, India
| | - Chinmoy Banerjee
- Division of Infectious Diseases and Immunology, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, West Bengal, India
| | - Manish Goyal
- Department of Molecular & Cell Biology, School of Dental Medicine, Boston University Medical Campus, Boston, MA, USA
| | - Asim Azhar Siddiqui
- Division of Infectious Diseases and Immunology, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, West Bengal, India
| | - Debanjan Saha
- Division of Infectious Diseases and Immunology, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, West Bengal, India
| | - Somnath Mazumder
- Division of Infectious Diseases and Immunology, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, West Bengal, India
- Department of Zoology, Raja Peary Mohan College, 1 Acharya Dhruba Pal Road, Uttarpara, West Bengal 712258, India
| | - Subhashis Debsharma
- Division of Infectious Diseases and Immunology, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, West Bengal, India
| | - Saikat Pramanik
- Division of Infectious Diseases and Immunology, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, West Bengal, India
| | - Shubhra Jyoti Saha
- Division of Infectious Diseases and Immunology, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, West Bengal, India
| | - Rudranil De
- Amity Institute of Biotechnology, Amity University, Kolkata, Plot No: 36, 37 & 38, Major Arterial Road, Action Area II, Kadampukur Village, Newtown, Kolkata, West Bengal 700135, India
| | - Uday Bandyopadhyay
- Division of Infectious Diseases and Immunology, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, West Bengal, India
- Division of Molecular Medicine, Bose Institute, Unified Academic Campus, EN 80, Sector V, Bidhan Nagar, Kolkata, West Bengal 700091, India
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5
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Tebben K, Yirampo S, Coulibaly D, Koné AK, Laurens MB, Stucke EM, Dembélé A, Tolo Y, Traoré K, Niangaly A, Berry AA, Kouriba B, Plowe CV, Doumbo OK, Lyke KE, Takala-Harrison S, Thera MA, Travassos MA, Serre D. Gene expression analyses reveal differences in children's response to malaria according to their age. Nat Commun 2024; 15:2021. [PMID: 38448421 PMCID: PMC10918175 DOI: 10.1038/s41467-024-46416-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 02/26/2024] [Indexed: 03/08/2024] Open
Abstract
In Bandiagara, Mali, children experience on average two clinical malaria episodes per year. However, even in the same transmission area, the number of uncomplicated symptomatic infections, and their parasitemia, can vary dramatically among children. We simultaneously characterize host and parasite gene expression profiles from 136 Malian children with symptomatic falciparum malaria and examine differences in the relative proportion of immune cells and parasite stages, as well as in gene expression, associated with infection and or patient characteristics. Parasitemia explains much of the variation in host and parasite gene expression, and infections with higher parasitemia display proportionally more neutrophils and fewer T cells, suggesting parasitemia-dependent neutrophil recruitment and/or T cell extravasation to secondary lymphoid organs. The child's age also strongly correlates with variations in gene expression: Plasmodium falciparum genes associated with age suggest that older children carry more male gametocytes, while variations in host gene expression indicate a stronger innate response in younger children and stronger adaptive response in older children. These analyses highlight the variability in host responses and parasite regulation during P. falciparum symptomatic infections and emphasize the importance of considering the children's age when studying and treating malaria infections.
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Affiliation(s)
- Kieran Tebben
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Salif Yirampo
- Malaria Research and Training Center, University of Sciences, Techniques and Technologies, Bamako, Mali
| | - Drissa Coulibaly
- Malaria Research and Training Center, University of Sciences, Techniques and Technologies, Bamako, Mali
| | - Abdoulaye K Koné
- Malaria Research and Training Center, University of Sciences, Techniques and Technologies, Bamako, Mali
| | - Matthew B Laurens
- Malaria Research Program, Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Emily M Stucke
- Malaria Research Program, Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Ahmadou Dembélé
- Malaria Research and Training Center, University of Sciences, Techniques and Technologies, Bamako, Mali
| | - Youssouf Tolo
- Malaria Research and Training Center, University of Sciences, Techniques and Technologies, Bamako, Mali
| | - Karim Traoré
- Malaria Research and Training Center, University of Sciences, Techniques and Technologies, Bamako, Mali
| | - Amadou Niangaly
- Malaria Research and Training Center, University of Sciences, Techniques and Technologies, Bamako, Mali
| | - Andrea A Berry
- Malaria Research Program, Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Bourema Kouriba
- Malaria Research and Training Center, University of Sciences, Techniques and Technologies, Bamako, Mali
| | - Christopher V Plowe
- Malaria Research Program, Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Ogobara K Doumbo
- Malaria Research and Training Center, University of Sciences, Techniques and Technologies, Bamako, Mali
| | - Kirsten E Lyke
- Malaria Research Program, Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Shannon Takala-Harrison
- Malaria Research Program, Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Mahamadou A Thera
- Malaria Research and Training Center, University of Sciences, Techniques and Technologies, Bamako, Mali
| | - Mark A Travassos
- Malaria Research Program, Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, USA
| | - David Serre
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA.
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA.
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6
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Tebben K, Yirampo S, Coulibaly D, Koné A, Laurens M, Stucke E, Dembélé A, Tolo Y, Traoré K, Niangaly A, Berry A, Kouriba B, Plowe C, Doumbo O, Lyke K, Takala-Harrison S, Thera M, Travassos M, Serre D. Gene expression analyses reveal differences in children's response to malaria according to their age. RESEARCH SQUARE 2023:rs.3.rs-3487114. [PMID: 37961587 PMCID: PMC10635353 DOI: 10.21203/rs.3.rs-3487114/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
In Bandiagara, Mali, children experience on average two clinical malaria episodes per season. However, even in the same transmission area, the number of uncomplicated symptomatic infections, and their parasitemia, vary dramatically among children. To examine the factors contributing to these variations, we simultaneously characterized the host and parasite gene expression profiles from 136 children with symptomatic falciparum malaria and analyzed the expression of 9,205 human and 2,484 Plasmodium genes. We used gene expression deconvolution to estimate the relative proportion of immune cells and parasite stages in each sample and to adjust the differential gene expression analyses. Parasitemia explained much of the variation in both host and parasite gene expression and revealed that infections with higher parasitemia had more neutrophils and fewer T cells, suggesting parasitemia-dependent neutrophil recruitment and/or T cell extravasation to secondary lymphoid organs. The child's age was also strongly correlated with gene expression variations. Plasmodium falciparum genes associated with age suggested that older children carried more male gametocytes, while host genes associated with age indicated a stronger innate response (through TLR and NLR signaling) in younger children and stronger adaptive immunity (through TCR and BCR signaling) in older children. These analyses highlight the variability in host responses and parasite regulation during P. falciparum symptomatic infections and emphasize the importance of considering the children's age when studying and treating malaria infections.
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Affiliation(s)
| | - Salif Yirampo
- Universite des Sciences des Techniques et des Technologies de Bamako
| | - Drissa Coulibaly
- Universite des Sciences des Techniques et des Technologies de Bamako
| | - Abdoulaye Koné
- Universite des Sciences des Techniques et des Technologies de Bamako
| | | | | | - Ahmadou Dembélé
- Universite des Sciences des Techniques et des Technologies de Bamako
| | - Youssouf Tolo
- Universite des Sciences des Techniques et des Technologies de Bamako
| | - Karim Traoré
- Universite des Sciences des Techniques et des Technologies de Bamako
| | - Ahmadou Niangaly
- Universite des Sciences des Techniques et des Technologies de Bamako
| | | | - Bourema Kouriba
- Universite des Sciences des Techniques et des Technologies de Bamako
| | | | - Ogobara Doumbo
- Universite des Sciences des Techniques et des Technologies de Bamako
| | | | | | - Mahamadou Thera
- Malaria Research and Training Centre-International Center for Excellence in Research (MRTC-ICER)
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7
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Tebben K, Yirampo S, Coulibaly D, Koné AK, Laurens MB, Stucke EM, Dembélé A, Tolo Y, Traoré K, Niangaly A, Berry AA, Kouriba B, Plowe CV, Doumbo OK, Lyke KE, Takala-Harrison S, Thera MA, Travassos MA, Serre D. Gene expression analyses reveal differences in children's response to malaria according to their age. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.24.563751. [PMID: 37961701 PMCID: PMC10634788 DOI: 10.1101/2023.10.24.563751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
In Bandiagara, Mali, children experience on average two clinical malaria episodes per season. However, even in the same transmission area, the number of uncomplicated symptomatic infections, and their parasitemia, vary dramatically among children. To examine the factors contributing to these variations, we simultaneously characterized the host and parasite gene expression profiles from 136 children with symptomatic falciparum malaria and analyzed the expression of 9,205 human and 2,484 Plasmodium genes. We used gene expression deconvolution to estimate the relative proportion of immune cells and parasite stages in each sample and to adjust the differential gene expression analyses. Parasitemia explained much of the variation in both host and parasite gene expression and revealed that infections with higher parasitemia had more neutrophils and fewer T cells, suggesting parasitemia-dependent neutrophil recruitment and/or T cell extravasation to secondary lymphoid organs. The child's age was also strongly correlated with gene expression variations. Plasmodium falciparum genes associated with age suggested that older children carried more male gametocytes, while host genes associated with age indicated a stronger innate response (through TLR and NLR signaling) in younger children and stronger adaptive immunity (through TCR and BCR signaling) in older children. These analyses highlight the variability in host responses and parasite regulation during P. falciparum symptomatic infections and emphasize the importance of considering the children's age when studying and treating malaria infections.
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Affiliation(s)
- Kieran Tebben
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
- Department of Microbiology and Immunology, University of Maryland School of Medicine; Baltimore, USA
| | - Salif Yirampo
- Malaria Research and Training Center, University of Sciences, Techniques and Technologies; Bamako, Mali
| | - Drissa Coulibaly
- Malaria Research and Training Center, University of Sciences, Techniques and Technologies; Bamako, Mali
| | - Abdoulaye K. Koné
- Malaria Research and Training Center, University of Sciences, Techniques and Technologies; Bamako, Mali
| | - Matthew B. Laurens
- Malaria Research Program, Center for Vaccine Development and Global Health, University of Maryland School of Medicine; Baltimore, USA
| | - Emily M. Stucke
- Malaria Research Program, Center for Vaccine Development and Global Health, University of Maryland School of Medicine; Baltimore, USA
| | - Ahmadou Dembélé
- Malaria Research and Training Center, University of Sciences, Techniques and Technologies; Bamako, Mali
| | - Youssouf Tolo
- Malaria Research and Training Center, University of Sciences, Techniques and Technologies; Bamako, Mali
| | - Karim Traoré
- Malaria Research and Training Center, University of Sciences, Techniques and Technologies; Bamako, Mali
| | - Amadou Niangaly
- Malaria Research and Training Center, University of Sciences, Techniques and Technologies; Bamako, Mali
| | - Andrea A. Berry
- Malaria Research Program, Center for Vaccine Development and Global Health, University of Maryland School of Medicine; Baltimore, USA
| | - Bourema Kouriba
- Malaria Research and Training Center, University of Sciences, Techniques and Technologies; Bamako, Mali
| | - Christopher V. Plowe
- Malaria Research Program, Center for Vaccine Development and Global Health, University of Maryland School of Medicine; Baltimore, USA
| | - Ogobara K Doumbo
- Malaria Research and Training Center, University of Sciences, Techniques and Technologies; Bamako, Mali
| | - Kirsten E. Lyke
- Malaria Research Program, Center for Vaccine Development and Global Health, University of Maryland School of Medicine; Baltimore, USA
| | - Shannon Takala-Harrison
- Malaria Research Program, Center for Vaccine Development and Global Health, University of Maryland School of Medicine; Baltimore, USA
| | - Mahamadou A. Thera
- Malaria Research and Training Center, University of Sciences, Techniques and Technologies; Bamako, Mali
| | - Mark A. Travassos
- Malaria Research Program, Center for Vaccine Development and Global Health, University of Maryland School of Medicine; Baltimore, USA
| | - David Serre
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
- Department of Microbiology and Immunology, University of Maryland School of Medicine; Baltimore, USA
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8
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Chandrasekar N, Steffi AP, Ramachandran B, Hwang MT, Faramarzi V, Govarthanan M. MXenes - Versatile 2D materials for identification of biomarkers and contaminants in large scale environments - A review. ENVIRONMENTAL RESEARCH 2023; 228:115900. [PMID: 37059325 DOI: 10.1016/j.envres.2023.115900] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 03/31/2023] [Accepted: 04/11/2023] [Indexed: 05/16/2023]
Abstract
Recent years have seen a lot of interest in transition metal carbides/carbonitrides (MXenes), Which is one of newly proliferating two-dimensional (2D) materials.The advantages and applications of synthesizing MXenes-based biosensing systems are interesting. There is an urgent requirement for synthesis of MXenes. Through foliation, physical adsorption, and interface modification,it has been proposed that many biological disorders are related to genetic mutation. Majority of mutations were discovered to be nucleotide mismatches. Consequently, accurate -nucleotide mismatched discrimination is crucial for both diagnosing and treating diseases. To differentiate between such a sensitivealterations in the DNA duplex, several detection methods, particularly Electrochemical-luminescence (ECL) ones, have really been investigated.Mn+1XnTx is common name for MXenes, a novel family of two-dimensional (2D) transition metal carbides, nitrides, and carbonitrides, where T stands for interface termination units (i.e. = O, OH, and/or F). These electronic characteristics of MXenes may be changed between conductive to semiconducting due to abundant organometallic chemistry.Solid-state ECL sensors predicated on MXene would provide the facile nucleotide detection and convenience for usage with minimal training, mobility and possibly minimal cost.This study emphasizes upcoming requirements and possibilities in this area while describing the accomplishments achieved in the usage and employing of MXenes in the research and development of facile biomarkerdetection and their significance in designing electrochemical sensors. Opportunities are addressed for creating 2D MXene materials sensors and devices with incorporated biomolecule sensing. MXenes Carry out this process sensors, address the advantages of using MXenes and their variants as detecting materials for gathering different types of data, and attempt to clarify the design principles and operation of related MXene-based sensors, such as nucleotide detection, Single nucleotide detectors, Cancer theranostics, Biosensing capabilities, Gliotoxin detection, SARS-COV-2 nucleocapsid detection, electrochemical sensors, visual sensors, and humidity sensors. Finally, we examine the major issues and prospects for MXene-based materials used in various sensing applications.
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Affiliation(s)
- Narendhar Chandrasekar
- Department of BioNano Technology, Gachon University, 1342 Seongnam-Daero, Sujeong-Gu, Seongnam-si, 13120, Gyeonggi-do, Republic of Korea
| | - Alexander Pinky Steffi
- Department of Nanoscience and Technology, Sri Ramakrishna Engineering College, Coimbatore, Tamil Nadu, India
| | - Balaji Ramachandran
- Department of Electronics and Communication Engineering, Koneru Lakshmaiah Education Foundation, Andhra Pradesh, 522302, India.
| | - Michael Taeyoung Hwang
- Department of BioNano Technology, Gachon University, 1342 Seongnam-Daero, Sujeong-Gu, Seongnam-si, 13120, Gyeonggi-do, Republic of Korea.
| | - Vahid Faramarzi
- Department of Electrical and Computer Engineering, Tarbiat Modares University, 14115-194, Tehran, Iran
| | - Muthusamy Govarthanan
- Department of Environmental Engineering, Kyungpook National University, Daehak-ro, Buk-gu, Daegu, 41566, South Korea; Department of Biomaterials, Saveetha Dental College and Hospital, Saveetha Institute of Medical and Technical Sciences, Chennai, 600077, Tamil Nadu, India.
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9
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Amambua-Ngwa A, Button-Simons KA, Li X, Kumar S, Brenneman KV, Ferrari M, Checkley LA, Haile MT, Shoue DA, McDew-White M, Tindall SM, Reyes A, Delgado E, Dalhoff H, Larbalestier JK, Amato R, Pearson RD, Taylor AB, Nosten FH, D'Alessandro U, Kwiatkowski D, Cheeseman IH, Kappe SHI, Avery SV, Conway DJ, Vaughan AM, Ferdig MT, Anderson TJC. Chloroquine resistance evolution in Plasmodium falciparum is mediated by the putative amino acid transporter AAT1. Nat Microbiol 2023; 8:1213-1226. [PMID: 37169919 PMCID: PMC10322710 DOI: 10.1038/s41564-023-01377-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 03/29/2023] [Indexed: 05/13/2023]
Abstract
Malaria parasites break down host haemoglobin into peptides and amino acids in the digestive vacuole for export to the parasite cytoplasm for growth: interrupting this process is central to the mode of action of several antimalarial drugs. Mutations in the chloroquine (CQ) resistance transporter, pfcrt, located in the digestive vacuole membrane, confer CQ resistance in Plasmodium falciparum, and typically also affect parasite fitness. However, the role of other parasite loci in the evolution of CQ resistance is unclear. Here we use a combination of population genomics, genetic crosses and gene editing to demonstrate that a second vacuolar transporter plays a key role in both resistance and compensatory evolution. Longitudinal genomic analyses of the Gambian parasites revealed temporal signatures of selection on a putative amino acid transporter (pfaat1) variant S258L, which increased from 0% to 97% in frequency between 1984 and 2014 in parallel with the pfcrt1 K76T variant. Parasite genetic crosses then identified a chromosome 6 quantitative trait locus containing pfaat1 that is selected by CQ treatment. Gene editing demonstrated that pfaat1 S258L potentiates CQ resistance but at a cost of reduced fitness, while pfaat1 F313S, a common southeast Asian polymorphism, reduces CQ resistance while restoring fitness. Our analyses reveal hidden complexity in CQ resistance evolution, suggesting that pfaat1 may underlie regional differences in the dynamics of resistance evolution, and modulate parasite resistance or fitness by manipulating the balance between both amino acid and drug transport.
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Affiliation(s)
- Alfred Amambua-Ngwa
- MRC Unit The Gambia at London School of Hygiene and Tropical Medicine, Banjul, The Gambia
| | - Katrina A Button-Simons
- Eck Institute for Global Health, Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
| | - Xue Li
- Disease Intervention and Prevention Program, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Sudhir Kumar
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - Katelyn Vendrely Brenneman
- Eck Institute for Global Health, Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
| | - Marco Ferrari
- Disease Intervention and Prevention Program, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Lisa A Checkley
- Eck Institute for Global Health, Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
| | - Meseret T Haile
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - Douglas A Shoue
- Eck Institute for Global Health, Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
| | - Marina McDew-White
- Disease Intervention and Prevention Program, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Sarah M Tindall
- School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Ann Reyes
- Disease Intervention and Prevention Program, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Elizabeth Delgado
- Disease Intervention and Prevention Program, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Haley Dalhoff
- Eck Institute for Global Health, Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
| | - James K Larbalestier
- Eck Institute for Global Health, Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
| | | | | | - Alexander B Taylor
- Department of Biochemistry & Structural Biology, University of Texas Health Science Center at San Antonio, Antonio, TX, USA
| | - François H Nosten
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Mae Sot, Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Umberto D'Alessandro
- MRC Unit The Gambia at London School of Hygiene and Tropical Medicine, Banjul, The Gambia
| | | | - Ian H Cheeseman
- Host Pathogen Interactions Program, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Stefan H I Kappe
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA, USA
- Department of Pediatrics, University of Washington, Seattle, WA, USA
- Department of Global Health, University of Washington, Seattle, WA, USA
| | - Simon V Avery
- School of Life Sciences, University of Nottingham, Nottingham, UK
| | - David J Conway
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, UK
| | - Ashley M Vaughan
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA, USA.
- Department of Pediatrics, University of Washington, Seattle, WA, USA.
| | - Michael T Ferdig
- Eck Institute for Global Health, Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA.
| | - Timothy J C Anderson
- Disease Intervention and Prevention Program, Texas Biomedical Research Institute, San Antonio, TX, USA.
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10
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Ehrlich HY, Somé AF, Bazié T, Ebou CN, Dembélé EL, Balma R, Goodwin J, Wade M, Bei AK, Ouédraogo JB, Foy BD, Dabiré RK, Parikh S. Tracking antimalarial drug resistance using mosquito blood meals: a cross-sectional study. THE LANCET. MICROBE 2023; 4:e461-e469. [PMID: 37086737 PMCID: PMC10365133 DOI: 10.1016/s2666-5247(23)00063-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 02/06/2023] [Accepted: 02/07/2023] [Indexed: 04/24/2023]
Abstract
BACKGROUND Strong surveillance systems with wide geographic coverage are needed to detect and respond to reports of antimalarial drug resistance on the African continent. We aimed to assess the utility and feasibility of using blood-fed mosquitos (xenomonitoring) to conduct rapid surveillance of molecular markers associated with resistance in human populations. METHODS We conducted three cross-sectional surveys in two rainy seasons and the interim dry season in southwest Burkina Faso between Oct 10, 2018, and Sept 17, 2019. We collected human blood samples and blood-fed mosquitos residing in household clusters across seven village sectors. Samples were assessed for Plasmodium falciparum with ultrasensitive quantitative PCR, genotyped for two markers of reduced drug susceptibility, pfmdr1 256A>T (Asn86Tyr) and pfcrt 227A>C (Lys76Thr), and sequenced for four markers of clonality. We assessed statistical equivalence using a 10% margin of equivalence. FINDINGS We identified 551 infections in 1483 human blood samples (mean multiplicity of infection [MOI] 1·94, SD 1·47) and 346 infections in 2151 mosquito blood meals (mean MOI 2·2, SD 1·67). The frequency of pfmdr1 Asn86Tyr was 4% in survey 1, 2% in survey 2, and 12% in survey 3 in human samples, and 3% in survey 1, 0% in survey 2, and 8% in survey 3 in mosquito blood meals, and inter-host frequencies were statistically equivalent in surveys 1 and 2 (p<0·0001) but not Survey 3 (p=0·062) within a tolerability of 0·10. The frequency of pfcrt Lys76Thr was 16% in survey 1, 55% in survey 2, and 11% in survey 3 in humans and 40% in survey 1, 72% in survey 2, and 13% in survey 3 in mosquitos, and inter-host frequencies were equivalent in survey 3 only (p=0·032) within a tolerability of 0·10. In simulations, multiple but not preferential feeding behaviour in mosquitos reduced the accuracy of frequency estimates between hosts, particularly for markers circulating at higher frequencies. INTERPRETATION Molecular markers in mosquito blood meals and in humans exhibited similar temporal trends but frequencies were not statistically equivalent in all scenarios. More work is needed to determine empirical and pragmatic thresholds of difference. Xenomonitoring might be an efficient tool to provide rapid information on emerging antimalarial resistance in regions with insufficient surveillance. FUNDING National Institute of Allergy and Infectious Diseases. TRANSLATION For the French translation of the abstract see Supplementary Materials section.
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Affiliation(s)
- Hanna Y Ehrlich
- Department of Epidemiology of Microbial Diseases, Yale University, New Haven, CT, USA; One Health Institute, University of California, Davis, CA, USA.
| | - A Fabrice Somé
- Department of Parasitology, Institut de Recherche en Sciences de la Santé, Bobo-Dioulasso, Burkina Faso
| | - Thomas Bazié
- Department of Parasitology, Institut de Recherche en Sciences de la Santé, Bobo-Dioulasso, Burkina Faso
| | - Cathérine Neya Ebou
- Department of Parasitology, Institut de Recherche en Sciences de la Santé, Bobo-Dioulasso, Burkina Faso
| | - Estelle Lotio Dembélé
- Department of Parasitology, Institut de Recherche en Sciences de la Santé, Bobo-Dioulasso, Burkina Faso
| | - Richard Balma
- Department of Medical Entomology, Institut de Recherche en Sciences de la Santé, Bobo-Dioulasso, Burkina Faso
| | - Justin Goodwin
- Department of Epidemiology of Microbial Diseases, Yale University, New Haven, CT, USA
| | - Martina Wade
- Department of Epidemiology of Microbial Diseases, Yale University, New Haven, CT, USA
| | - Amy K Bei
- Department of Epidemiology of Microbial Diseases, Yale University, New Haven, CT, USA
| | - Jean-Bosco Ouédraogo
- Department of Epidemiology of Microbial Diseases, Yale University, New Haven, CT, USA; Department of Parasitology, Institut de Recherche en Sciences de la Santé, Bobo-Dioulasso, Burkina Faso
| | - Brian D Foy
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO, USA
| | - Roch K Dabiré
- Department of Medical Entomology, Institut de Recherche en Sciences de la Santé, Bobo-Dioulasso, Burkina Faso
| | - Sunil Parikh
- Department of Epidemiology of Microbial Diseases, Yale University, New Haven, CT, USA
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11
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Banerjee C, Nag S, Goyal M, Saha D, Siddiqui AA, Mazumder S, Debsharma S, Pramanik S, Bandyopadhyay U. Nuclease activity of Plasmodium falciparum Alba family protein PfAlba3. Cell Rep 2023; 42:112292. [PMID: 36947546 DOI: 10.1016/j.celrep.2023.112292] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 01/06/2023] [Accepted: 03/06/2023] [Indexed: 03/23/2023] Open
Abstract
Plasmodium falciparum Alba domain-containing protein Alba3 (PfAlba3) is ubiquitously expressed in intra-erythrocytic stages of Plasmodium falciparum, but the function of this protein is not yet established. Here, we report an apurinic/apyrimidinic site-driven intrinsic nuclease activity of PfAlba3 assisted by divalent metal ions. Surface plasmon resonance and atomic force microscopy confirm sequence non-specific DNA binding by PfAlba3. Upon binding, PfAlba3 cleaves double-stranded DNA (dsDNA) hydrolytically. Mutational studies coupled with mass spectrometric analysis indicate that K23 is the essential residue in modulating the binding to DNA through acetylation-deacetylation. We further demonstrate that PfSir2a interacts and deacetylates K23-acetylated PfAlba3 in favoring DNA binding. Hence, K23 serves as a putative molecular switch regulating the nuclease activity of PfAlba3. Thus, the nuclease activity of PfAlba3, along with its apurinic/apyrimidinic (AP) endonuclease feature identified in this study, indicates a role of PfAlba3 in DNA-damage response that may have a far-reaching consequence in Plasmodium pathogenicity.
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Affiliation(s)
- Chinmoy Banerjee
- Division of Infectious Diseases and Immunology, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Jadavpur, Kolkata, West Bengal 700032, India
| | - Shiladitya Nag
- Division of Infectious Diseases and Immunology, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Jadavpur, Kolkata, West Bengal 700032, India
| | - Manish Goyal
- Division of Infectious Diseases and Immunology, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Jadavpur, Kolkata, West Bengal 700032, India
| | - Debanjan Saha
- Division of Infectious Diseases and Immunology, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Jadavpur, Kolkata, West Bengal 700032, India
| | - Asim Azhar Siddiqui
- Division of Infectious Diseases and Immunology, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Jadavpur, Kolkata, West Bengal 700032, India
| | - Somnath Mazumder
- Division of Infectious Diseases and Immunology, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Jadavpur, Kolkata, West Bengal 700032, India
| | - Subhashis Debsharma
- Division of Infectious Diseases and Immunology, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Jadavpur, Kolkata, West Bengal 700032, India
| | - Saikat Pramanik
- Division of Infectious Diseases and Immunology, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Jadavpur, Kolkata, West Bengal 700032, India
| | - Uday Bandyopadhyay
- Division of Infectious Diseases and Immunology, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Jadavpur, Kolkata, West Bengal 700032, India; Division of Molecular Medicine, Bose Institute, EN 80, Sector V, Bidhan Nagar Kolkata, 700091, West Bengal, India.
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12
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Honma H, Takahashi N, Arisue N, Sugishita T. Analysis of genome instability and implications for the consequent phenotype in Plasmodium falciparum containing mutated MSH2-1 (P513T). Microb Genom 2023; 9. [PMID: 37083479 DOI: 10.1099/mgen.0.001003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/22/2023] Open
Abstract
Malarial parasites exhibit extensive genomic plasticity, which induces the antigen diversification and the development of antimalarial drug resistance. Only a few studies have examined the genome maintenance mechanisms of parasites. The study aimed at elucidating the impact of a mutation in a DNA mismatch repair gene on genome stability by maintaining the mutant and wild-type parasites through serial in vitro cultures for approximately 400 days and analysing the subsequent spontaneous mutations. A P513T mutant of the DNA mismatch repair protein PfMSH2-1 from Plasmodium falciparum 3D7 was created. The mutation did not influence the base substitution rate but significantly increased the insertion/deletion (indel) mutation rate in short tandem repeats (STRs) and minisatellite loci. STR mutability was affected by allele size, genomic category and certain repeat motifs. In the mutants, significant telomere healing and homologous recombination at chromosomal ends caused extensive gene loss and generation of chimeric genes, resulting in large-scale chromosomal alteration. Additionally, the mutant showed increased tolerance to N-methyl-N'-nitro-N-nitrosoguanidine, suggesting that PfMSH2-1 was involved in recognizing DNA methylation damage. This work provides valuable insights into the role of PfMSH2-1 in genome stability and demonstrates that the genomic destabilization caused by its dysfunction may lead to antigen diversification.
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Affiliation(s)
- Hajime Honma
- Section of Global Health, Division of Public Health, Department of Hygiene and Public Health, Tokyo Women's Medical University, 8-1 Kawada-cho, Shinjuku, Tokyo 162-8666, Japan
- Department of International Affairs and Tropical Medicine, Tokyo Women's Medical University, 8-1 Kawada-cho, Shinjuku, Tokyo 162-8666, Japan
| | - Nobuyuki Takahashi
- Section of Global Health, Division of Public Health, Department of Hygiene and Public Health, Tokyo Women's Medical University, 8-1 Kawada-cho, Shinjuku, Tokyo 162-8666, Japan
- Department of International Affairs and Tropical Medicine, Tokyo Women's Medical University, 8-1 Kawada-cho, Shinjuku, Tokyo 162-8666, Japan
| | - Nobuko Arisue
- Section of Global Health, Division of Public Health, Department of Hygiene and Public Health, Tokyo Women's Medical University, 8-1 Kawada-cho, Shinjuku, Tokyo 162-8666, Japan
| | - Tomohiko Sugishita
- Section of Global Health, Division of Public Health, Department of Hygiene and Public Health, Tokyo Women's Medical University, 8-1 Kawada-cho, Shinjuku, Tokyo 162-8666, Japan
- Department of International Affairs and Tropical Medicine, Tokyo Women's Medical University, 8-1 Kawada-cho, Shinjuku, Tokyo 162-8666, Japan
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13
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Mohammed M, Dziedziech A, Sekar V, Ernest M, Alves E Silva TL, Balan B, Emami SN, Biryukova I, Friedländer MR, Jex A, Jacobs-Lorena M, Henriksson J, Vega-Rodriguez J, Ankarklev J. Single-Cell Transcriptomics To Define Plasmodium falciparum Stage Transition in the Mosquito Midgut. Microbiol Spectr 2023; 11:e0367122. [PMID: 36847501 PMCID: PMC10100735 DOI: 10.1128/spectrum.03671-22] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 02/05/2023] [Indexed: 03/01/2023] Open
Abstract
Malaria inflicts the highest rate of morbidity and mortality among the vector-borne diseases. The dramatic bottleneck of parasite numbers that occurs in the gut of the obligatory mosquito vector provides a promising target for novel control strategies. Using single-cell transcriptomics, we analyzed Plasmodium falciparum development in the mosquito gut, from unfertilized female gametes through the first 20 h after blood feeding, including the zygote and ookinete stages. This study revealed the temporal gene expression of the ApiAP2 family of transcription factors and of parasite stress genes in response to the harsh environment of the mosquito midgut. Further, employing structural protein prediction analyses, we found several upregulated genes predicted to encode intrinsically disordered proteins (IDPs), a category of proteins known for their importance in regulation of transcription, translation, and protein-protein interactions. IDPs are known for their antigenic properties and may serve as suitable targets for antibody- or peptide-based transmission suppression strategies. In total, this study uncovers the P. falciparum transcriptome from early to late parasite development in the mosquito midgut, inside its natural vector, which provides an important resource for future malaria transmission-blocking initiatives. IMPORTANCE The malaria parasite Plasmodium falciparum causes more than half a million deaths per year. The current treatment regimen targets the symptom-causing blood stage inside the human host. However, recent incentives in the field call for novel interventions to block parasite transmission from humans to the mosquito vector. Therefore, we need to better understand the parasite biology during its development inside the mosquito, including a deeper understanding of the expression of genes controlling parasite progression during these stages. Here, we have generated single-cell transcriptome data, covering P. falciparum's development, from gamete to ookinete inside the mosquito midgut, uncovering previously untapped parasite biology, including a repertoire of novel biomarkers to be explored in future transmission-blocking efforts. We anticipate that our study provides an important resource, which can be further explored to improve our understanding of the parasite biology as well as aid in guiding future malaria intervention strategies.
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Affiliation(s)
- Mubasher Mohammed
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Alexis Dziedziech
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Vaishnovi Sekar
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Medard Ernest
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland, USA
| | - Thiago Luiz Alves E Silva
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland, USA
| | - Balu Balan
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, Australia
| | - S. Noushin Emami
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Inna Biryukova
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Marc R. Friedländer
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Aaron Jex
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Marcelo Jacobs-Lorena
- Department of Molecular Microbiology and Immunology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, USA
| | - Johan Henriksson
- Laboratory for Molecular Infection Medicine Sweden (MIMS), Department of Molecular Biology, Umeå University, Umeå, Sweden
| | - Joel Vega-Rodriguez
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland, USA
| | - Johan Ankarklev
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
- Microbial Single Cell Genomics, Department of Cell and Molecular Biology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
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14
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Adjalley S, Lee MCS. CRISPR/Cas9 Editing of the Plasmodium falciparum Genome. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2022; 2470:221-239. [PMID: 35881349 DOI: 10.1007/978-1-0716-2189-9_17] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The ability to interrogate gene function in Plasmodium parasites has been greatly enhanced by the advent of CRISPR/Cas9 systems. The breadth of genome manipulations ranges from single point mutations to large multigene deletions, however many of the technical considerations for designing CRISPR-based experiments are common to any editing approach. This review will discuss protocols for vector construction and donor design for genome editing P. falciparum, including pitfalls, variables, and validation methods.
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Affiliation(s)
- Sophie Adjalley
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
- Micrographia Bio, Translation and Innovation Hub, London, UK
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15
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Yoshikawa Y, Kimura S, Soga A, Sugiyama M, Ueno A, Kondo H, Zhu Z, Ochiai K, Nakayama K, Hakozaki J, Kusakisako K, Haraguchi A, Kitano T, Orino K, Fukumoto S, Ikadai H. Plasmodium berghei Brca2 is required for normal development and differentiation in mice and mosquitoes. Parasit Vectors 2022; 15:244. [PMID: 35804459 PMCID: PMC9270840 DOI: 10.1186/s13071-022-05357-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 06/10/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Malaria is a major global parasitic disease caused by species of the genus Plasmodium. Zygotes of Plasmodium spp. undergo meiosis and develop into tetraploid ookinetes, which differentiate into oocysts that undergo sporogony. Homologous recombination (HR) occurs during meiosis and introduces genetic variation. However, the mechanisms of HR in Plasmodium are unclear. In humans, the recombinases DNA repair protein Rad51 homolog 1 (Rad51) and DNA meiotic recombinase 1 (Dmc1) are required for HR and are regulated by breast cancer susceptibility protein 2 (BRCA2). Most eukaryotes harbor BRCA2 homologs. Nevertheless, these have not been reported for Plasmodium. METHODS A Brca2 candidate was salvaged from a database to identify Brca2 homologs in Plasmodium. To confirm that the candidate protein was Brca2, interaction activity between Plasmodium berghei (Pb) Brca2 (PbBrca2) and Rad51 (PbRad51) was investigated using a mammalian two-hybrid assay. To elucidate the functions of PbBrca2, PbBrca2 was knocked out and parasite proliferation and differentiation were assessed in mice and mosquitoes. Transmission electron microscopy was used to identify sporogony. RESULTS The candidate protein was conserved among Plasmodium species, and it was indicated that it harbors critical BRCA2 domains including BRC repeats, tower, and oligonucleotide/oligosaccharide-binding-fold domains. The P. berghei BRC repeats interacted with PbRad51. Hence, the candidate was considered a Brca2 homolog. PbBrca2 knockout parasites were associated with reduced parasitemia with increased ring stage and decreased trophozoite stage counts, gametocytemia, female gametocyte ratio, oocyst number, and ookinete development in both mice and mosquitoes. Nevertheless, the morphology of the blood stages in mice and the ookinete stage was comparable to those of the wild type parasites. Transmission electron microscopy results showed that sporogony never progressed in Brca2-knockout parasites. CONCLUSIONS Brca2 is implicated in nearly all Plasmodium life cycle stages, and especially in sporogony. PbBrca2 contributes to HR during meiosis.
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Affiliation(s)
- Yasunaga Yoshikawa
- Laboratory of Veterinary Biochemistry, School of Veterinary Medicine, Kitasato University, Towada, Aomori, 034-8628, Japan.
| | - Shunta Kimura
- Laboratory of Veterinary Biochemistry, School of Veterinary Medicine, Kitasato University, Towada, Aomori, 034-8628, Japan
| | - Akira Soga
- National Research Center for Protozoan Diseases, Obihiro University of Agriculture and Veterinary Medicine, Inada, Obihiro, 080-8555, Japan
| | - Makoto Sugiyama
- Laboratory of Veterinary Anatomy, School of Veterinary Medicine, Kitasato University, Towada, Aomori, 034-8628, Japan
| | - Aki Ueno
- Laboratory of Veterinary Biochemistry, School of Veterinary Medicine, Kitasato University, Towada, Aomori, 034-8628, Japan
| | - Hiroki Kondo
- Laboratory of Veterinary Biochemistry, School of Veterinary Medicine, Kitasato University, Towada, Aomori, 034-8628, Japan
| | - Zida Zhu
- Laboratory of Veterinary Biochemistry, School of Veterinary Medicine, Kitasato University, Towada, Aomori, 034-8628, Japan
| | - Kazuhiko Ochiai
- Laboratory of Veterinary Hygiene, School of Veterinary Medicine, Nippon Veterinary and Life Science University, Musashino, Tokyo, 180-8602, Japan
| | - Kazuhiko Nakayama
- Laboratory of Veterinary Parasitology, School of Veterinary Medicine, Kitasato University, Towada, Aomori, 034-8628, Japan
| | - Jun Hakozaki
- Laboratory of Veterinary Parasitology, School of Veterinary Medicine, Kitasato University, Towada, Aomori, 034-8628, Japan
| | - Kodai Kusakisako
- Laboratory of Veterinary Parasitology, School of Veterinary Medicine, Kitasato University, Towada, Aomori, 034-8628, Japan
| | - Asako Haraguchi
- Laboratory of Veterinary Parasitology, School of Veterinary Medicine, Kitasato University, Towada, Aomori, 034-8628, Japan
| | - Taisuke Kitano
- Laboratory of Veterinary Biochemistry, School of Veterinary Medicine, Kitasato University, Towada, Aomori, 034-8628, Japan
| | - Koichi Orino
- Laboratory of Veterinary Biochemistry, School of Veterinary Medicine, Kitasato University, Towada, Aomori, 034-8628, Japan
| | - Shinya Fukumoto
- National Research Center for Protozoan Diseases, Obihiro University of Agriculture and Veterinary Medicine, Inada, Obihiro, 080-8555, Japan
| | - Hiromi Ikadai
- Laboratory of Veterinary Parasitology, School of Veterinary Medicine, Kitasato University, Towada, Aomori, 034-8628, Japan
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16
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A tale of topoisomerases and the knotty genetic material in the backdrop of Plasmodium biology. Biosci Rep 2022; 42:231351. [PMID: 35699968 PMCID: PMC9261774 DOI: 10.1042/bsr20212847] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 05/05/2022] [Accepted: 05/24/2022] [Indexed: 11/17/2022] Open
Abstract
The untangling or overwinding of genetic material is an inevitable part of DNA
replication, repair, recombination, and transcription. Topoisomerases belong to
a conserved enzyme family that amends DNA topology during various processes of
DNA metabolism. To relax the genetic material, topoisomerases transiently break
the phosphodiester bond on one or both DNA strands and remain associated with
the cleavage site by forming a covalent enzyme–DNA intermediate. This
releases torsional stress and allows the broken DNA to be re-ligated by the
enzyme. The biological function of topoisomerases ranges from the separation of
sister chromatids following DNA replication to the aiding of chromosome
condensation and segregation during mitosis. Topoisomerases are also actively
involved in meiotic recombination. The unicellular apicomplexan parasite,
Plasmodium falciparum, harbors different topoisomerase
subtypes, some of which have substantially different sequences and functions
from their human counterparts. This review highlights the biological function of
each identified Plasmodium topoisomerase along with a
comparative analysis of their orthologs in human or other model organisms. There
is also a focus on recent advancements towards the development of topoisomerase
chemical inhibitors, underscoring the druggability of unique topoisomerase
subunits that are absent in humans. Plasmodium harbors three
distinct genomes in the nucleus, apicoplast, and mitochondria, respectively, and
undergoes non-canonical cell division during the schizont stage of development.
This review emphasizes the specific developmental stages of
Plasmodium on which future topoisomerase research should
focus.
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17
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Ishizaki T, Hernandez S, Paoletta MS, Sanderson T, Bushell ES. CRISPR/Cas9 and genetic screens in malaria parasites: small genomes, big impact. Biochem Soc Trans 2022; 50:1069-1079. [PMID: 35621119 PMCID: PMC9246331 DOI: 10.1042/bst20210281] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 04/20/2022] [Accepted: 04/29/2022] [Indexed: 12/19/2022]
Abstract
The ∼30 Mb genomes of the Plasmodium parasites that cause malaria each encode ∼5000 genes, but the functions of the majority remain unknown. This is due to a paucity of functional annotation from sequence homology, which is compounded by low genetic tractability compared with many model organisms. In recent years technical breakthroughs have made forward and reverse genome-scale screens in Plasmodium possible. Furthermore, the adaptation of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and CRISPR-Associated protein 9 (CRISPR/Cas9) technology has dramatically improved gene editing efficiency at the single gene level. Here, we review the arrival of genetic screens in malaria parasites to analyse parasite gene function at a genome-scale and their impact on understanding parasite biology. CRISPR/Cas9 screens, which have revolutionised human and model organism research, have not yet been implemented in malaria parasites due to the need for more complex CRISPR/Cas9 gene targeting vector libraries. We therefore introduce the reader to CRISPR-based screens in the related apicomplexan Toxoplasma gondii and discuss how these approaches could be adapted to develop CRISPR/Cas9 based genome-scale genetic screens in malaria parasites. Moreover, since more than half of Plasmodium genes are required for normal asexual blood-stage reproduction, and cannot be targeted using knockout methods, we discuss how CRISPR/Cas9 could be used to scale up conditional gene knockdown approaches to systematically assign function to essential genes.
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Affiliation(s)
- Takahiro Ishizaki
- Department of Molecular Biology, Umeå University, 901 87 Umeå, Sweden
- The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå, Sweden
| | - Sophia Hernandez
- Department of Molecular Biology, Umeå University, 901 87 Umeå, Sweden
- The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå, Sweden
| | - Martina S. Paoletta
- Department of Molecular Biology, Umeå University, 901 87 Umeå, Sweden
- The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå, Sweden
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), INTA - CONICET, Hurlingham, Argentina
| | - Theo Sanderson
- Francis Crick Institute, 1 Midland Rd, London NW1 1AT, U.K
| | - Ellen S.C. Bushell
- Department of Molecular Biology, Umeå University, 901 87 Umeå, Sweden
- The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå, Sweden
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18
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Chahine Z, Le Roch KG. Decrypting the complexity of the human malaria parasite biology through systems biology approaches. FRONTIERS IN SYSTEMS BIOLOGY 2022; 2:940321. [PMID: 37200864 PMCID: PMC10191146 DOI: 10.3389/fsysb.2022.940321] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The human malaria parasite, Plasmodium falciparum, is a unicellular protozoan responsible for over half a million deaths annually. With a complex life cycle alternating between human and invertebrate hosts, this apicomplexan is notoriously adept at evading host immune responses and developing resistance to all clinically administered treatments. Advances in omics-based technologies, increased sensitivity of sequencing platforms and enhanced CRISPR based gene editing tools, have given researchers access to more in-depth and untapped information about this enigmatic micro-organism, a feat thought to be infeasible in the past decade. Here we discuss some of the most important scientific achievements made over the past few years with a focus on novel technologies and platforms that set the stage for subsequent discoveries. We also describe some of the systems-based methods applied to uncover gaps of knowledge left through single-omics applications with the hope that we will soon be able to overcome the spread of this life-threatening disease.
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19
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Davis JA, Chakrabarti K. Telomerase ribonucleoprotein and genome integrity-An emerging connection in protozoan parasites. WILEY INTERDISCIPLINARY REVIEWS. RNA 2021; 13:e1710. [PMID: 34973045 DOI: 10.1002/wrna.1710] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Revised: 12/08/2021] [Accepted: 12/10/2021] [Indexed: 12/20/2022]
Abstract
Telomerase has an established role in telomere maintenance in eukaryotes. However, recent studies have begun to implicate telomerase in cellular roles beyond telomere maintenance. Specifically, evidence is emerging of cross-talks between telomerase mediated telomere homeostasis and DNA repair pathways. Telomere shortening due to the end replication problem is a constant threat to genome integrity in eukaryotic cells. This poses a particular problem in unicellular parasitic protists because their major virulence genes are located at the subtelomeric loci. Although telomerase is the major regulator of telomere lengthening in eukaryotes, it is less studied in the ancient eukaryotes, including clinically important human pathogens. Recent research is highlighting interplay between telomerase and the DNA damage response in human parasites. The importance of this interplay in pathogen virulence is only beginning to be illuminated, including the potential to highlight novel developmental regulation of telomerase in parasites who transition between multiple developmental stages throughout their life cycle. In this review, we will discuss the telomerase ribonucleoprotein enzyme and DNA repair pathways with emerging views in human parasites to give a broader perspective of the possible connection of telomere, telomerase, and DNA repair pathways across eukaryotic lineages and highlight their potential role in pathogen virulence. This article is categorized under: RNA Structure and Dynamics > Influence of RNA Structure in Biological Systems RNA Evolution and Genomics > RNA and Ribonucleoprotein Evolution RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications.
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Affiliation(s)
| | - Kausik Chakrabarti
- University of North Carolina at Charlotte, Charlotte, North Carolina, USA
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20
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Luo S, Wang Y, Tao Y, Li S, Wang Z, He W, Wang H, Wang N, Xu J, Song H. Application in Gene Editing in Ovarian Cancer Therapy. Cancer Invest 2021; 40:387-399. [PMID: 34758691 DOI: 10.1080/07357907.2021.1998521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
The onset and progression of ovarian cancer (OC) are closely related to dysregulated gene expression. Current treatments for OC are mainly limited to surgery and chemotherapy. However, due to low drug sensitivity, the prognosis OC is exceptionally poor and the recurrence rate remains high. Hence, it is vital to develop new treatment strategies. Gene editing for site-specific genomic modification is a powerful novel tool for the treatment of OC. In this article, current gene editing research for the treatment of OC is reviewed to provide a reference for the clinical application of new approaches to improve treatment outcomes and prognosis.
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Affiliation(s)
- Shuang Luo
- National Joint Local Engineering Laboratory for Cell Engineering and Biomedicine Technique, Guizhou Province Key Laboratory of Regenerative Medicine, Key Laboratory of Adult Stem Cell Translational Research (Chinese Academy of Medical Sciences), Guizhou Medical University, Guiyang, China.,Department of Clinical Medical College, Guizhou Medical University, Guiyang, China
| | - Yujiao Wang
- Second Clinical Medical College of Lanzhou University, Lanzhou, China
| | - Yongyu Tao
- Department of Clinical Medical College, Guizhou Medical University, Guiyang, China
| | - Shuo Li
- Second Clinical Medical College of Lanzhou University, Lanzhou, China
| | - Zirui Wang
- Second Clinical Medical College of Lanzhou University, Lanzhou, China
| | - Wei He
- Second Clinical Medical College of Lanzhou University, Lanzhou, China
| | - Hangxing Wang
- Department of Clinical Medical College, Guizhou Medical University, Guiyang, China
| | - Nan Wang
- Department of Clinical Medical College, Guizhou Medical University, Guiyang, China
| | - Jianwei Xu
- National Joint Local Engineering Laboratory for Cell Engineering and Biomedicine Technique, Guizhou Province Key Laboratory of Regenerative Medicine, Key Laboratory of Adult Stem Cell Translational Research (Chinese Academy of Medical Sciences), Guizhou Medical University, Guiyang, China.,Department of Clinical Medical College, Guizhou Medical University, Guiyang, China.,Department of General Surgery, Dalang Hospital, Dongguan, China.,Department of Pharmacology, School of Basic Medicine, Guizhou Medical University, Guiyang, China
| | - Hailiang Song
- Department of General Surgery, Dalang Hospital, Dongguan, China
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21
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Maneekesorn S, Knuepfer E, Green JL, Prommana P, Uthaipibull C, Srichairatanakool S, Holder AA. Deletion of Plasmodium falciparum ubc13 increases parasite sensitivity to the mutagen, methyl methanesulfonate and dihydroartemisinin. Sci Rep 2021; 11:21791. [PMID: 34750454 PMCID: PMC8575778 DOI: 10.1038/s41598-021-01267-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 10/18/2021] [Indexed: 12/18/2022] Open
Abstract
The inducible Di-Cre system was used to delete the putative ubiquitin-conjugating enzyme 13 gene (ubc13) of Plasmodium falciparum to study its role in ubiquitylation and the functional consequence during the parasite asexual blood stage. Deletion resulted in a significant reduction of parasite growth in vitro, reduced ubiquitylation of the Lys63 residue of ubiquitin attached to protein substrates, and an increased sensitivity of the parasite to both the mutagen, methyl methanesulfonate and the antimalarial drug dihydroartemisinin (DHA), but not chloroquine. The parasite was also sensitive to the UBC13 inhibitor NSC697923. The data suggest that this gene does code for an ubiquitin conjugating enzyme responsible for K63 ubiquitylation, which is important in DNA repair pathways as was previously demonstrated in other organisms. The increased parasite sensitivity to DHA in the absence of ubc13 function indicates that DHA may act primarily through this pathway and that inhibitors of UBC13 may both enhance the efficacy of this antimalarial drug and directly inhibit parasite growth.
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Affiliation(s)
- Supawadee Maneekesorn
- Department of Biochemistry, Faculty of Medicine, Chiang Mai University, Chiang Mai, 50200, Thailand
- Malaria Parasitology Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Ellen Knuepfer
- Malaria Parasitology Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- Molecular and Cellular Parasitology Laboratory, Department of Pathobiology and Population Sciences, The Royal Veterinary College, Hawkshead Lane, Hatfield, AL9 7TA, UK
| | - Judith L Green
- Malaria Parasitology Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Parichat Prommana
- Medical Molecular Biotechnology Research Group, National Center for Genetic Engineering and Biotechnology (BIOTEC), 113 Thailand Science Park, Phahonyothin Road, Khlong Nueng, Khlong Luang, 12120, Pathum Thani, Thailand
| | - Chairat Uthaipibull
- Medical Molecular Biotechnology Research Group, National Center for Genetic Engineering and Biotechnology (BIOTEC), 113 Thailand Science Park, Phahonyothin Road, Khlong Nueng, Khlong Luang, 12120, Pathum Thani, Thailand
- Thailand Center of Excellence for Life Sciences (TCELS), Phayathai, 10400, Bangkok, Thailand
| | - Somdet Srichairatanakool
- Department of Biochemistry, Faculty of Medicine, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Anthony A Holder
- Malaria Parasitology Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.
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22
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Comparative Analysis of Plasmodium falciparum Genotyping via SNP Detection, Microsatellite Profiling, and Whole-Genome Sequencing. Antimicrob Agents Chemother 2021; 66:e0116321. [PMID: 34694871 PMCID: PMC8765236 DOI: 10.1128/aac.01163-21] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Research efforts to combat antimalarial drug resistance rely on quick, robust, and sensitive methods to genetically characterize Plasmodium falciparum parasites. We developed a single-nucleotide polymorphism (SNP)-based genotyping method that can assess 33 drug resistance-conferring SNPs in dhfr, dhps, pfmdr1, pfcrt, and k13 in nine PCRs, performed directly from P. falciparum cultures or infected blood. We also optimized multiplexed fragment analysis and gel electrophoresis-based microsatellite typing methods using a set of five markers that can distinguish 12 laboratory strains of diverse geographical and temporal origin. We demonstrate how these methods can be applied to screen for the multidrug-resistant KEL1/PLA1/PfPailin (KelPP) lineage that has been sweeping across the Greater Mekong Subregion, verify parasite in vitro SNP-editing, identify novel recombinant genetic cross progeny, or cluster strains to infer their geographical origins. Results were compared with Illumina-based whole-genome sequence analysis that provides the most detailed sequence information but is cost-prohibitive. These adaptable, simple, and inexpensive methods can be easily implemented into routine genotyping of P. falciparum parasites in both laboratory and field settings.
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23
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Recent Advances in Molecular Genetic Tools for Babesia. Vet Sci 2021; 8:vetsci8100222. [PMID: 34679052 PMCID: PMC8541370 DOI: 10.3390/vetsci8100222] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 09/15/2021] [Accepted: 10/02/2021] [Indexed: 11/21/2022] Open
Abstract
Development of in vitro culture and completion of genome sequencing of several Babesia parasites promoted the efforts to establish transfection systems for these parasites to dissect the gene functions. It has been more than a decade since the establishment of first transfection for Babesia bovis, the causative agent of bovine babesiosis. However, the number of genes that were targeted by genetic tools in Babesia parasites is limited. This is partially due to the low efficiencies of these methods. The recent adaptation of CRISPR/Cas9 for genome editing of Babesia bovis can accelerate the efforts for dissecting this parasite’s genome and extend the knowledge on biological aspects of erythrocytic and tick stages of Babesia. Additionally, glmS ribozyme as a conditional knockdown system is available that could be used for the characterization of essential genes. The development of high throughput genetic tools is needed to dissect the function of multigene families, targeting several genes in a specific pathway, and finally genome-wide identification of essential genes to find novel drug targets. In this review, we summarized the current tools that are available for Babesia and the genes that are being targeted by these tools. This may draw a perspective for the future development of genetic tools and pave the way for the identification of novel drugs or vaccine targets.
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24
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Goyal M, Singh BK, Simantov K, Kaufman Y, Eshar S, Dzikowski R. An SR protein is essential for activating DNA repair in malaria parasites. J Cell Sci 2021; 134:271848. [PMID: 34291805 PMCID: PMC8435287 DOI: 10.1242/jcs.258572] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 07/14/2021] [Indexed: 11/24/2022] Open
Abstract
Plasmodium falciparum, the parasite responsible for the deadliest form of human malaria, replicates within the erythrocytes of its host, where it encounters numerous pressures that cause extensive DNA damage, which must be repaired efficiently to ensure parasite survival. Malaria parasites, which have lost the non-homologous end joining (NHEJ) pathway for repairing DNA double-strand breaks, have evolved unique mechanisms that enable them to robustly maintain genome integrity under such harsh conditions. However, the nature of these adaptations is unknown. We show that a highly conserved RNA splicing factor, P. falciparum (Pf)SR1, plays an unexpected and crucial role in DNA repair in malaria parasites. Using an inducible and reversible system to manipulate PfSR1 expression, we demonstrate that this protein is recruited to foci of DNA damage. Although loss of PfSR1 does not impair parasite viability, the protein is essential for their recovery from DNA-damaging agents or exposure to artemisinin, the first-line antimalarial drug, demonstrating its necessity for DNA repair. These findings provide key insights into the evolution of DNA repair pathways in malaria parasites as well as the ability of the parasite to recover from antimalarial treatment. Summary: There is an unexpected role for the alternative splicing factor PfSR1 in activating the DNA damage response in the human malaria parasite Plasmodium falciparum.
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Affiliation(s)
- Manish Goyal
- Department of Microbiology & Molecular Genetics, The Kuvin Center for the Study of Infectious and Tropical Diseases, IMRIC, The Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel
| | - Brajesh Kumar Singh
- Department of Microbiology & Molecular Genetics, The Kuvin Center for the Study of Infectious and Tropical Diseases, IMRIC, The Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel
| | - Karina Simantov
- Department of Microbiology & Molecular Genetics, The Kuvin Center for the Study of Infectious and Tropical Diseases, IMRIC, The Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel
| | - Yotam Kaufman
- Department of Microbiology & Molecular Genetics, The Kuvin Center for the Study of Infectious and Tropical Diseases, IMRIC, The Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel
| | - Shiri Eshar
- Department of Microbiology & Molecular Genetics, The Kuvin Center for the Study of Infectious and Tropical Diseases, IMRIC, The Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel
| | - Ron Dzikowski
- Department of Microbiology & Molecular Genetics, The Kuvin Center for the Study of Infectious and Tropical Diseases, IMRIC, The Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel
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25
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Tabassum W, Singh P, Suthram N, Bhattacharyya S, Bhattacharyya MK. Synergistic Action between PfHsp90 Inhibitor and PfRad51 Inhibitor Induces Elevated DNA Damage Sensitivity in the Malaria Parasite. Antimicrob Agents Chemother 2021; 65:e0045721. [PMID: 34097485 PMCID: PMC8370194 DOI: 10.1128/aac.00457-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Accepted: 05/19/2021] [Indexed: 12/18/2022] Open
Abstract
The DNA recombinase Rad51 from the human malaria parasite Plasmodium falciparum has emerged as a potential drug target due to its central role in the homologous recombination (HR)-mediated double-strand break (DSB) repair pathway. Inhibition of the ATPase and strand exchange activity of P. falciparum Rad51 (PfRad51) by a small-molecule inhibitor, B02 [3-(phenylmethyl)-2-[(1E)-2-(3-pyridinyl)ethenyl]-4(3H)-quinazolinone], renders the parasite more sensitive to genotoxic agents. Here, we investigated whether the inhibition of the molecular chaperone PfHsp90 potentiates the antimalarial action of B02. We found that the PfHsp90 inhibitor 17-AAG [17-(allylamino)-17-demethoxygeldanamycin] exhibits strong synergism with B02 in both drug-sensitive (strain 3D7) and multidrug-resistant (strain Dd2) P. falciparum parasites. 17-AAG causes a greater than 200-fold decrease in the half-maximal inhibitory concentration (IC50) of B02 in 3D7 parasites. Our results provide mechanistic insights into such profound synergism between 17-AAG and B02. We report that PfHsp90 physically interacts with PfRad51 and promotes the UV irradiation-induced DNA repair activity of PfRad51 by controlling its stability. We find that 17-AAG reduces PfRad51 protein levels by accelerating proteasomal degradation. Consequently, PfHsp90 inhibition renders the parasites more susceptible to the potent DNA-damaging agent methyl methanesulfonate (MMS) in a dose-dependent manner. Thus, our study provides a rationale for targeting PfHsp90 along with the recombinase PfRad51 for controlling malaria propagation.
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Affiliation(s)
- Wahida Tabassum
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - Priyanka Singh
- Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - Niranjan Suthram
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - Sunanda Bhattacharyya
- Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad, India
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26
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You H, Mayer JU, Johnston RL, Sivakumaran H, Ranasinghe S, Rivera V, Kondrashova O, Koufariotis LT, Du X, Driguez P, French JD, Waddell N, Duke MG, Ittiprasert W, Mann VH, Brindley PJ, Jones MK, McManus DP. CRISPR/Cas9-mediated genome editing of Schistosoma mansoni acetylcholinesterase. FASEB J 2021; 35:e21205. [PMID: 33337558 DOI: 10.1096/fj.202001745rr] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Revised: 10/16/2020] [Accepted: 11/03/2020] [Indexed: 12/21/2022]
Abstract
CRISPR/Cas9-mediated genome editing shows cogent potential for the genetic modification of helminth parasites. We report successful gene knock-in (KI) into the genome of the egg of Schistosoma mansoni by combining CRISPR/Cas9 with single-stranded oligodeoxynucleotides (ssODNs). We edited the acetylcholinesterase (AChE) gene of S. mansoni targeting two guide RNAs (gRNAs), X5 and X7, located on exon 5 and exon 7 of Smp_154600, respectively. Eggs recovered from livers of experimentally infected mice were transfected by electroporation with a CRISPR/Cas9-vector encoding gRNA X5 or X7 combining with/ without a ssODN donor. Next generation sequencing analysis of reads of amplicon libraries spanning targeted regions revealed that the major modifications induced by CRISPR/Cas9 in the eggs were generated by homology directed repair (HDR). Furthermore, soluble egg antigen from AChE-edited eggs exhibited markedly reduced AChE activity, indicative that programed Cas9 cleavage mutated the AChE gene. Following injection of AChE-edited schistosome eggs into the tail veins of mice, an significantly enhanced Th2 response involving IL-4, -5, -10, and-13 was detected in lung cells and splenocytes in mice injected with X5-KI eggs in comparison to control mice injected with unmutated eggs. A Th2-predominant response, with increased levels of IL-4, -13, and GATA3, also was induced by X5 KI eggs in small intestine-draining mesenteric lymph node cells when the gene-edited eggs were introduced into the subserosa of the ileum of the mice. These findings confirmed the potential and the utility of CRISPR/Cas9-mediated genome editing for functional genomics in schistosomes.
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Affiliation(s)
- Hong You
- Immunology Department, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | | | - Rebecca L Johnston
- Genetics & Computational Biology Department, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Haran Sivakumaran
- Genetics & Computational Biology Department, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Shiwanthi Ranasinghe
- Immunology Department, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Vanessa Rivera
- Immunology Department, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia.,School of Medicine, Deakin University, Geelong, VIC, Australia
| | - Olga Kondrashova
- Genetics & Computational Biology Department, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Lambros T Koufariotis
- Genetics & Computational Biology Department, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Xiaofeng Du
- Immunology Department, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Patrick Driguez
- King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
| | - Juliet D French
- Genetics & Computational Biology Department, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Nicola Waddell
- Genetics & Computational Biology Department, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Mary G Duke
- Immunology Department, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Wannaporn Ittiprasert
- Department of Microbiology, Immunology & Tropical Medicine, & Research Center for Neglected Diseases of Poverty, School of Medicine & Health Sciences, George Washington University, Washington, DC, USA
| | - Victoria H Mann
- Department of Microbiology, Immunology & Tropical Medicine, & Research Center for Neglected Diseases of Poverty, School of Medicine & Health Sciences, George Washington University, Washington, DC, USA
| | - Paul J Brindley
- Department of Microbiology, Immunology & Tropical Medicine, & Research Center for Neglected Diseases of Poverty, School of Medicine & Health Sciences, George Washington University, Washington, DC, USA
| | - Malcolm K Jones
- Immunology Department, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia.,School of Veterinary Science, The University of Queensland, Gatton, QLD, Australia
| | - Donald P McManus
- Immunology Department, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
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27
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Kirti A, Sharma M, Rani K, Bansal A. CRISPRing protozoan parasites to better understand the biology of diseases. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2021; 180:21-68. [PMID: 33934837 DOI: 10.1016/bs.pmbts.2021.01.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Precise gene editing techniques are paramount to gain deeper insights into the biological processes such as host-parasite interactions, drug resistance mechanisms, and gene-function relationships. Discovery of CRISPR-Cas9 system has spearheaded mechanistic understanding of protozoan parasite biology as evident from the number of reports in the last decade. Here, we have described the use of CRISPR-Cas9 in understanding the biology of medically important protozoan parasites such as Plasmodium, Leishmania, Trypanosoma, Babesia and Trichomonas. In spite of intrinsic difficulties in genome editing in these protozoan parasites, CRISPR-Cas9 has acted as a catalyst for faster generation of desired transgenic parasites. Modifications in the CRISPR-Cas9 system for improving the efficiency have been useful in better understanding the molecular mechanisms associated with repair of double strand breaks in the parasites. Moreover, improvement in reagents used for CRISPR mediated gene editing have been instrumental in addressing the issue of non-specificity and toxicity for therapeutic use. These application-based modifications may help in further increasing the efficiency of gene editing in protozoan parasites.
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Affiliation(s)
- Apurva Kirti
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Manish Sharma
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Komal Rani
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Abhisheka Bansal
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India.
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Zhou M, Varol A, Efferth T. Multi-omics approaches to improve malaria therapy. Pharmacol Res 2021; 167:105570. [PMID: 33766628 DOI: 10.1016/j.phrs.2021.105570] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 03/02/2021] [Accepted: 03/16/2021] [Indexed: 01/07/2023]
Abstract
Malaria contributes to the most widespread infectious diseases worldwide. Even though current drugs are commercially available, the ever-increasing drug resistance problem by malaria parasites poses new challenges in malaria therapy. Hence, searching for efficient therapeutic strategies is of high priority in malaria control. In recent years, multi-omics technologies have been extensively applied to provide a more holistic view of functional principles and dynamics of biological mechanisms. We briefly review multi-omics technologies and focus on recent malaria progress conducted with the help of various omics methods. Then, we present up-to-date advances for multi-omics approaches in malaria. Next, we describe resistance phenomena to established antimalarial drugs and underlying mechanisms. Finally, we provide insight into novel multi-omics approaches, new drugs and vaccine developments and analyze current gaps in multi-omics research. Although multi-omics approaches have been successfully used in malaria studies, they are still limited. Many gaps need to be filled to bridge the gap between basic research and treatment of malaria patients. Multi-omics approaches will foster a better understanding of the molecular mechanisms of Plasmodium that are essential for the development of novel drugs and vaccines to fight this disastrous disease.
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Affiliation(s)
- Min Zhou
- Department of Pharmaceutical Biology, Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University, Staudinger Weg 5, 55128 Mainz, Germany
| | - Ayşegül Varol
- Department of Pharmaceutical Biology, Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University, Staudinger Weg 5, 55128 Mainz, Germany
| | - Thomas Efferth
- Department of Pharmaceutical Biology, Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University, Staudinger Weg 5, 55128 Mainz, Germany.
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Hitz E, Grüninger O, Passecker A, Wyss M, Scheurer C, Wittlin S, Beck HP, Brancucci NMB, Voss TS. The catalytic subunit of Plasmodium falciparum casein kinase 2 is essential for gametocytogenesis. Commun Biol 2021; 4:336. [PMID: 33712726 PMCID: PMC7954856 DOI: 10.1038/s42003-021-01873-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 02/17/2021] [Indexed: 01/31/2023] Open
Abstract
Casein kinase 2 (CK2) is a pleiotropic kinase phosphorylating substrates in different cellular compartments in eukaryotes. In the malaria parasite Plasmodium falciparum, PfCK2 is vital for asexual proliferation of blood-stage parasites. Here, we applied CRISPR/Cas9-based gene editing to investigate the function of the PfCK2α catalytic subunit in gametocytes, the sexual forms of the parasite that are essential for malaria transmission. We show that PfCK2α localizes to the nucleus and cytoplasm in asexual and sexual parasites alike. Conditional knockdown of PfCK2α expression prevented the transition of stage IV into transmission-competent stage V gametocytes, whereas the conditional knockout of pfck2a completely blocked gametocyte maturation already at an earlier stage of sexual differentiation. In summary, our results demonstrate that PfCK2α is not only essential for asexual but also sexual development of P. falciparum blood-stage parasites and encourage studies exploring PfCK2α as a potential target for dual-active antimalarial drugs.
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Affiliation(s)
- Eva Hitz
- grid.416786.a0000 0004 0587 0574Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, 4051 Basel, Switzerland ,grid.6612.30000 0004 1937 0642University of Basel, 4001 Basel, Switzerland
| | - Olivia Grüninger
- grid.416786.a0000 0004 0587 0574Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, 4051 Basel, Switzerland ,grid.6612.30000 0004 1937 0642University of Basel, 4001 Basel, Switzerland
| | - Armin Passecker
- grid.416786.a0000 0004 0587 0574Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, 4051 Basel, Switzerland ,grid.6612.30000 0004 1937 0642University of Basel, 4001 Basel, Switzerland
| | - Matthias Wyss
- grid.416786.a0000 0004 0587 0574Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, 4051 Basel, Switzerland ,grid.6612.30000 0004 1937 0642University of Basel, 4001 Basel, Switzerland
| | - Christian Scheurer
- grid.416786.a0000 0004 0587 0574Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, 4051 Basel, Switzerland ,grid.6612.30000 0004 1937 0642University of Basel, 4001 Basel, Switzerland
| | - Sergio Wittlin
- grid.416786.a0000 0004 0587 0574Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, 4051 Basel, Switzerland ,grid.6612.30000 0004 1937 0642University of Basel, 4001 Basel, Switzerland
| | - Hans-Peter Beck
- grid.416786.a0000 0004 0587 0574Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, 4051 Basel, Switzerland ,grid.6612.30000 0004 1937 0642University of Basel, 4001 Basel, Switzerland
| | - Nicolas M. B. Brancucci
- grid.416786.a0000 0004 0587 0574Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, 4051 Basel, Switzerland ,grid.6612.30000 0004 1937 0642University of Basel, 4001 Basel, Switzerland
| | - Till S. Voss
- grid.416786.a0000 0004 0587 0574Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, 4051 Basel, Switzerland ,grid.6612.30000 0004 1937 0642University of Basel, 4001 Basel, Switzerland
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Abstract
Plasmodium falciparum is the deadliest human parasite that causes malaria when it reaches the bloodstream and begins proliferating inside red blood cells, where the parasites are particularly prone to DNA damage. The molecular mechanisms that allow these pathogens to maintain their genome integrity under such conditions are also the driving force for acquiring genome plasticity that enables them to create antigenic variation and become resistant to essentially all available drugs. Plasmodium falciparum parasites proliferate within circulating red blood cells and are responsible for the deadliest form of human malaria. These parasites are exposed to numerous intrinsic and external sources that could cause DNA damage; therefore, they have evolved efficient mechanisms to protect their genome integrity and allow them to proliferate under such conditions. In higher eukaryotes, double-strand breaks rapidly lead to phosphorylation of the core histone variant H2A.X, which marks the site of damaged DNA. We show that in P. falciparum that lacks the H2A.X variant, the canonical P. falciparum H2A (PfH2A) is phosphorylated on serine 121 upon exposure to sources of DNA damage. We further demonstrate that phosphorylated PfH2A is recruited to foci of damaged chromatin shortly after exposure to sources of damage, while the nonphosphorylated PfH2A remains spread throughout the nucleoplasm. In addition, we found that PfH2A phosphorylation is dynamic and that over time, as the parasite activates the repair machinery, this phosphorylation is removed. Finally, we demonstrate that these phosphorylation dynamics could be used to establish a novel and direct DNA repair assay in P. falciparum. IMPORTANCEPlasmodium falciparum is the deadliest human parasite that causes malaria when it reaches the bloodstream and begins proliferating inside red blood cells, where the parasites are particularly prone to DNA damage. The molecular mechanisms that allow these pathogens to maintain their genome integrity under such conditions are also the driving force for acquiring genome plasticity that enables them to create antigenic variation and become resistant to essentially all available drugs. However, mechanisms of DNA damage response and repair have not been extensively studied for these parasites. The paper addresses our recent discovery that P. falciparum that lacks the histone variant H2A.X phosphorylates its canonical core histone PfH2A in response to exposure to DNA damage. The process of DNA repair in Plasmodium was mostly studied indirectly. Our findings enabled us to establish a direct DNA repair assay for P. falciparum similar to assays that are widely used in model organisms.
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Guttery DS, Ramaprasad A, Ferguson DJP, Zeeshan M, Pandey R, Brady D, Holder AA, Pain A, Tewari R. MRE11 Is Crucial for Malaria Parasite Transmission and Its Absence Affects Expression of Interconnected Networks of Key Genes Essential for Life. Cells 2020; 9:E2590. [PMID: 33287434 PMCID: PMC7761864 DOI: 10.3390/cells9122590] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 11/30/2020] [Accepted: 12/01/2020] [Indexed: 11/16/2022] Open
Abstract
The meiotic recombination 11 protein (MRE11) plays a key role in DNA damage response and maintenance of genome stability. However, little is known about its function during development of the malaria parasite Plasmodium. Here, we present a functional, ultrastructural and transcriptomic analysis of Plasmodium parasites lacking MRE11 during its life cycle in both mammalian and mosquito vector hosts. Genetic disruption of Plasmodium berghei mre11 (PbMRE11) results in significant retardation of oocyst development in the mosquito midgut associated with cytoplasmic and nuclear degeneration, along with concomitant ablation of sporogony and subsequent parasite transmission. Further, absence of PbMRE11 results in significant transcriptional downregulation of genes involved in key interconnected biological processes that are fundamental to all eukaryotic life including ribonucleoprotein biogenesis, spliceosome function and iron-sulfur cluster assembly. Overall, our study provides a comprehensive functional analysis of MRE11's role in Plasmodium development during the mosquito stages and offers a potential target for therapeutic intervention during malaria parasite transmission.
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Affiliation(s)
- David S. Guttery
- Queens Medical Centre, School of Life Sciences, University of Nottingham, Nottingham NG7 2UH, UK; (M.Z.); (R.P.); (D.B.)
| | - Abhinay Ramaprasad
- Biological and Environmental Sciences and Engineering (BESE) Division, King Abdullah University of Science and Technology, Thuwal 23955, Saudi Arabia; (A.R.); (A.P.)
- The Francis Crick Institute, London NW1 1AT, UK;
| | - David J. P. Ferguson
- Nuffield Department of Clinical Laboratory Science, University of Oxford, John Radcliffe Hospital, Oxford OX1 2JD, UK;
- Department Biological & Medical Sciences, Oxford Brookes University, Oxford OX3 0BP, UK
| | - Mohammad Zeeshan
- Queens Medical Centre, School of Life Sciences, University of Nottingham, Nottingham NG7 2UH, UK; (M.Z.); (R.P.); (D.B.)
| | - Rajan Pandey
- Queens Medical Centre, School of Life Sciences, University of Nottingham, Nottingham NG7 2UH, UK; (M.Z.); (R.P.); (D.B.)
| | - Declan Brady
- Queens Medical Centre, School of Life Sciences, University of Nottingham, Nottingham NG7 2UH, UK; (M.Z.); (R.P.); (D.B.)
| | | | - Arnab Pain
- Biological and Environmental Sciences and Engineering (BESE) Division, King Abdullah University of Science and Technology, Thuwal 23955, Saudi Arabia; (A.R.); (A.P.)
- Nuffield Department of Clinical Laboratory Science, University of Oxford, John Radcliffe Hospital, Oxford OX1 2JD, UK;
- Research Center for Zoonosis Control, Global Institution for Collaborative Research and Education (GI-CoRE), Hokkaido University, Sapporo 060-0808, Japan
| | - Rita Tewari
- Queens Medical Centre, School of Life Sciences, University of Nottingham, Nottingham NG7 2UH, UK; (M.Z.); (R.P.); (D.B.)
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Expansion of a Specific Plasmodium falciparum PfMDR1 Haplotype in Southeast Asia with Increased Substrate Transport. mBio 2020; 11:mBio.02093-20. [PMID: 33262257 PMCID: PMC7733942 DOI: 10.1128/mbio.02093-20] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Global efforts to eliminate malaria depend on the continued success of artemisinin-based combination therapies (ACTs) that target Plasmodium asexual blood-stage parasites. Resistance to ACTs, however, has emerged, creating the need to define the underlying mechanisms. Mutations in the P. falciparum multidrug resistance protein 1 (PfMDR1) transporter constitute an important determinant of resistance. Applying gene editing tools combined with an analysis of a public database containing thousands of parasite genomes, we show geographic selection and expansion of a pfmdr1 gene amplification encoding the N86/184F haplotype in Southeast Asia. Parasites expressing this PfMDR1 variant possess a higher transport capacity that modulates their responses to antimalarials. These data could help tailor and optimize antimalarial drug usage in different regions where malaria is endemic by taking into account the regional prevalence of pfmdr1 polymorphisms. Artemisinin-based combination therapies (ACTs) have been vital in reducing malaria mortality rates since the 2000s. Their efficacy, however, is threatened by the emergence and spread of artemisinin resistance in Southeast Asia. The Plasmodium falciparum multidrug resistance protein 1 (PfMDR1) transporter plays a central role in parasite resistance to ACT partner drugs through gene copy number variations (CNV) and/or single nucleotide polymorphisms (SNPs). Using genomic epidemiology, we show that multiple pfmdr1 copies encoding the N86 and 184F haplotype are prevalent across Southeast Asia. Applying genome editing tools on the Southeast Asian Dd2 strain and using a surrogate assay to measure transporter activity in infected red blood cells, we demonstrate that parasites harboring multicopy N86/184F PfMDR1 have a higher Fluo-4 transport capacity compared with those expressing the wild-type N86/Y184 haplotype. Multicopy N86/184F PfMDR1 is also associated with decreased parasite susceptibility to lumefantrine. These findings provide evidence of the geographic selection and expansion of specific multicopy PfMDR1 haplotypes associated with multidrug resistance in Southeast Asia.
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Zhang X, Deitsch KW, Kirkman LA. The contribution of extrachromosomal DNA to genome plasticity in malaria parasites. Mol Microbiol 2020; 115:503-507. [PMID: 33103309 DOI: 10.1111/mmi.14632] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 10/19/2020] [Accepted: 10/19/2020] [Indexed: 01/20/2023]
Abstract
Malaria caused by the protozoan parasite Plasmodium falciparum continues to impose significant morbidity and mortality, despite substantial investment into drug and vaccine development and deployment. Underlying the resilience of this parasite is its remarkable ability to undergo genome modifications, thus, providing parasite populations with extensive genetic variability that accelerates selection of drug resistance and limits the efficacy of most vaccines. This genome plasticity is rooted in the mechanisms of DNA repair that parasites employ to maintain genome integrity, a process skewed toward homologous recombination through the evolutionary loss of classical nonhomologous end joining. Repair of DNA double-strand breaks have been shown to enable "shuffling" of antigen-encoding gene sequences to vastly increase antigen diversity and to enable copy number expansion of genes that contribute to drug resistance. The latter phenomenon has been proposed to be a major contributor to the rise of resistance to several classes of antimalarial drugs. In this issue of Molecular Microbiology, McDaniels and colleagues add yet another mechanism that malaria parasites use to reduce drug susceptibility by demonstrating that P. falciparum can maintain expanded arrays of drug resistance cassettes as stably replicating, circular, extrachromosomal DNAs, thus, expanding genome plasticity beyond the parasite's 14 nuclear chromosomes.
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Affiliation(s)
- Xu Zhang
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY, USA
| | - Kirk W Deitsch
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY, USA
| | - Laura A Kirkman
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY, USA.,Department of Internal Medicine, Division of Infectious Diseases, Weill Cornell Medical College, New York, NY, USA
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Plasmodium berghei K13 Mutations Mediate In Vivo Artemisinin Resistance That Is Reversed by Proteasome Inhibition. mBio 2020; 11:mBio.02312-20. [PMID: 33173001 PMCID: PMC7667033 DOI: 10.1128/mbio.02312-20] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Recent successes in malaria control have been seriously threatened by the emergence of Plasmodium falciparum parasite resistance to the frontline artemisinin drugs in Southeast Asia. P. falciparum artemisinin resistance is associated with mutations in the parasite K13 protein, which associates with a delay in the time required to clear the parasites upon drug treatment. Gene editing technologies have been used to validate the role of several candidate K13 mutations in mediating P. falciparum artemisinin resistance in vitro under laboratory conditions. Nonetheless, the causal role of these mutations under in vivo conditions has been a matter of debate. Here, we have used CRISPR/Cas9 gene editing to introduce K13 mutations associated with artemisinin resistance into the related rodent-infecting parasite, Plasmodium berghei. Phenotyping of these P. berghei K13 mutant parasites provides evidence of their role in mediating artemisinin resistance in vivo, which supports in vitro artemisinin resistance observations. However, we were unable to introduce some of the P. falciparum K13 mutations (C580Y and I543T) into the corresponding amino acid residues, while other introduced mutations (M476I and R539T equivalents) carried pronounced fitness costs. Our study provides evidence of a clear causal role of K13 mutations in modulating susceptibility to artemisinins in vitro and in vivo using the well-characterized P. berghei model. We also show that inhibition of the P. berghei proteasome offsets parasite resistance to artemisinins in these mutant lines. The recent emergence of Plasmodium falciparum parasite resistance to the first line antimalarial drug artemisinin is of particular concern. Artemisinin resistance is primarily driven by mutations in the P. falciparum K13 protein, which enhance survival of early ring-stage parasites treated with the artemisinin active metabolite dihydroartemisinin in vitro and associate with delayed parasite clearance in vivo. However, association of K13 mutations with in vivo artemisinin resistance has been problematic due to the absence of a tractable model. Herein, we have employed CRISPR/Cas9 genome editing to engineer selected orthologous P. falciparum K13 mutations into the K13 gene of an artemisinin-sensitive Plasmodium berghei rodent model of malaria. Introduction of the orthologous P. falciparum K13 F446I, M476I, Y493H, and R539T mutations into P. berghei K13 yielded gene-edited parasites with reduced susceptibility to dihydroartemisinin in the standard 24-h in vitro assay and increased survival in an adapted in vitro ring-stage survival assay. Mutant P. berghei K13 parasites also displayed delayed clearance in vivo upon treatment with artesunate and achieved faster recrudescence upon treatment with artemisinin. Orthologous C580Y and I543T mutations could not be introduced into P. berghei, while the equivalents of the M476I and R539T mutations resulted in significant growth defects. Furthermore, a Plasmodium-selective proteasome inhibitor strongly synergized dihydroartemisinin action in these P. berghei K13 mutant lines, providing further evidence that the proteasome can be targeted to overcome artemisinin resistance. Taken together, our findings provide clear experimental evidence for the involvement of K13 polymorphisms in mediating susceptibility to artemisinins in vitro and, most importantly, under in vivo conditions.
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35
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Su XZ, Zhang C, Joy DA. Host-Malaria Parasite Interactions and Impacts on Mutual Evolution. Front Cell Infect Microbiol 2020; 10:587933. [PMID: 33194831 PMCID: PMC7652737 DOI: 10.3389/fcimb.2020.587933] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 09/22/2020] [Indexed: 12/22/2022] Open
Abstract
Malaria is the most deadly parasitic disease, affecting hundreds of millions of people worldwide. Malaria parasites have been associated with their hosts for millions of years. During the long history of host-parasite co-evolution, both parasites and hosts have applied pressure on each other through complex host-parasite molecular interactions. Whereas the hosts activate various immune mechanisms to remove parasites during an infection, the parasites attempt to evade host immunity by diversifying their genome and switching expression of targets of the host immune system. Human intervention to control the disease such as antimalarial drugs and vaccination can greatly alter parasite population dynamics and evolution, particularly the massive applications of antimalarial drugs in recent human history. Vaccination is likely the best method to prevent the disease; however, a partially protective vaccine may have unwanted consequences that require further investigation. Studies of host-parasite interactions and co-evolution will provide important information for designing safe and effective vaccines and for preventing drug resistance. In this essay, we will discuss some interesting molecules involved in host-parasite interactions, including important parasite antigens. We also discuss subjects relevant to drug and vaccine development and some approaches for studying host-parasite interactions.
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Affiliation(s)
- Xin-Zhuan Su
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Cui Zhang
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Deirdre A Joy
- Parasitology and International Programs Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
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Sheriff O, Yaw A, Lai SK, Loo HL, Sze SK, Preiser PR. Plasmodium falciparum replication factor C subunit 1 is involved in genotoxic stress response. Cell Microbiol 2020; 23:e13277. [PMID: 33040440 DOI: 10.1111/cmi.13277] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 10/05/2020] [Accepted: 10/06/2020] [Indexed: 02/03/2023]
Abstract
About half the world's population is at risk of malaria, with Plasmodium falciparum malaria being responsible for the most malaria related deaths globally. Antimalarial drugs such as chloroquine and artemisinin are directed towards the proliferating intra-erythrocytic stages of the parasite, which is responsible for all the clinical symptoms of the disease. These antimalarial drugs have been reported to function via multiple pathways, one of which induces DNA damage via the generation of free radicals and reactive oxygen species. An urgent need to understand the mechanistic details of drug response and resistance is highlighted by the decreasing clinical efficacy of the front line drug, Artemisinin. The replication factor C subunit 1 is an important component of the DNA replication machinery and DNA damage response mechanism. Here we show the translocation of PfRFC1 from an intranuclear localisation to the nuclear periphery, indicating an orchestrated progression of distinct patterns of replication in the developing parasites. PfRFC1 responds to genotoxic stress via elevated protein levels in soluble and chromatin bound fractions. Reduction of PfRFC1 protein levels upon treatment with antimalarials suggests an interplay of replication, apoptosis and DNA repair pathways leading to cell death. Additionally, mislocalisation of the endogenously tagged protein confirmed its essential role in parasites' replication and DNA repair. This study provides key insights into DNA replication, DNA damage response and cell death in P. falciparum.
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Affiliation(s)
- Omar Sheriff
- School of Biological Sciences, Nanyang Technological University Singapore, Singapore, Singapore
| | - Aniweh Yaw
- West African Centre for Cell Biology of Infectious Pathogens, University of Ghana, Legon, Ghana
| | - Soak Kuan Lai
- School of Biological Sciences, Nanyang Technological University Singapore, Singapore, Singapore
| | - Hooi Linn Loo
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore, Singapore
| | - Siu Kwan Sze
- School of Biological Sciences, Nanyang Technological University Singapore, Singapore, Singapore
| | - Peter Rainer Preiser
- School of Biological Sciences, Nanyang Technological University Singapore, Singapore, Singapore.,Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore, Singapore
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Zhou W, Wang H, Yang Y, Chen ZS, Zou C, Zhang J. Chloroquine against malaria, cancers and viral diseases. Drug Discov Today 2020; 25:S1359-6446(20)30367-6. [PMID: 32947043 PMCID: PMC7492153 DOI: 10.1016/j.drudis.2020.09.010] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 07/13/2020] [Accepted: 09/10/2020] [Indexed: 02/08/2023]
Abstract
Quinoline (QN) derivatives are often used for the prophylaxis and treatment of malaria. Chloroquine (CQ), a protonated, weakly basic drug, exerts its antimalarial effect mainly by increasing pH and accumulating in the food vacuole of the parasites. Repurposing CQ is an emerging strategy for new indications. Given the inhibition of autophagy and its immunomodulatory action, CQ shows positive efficacy against cancer and viral diseases, including Coronavirus 2019 (COVID-19). Here, we review the underlying mechanisms behind the antimalarial, anticancer and antiviral effects of CQ. We also discuss the clinical evidence for the use of CQ and hydroxychloroquine (HCQ) against COVID-19.
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Affiliation(s)
- Wenmin Zhou
- Key Laboratory of Molecular Target & Clinical Pharmacology and the State Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences & the Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou, 511436, PR China
| | - Hui Wang
- Key Laboratory of Molecular Target & Clinical Pharmacology and the State Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences & the Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou, 511436, PR China; Guangzhou Institute of Pediatrics/Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, 510623, PR China; The First Affiliated Hospital, Hainan Medical University, Haikou, 571199, PR China
| | - Yuqi Yang
- College of Pharmacy and Health Sciences, St John's University, Queens, New York, NY 11439, USA
| | - Zhe-Sheng Chen
- College of Pharmacy and Health Sciences, St John's University, Queens, New York, NY 11439, USA.
| | - Chang Zou
- The Second Clinical Medical College of Jinan University, Shenzhen, 518020, PR China.
| | - Jianye Zhang
- Key Laboratory of Molecular Target & Clinical Pharmacology and the State Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences & the Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou, 511436, PR China; Guangzhou Institute of Pediatrics/Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, 510623, PR China; The First Affiliated Hospital, Hainan Medical University, Haikou, 571199, PR China.
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38
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Francis AT, Shears MJ, Murphy SC, Fu D. Direct Quantification of Single Red Blood Cell Hemoglobin Concentration with Multiphoton Microscopy. Anal Chem 2020; 92:12235-12241. [PMID: 32786430 DOI: 10.1021/acs.analchem.0c01609] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Blood disorders, diseases, and infections often affect the shape, number, and content of red blood cells (RBCs) dramatically. To combat these pathologies, many therapies target RBCs and their contents directly. Mean corpuscular hemoglobin concentration (MCHC) is an important pathological metric in both identification and treatment. However, current methods for RBC analysis and MCHC quantification rely on bulk measurements. Single RBC measurements could provide necessary insight into the heterogeneity of RBC health and improve therapeutic efficacy. In this study, we present a novel multimodal multiphoton approach for quantifying hemoglobin concentration at single RBC resolution. We achieve this by collecting two images simultaneously that allows us to excite water with stimulated Raman scattering and hemoglobin with transient absorption. This multimodal imaging is enabled by a newly designed orthogonal modulation theme for dual-channel lock-in detection. By leveraging water as an internal standard, we quantify MCHC of healthy RBCs and RBCs infected with Plasmodium yoelii, a commonly studied rodent parasite model.
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Affiliation(s)
- Andrew T Francis
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Melanie J Shears
- Department of Laboratory Medicine and Center for Emerging and Re-emerging Infectious Diseases, University of Washington, 750 Republican Street, Seattle, Washington 98109, United States
| | - Sean C Murphy
- Department of Laboratory Medicine and Center for Emerging and Re-emerging Infectious Diseases, University of Washington, 750 Republican Street, Seattle, Washington 98109, United States
| | - Dan Fu
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
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39
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Rapid and quantitative antimalarial drug efficacy testing via the magneto-optical detection of hemozoin. Sci Rep 2020; 10:14025. [PMID: 32820190 PMCID: PMC7441145 DOI: 10.1038/s41598-020-70860-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Accepted: 07/24/2020] [Indexed: 01/24/2023] Open
Abstract
Emergence of resistant Plasmodium species makes drug efficacy testing a crucial part of malaria control. Here we describe a novel assay for sensitive, fast and simple drug screening via the magneto-optical detection of hemozoin, a natural biomarker formed during the hemoglobin metabolism of Plasmodium species. By quantifying hemozoin production over the intraerythrocytic cycle, we reveal that hemozoin formation is already initiated by ~ 6–12 h old ring-stage parasites. We demonstrate that the new assay is capable of drug efficacy testing with incubation times as short as 6–10 h, using synchronized P. falciparum 3D7 cultures incubated with chloroquine, piperaquine and dihydroartemisinin. The determined 50% inhibitory concentrations agree well with values established by standard assays requiring significantly longer testing time. Accordingly, we conclude that magneto-optical hemozoin detection provides a practical approach for the quick assessment of drug effect with short incubation times, which may also facilitate stage-specific assessment of drug inhibitory effects.
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40
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Sex in Symbiodiniaceae dinoflagellates: genomic evidence for independent loss of the canonical synaptonemal complex. Sci Rep 2020; 10:9792. [PMID: 32555361 PMCID: PMC7299967 DOI: 10.1038/s41598-020-66429-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2020] [Accepted: 05/19/2020] [Indexed: 01/07/2023] Open
Abstract
Dinoflagellates of the Symbiodiniaceae family encompass diverse symbionts that are critical to corals and other species living in coral reefs. It is well known that sexual reproduction enhances adaptive evolution in changing environments. Although genes related to meiotic functions were reported in Symbiodiniaceae, cytological evidence of meiosis and fertilisation are however yet to be observed in these taxa. Using transcriptome and genome data from 21 Symbiodiniaceae isolates, we studied genes that encode proteins associated with distinct stages of meiosis and syngamy. We report the absence of genes that encode main components of the synaptonemal complex (SC), a protein structure that mediates homologous chromosomal pairing and class I crossovers. This result suggests an independent loss of canonical SCs in the alveolates, that also includes the SC-lacking ciliates. We hypothesise that this loss was due in part to permanently condensed chromosomes and repeat-rich sequences in Symbiodiniaceae (and other dinoflagellates) which favoured the SC-independent class II crossover pathway. Our results reveal novel insights into evolution of the meiotic molecular machinery in the ecologically important Symbiodiniaceae and in other eukaryotes.
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Rose E, Carvalho JL, Hecht M. Mechanisms of DNA repair in Trypanosoma cruzi: What do we know so far? DNA Repair (Amst) 2020; 91-92:102873. [PMID: 32505694 DOI: 10.1016/j.dnarep.2020.102873] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 03/27/2020] [Accepted: 05/22/2020] [Indexed: 12/13/2022]
Abstract
Trypanosoma cruzi is the etiological agent of Chagas Disease, which affects 6-7 million people worldwide. Since the early stages of infection and throughout its life cycle, the parasite is exposed to several genotoxic agents. Furthermore, DNA damage is also part of the mechanism of action of at least a few trypanocidal drugs, including Benznidazole. Thus, it is paramount for the parasite to count on an efficient DNA repair machinery to guarantee genome integrity and survival. The present work provides an up-to-date review of both the conserved and peculiar DNA repair mechanisms described in T. cruzi against oxidative stress, ultraviolet and ionizing radiation, DNA adduct-inducing agents, and Benznidazole. The comprehension of the DNA repair mechanisms of the parasite may shed light on the parasite evolution and possibly pave the way for the development of novel and more effective trypanocidal drugs.
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Affiliation(s)
- Ester Rose
- Interdisciplinary Laboratory of Biosciences, Faculty of Medicine, University of Brasília, Brasília, Brazil.
| | - Juliana Lott Carvalho
- Interdisciplinary Laboratory of Biosciences, Faculty of Medicine, University of Brasília, Brasília, Brazil; Genomic Sciences and Biotechnology Program, Catholic University of Brasília, Brasília, Brazil
| | - Mariana Hecht
- Interdisciplinary Laboratory of Biosciences, Faculty of Medicine, University of Brasília, Brasília, Brazil
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42
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Stanway RR, Bushell E, Chiappino-Pepe A, Roques M, Sanderson T, Franke-Fayard B, Caldelari R, Golomingi M, Nyonda M, Pandey V, Schwach F, Chevalley S, Ramesar J, Metcalf T, Herd C, Burda PC, Rayner JC, Soldati-Favre D, Janse CJ, Hatzimanikatis V, Billker O, Heussler VT. Genome-Scale Identification of Essential Metabolic Processes for Targeting the Plasmodium Liver Stage. Cell 2020; 179:1112-1128.e26. [PMID: 31730853 PMCID: PMC6904910 DOI: 10.1016/j.cell.2019.10.030] [Citation(s) in RCA: 73] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 07/23/2019] [Accepted: 10/23/2019] [Indexed: 12/11/2022]
Abstract
Plasmodium gene functions in mosquito and liver stages remain poorly characterized due to limitations in the throughput of phenotyping at these stages. To fill this gap, we followed more than 1,300 barcoded P. berghei mutants through the life cycle. We discover 461 genes required for efficient parasite transmission to mosquitoes through the liver stage and back into the bloodstream of mice. We analyze the screen in the context of genomic, transcriptomic, and metabolomic data by building a thermodynamic model of P. berghei liver-stage metabolism, which shows a major reprogramming of parasite metabolism to achieve rapid growth in the liver. We identify seven metabolic subsystems that become essential at the liver stages compared with asexual blood stages: type II fatty acid synthesis and elongation (FAE), tricarboxylic acid, amino sugar, heme, lipoate, and shikimate metabolism. Selected predictions from the model are individually validated in single mutants to provide future targets for drug development. 1,342 barcoded P. berghei knockout (KO) mutants analyzed for stage-specific phenotypes Life-stage-specific metabolic models reveal reprogramming of cellular function High agreement between blood/liver stage metabolic models and genetic screening data Essential metabolic pathways for parasite development and mechanistic origin revealed
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Affiliation(s)
- Rebecca R Stanway
- Institute of Cell Biology, University of Bern, Bern 3012, Switzerland
| | - Ellen Bushell
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK; Molecular Infection Medicine Sweden (MIMS), Department of Molecular Biology, Umeå University, Umeå 901 87, Sweden
| | - Anush Chiappino-Pepe
- Laboratory of Computational Systems Biotechnology, École Polytechnique Fédérale de Lausanne, EPFL, Lausanne 1015, Switzerland
| | - Magali Roques
- Institute of Cell Biology, University of Bern, Bern 3012, Switzerland
| | - Theo Sanderson
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Blandine Franke-Fayard
- Leiden Malaria Research Group, Parasitology, Center of Infectious Diseases, Leiden University Medical Center (LUMC), Leiden 2333ZA, the Netherlands
| | - Reto Caldelari
- Institute of Cell Biology, University of Bern, Bern 3012, Switzerland
| | | | - Mary Nyonda
- Department of Microbiology & Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva 1211, Switzerland
| | - Vikash Pandey
- Laboratory of Computational Systems Biotechnology, École Polytechnique Fédérale de Lausanne, EPFL, Lausanne 1015, Switzerland; Molecular Infection Medicine Sweden (MIMS), Department of Molecular Biology, Umeå University, Umeå 901 87, Sweden
| | - Frank Schwach
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Séverine Chevalley
- Leiden Malaria Research Group, Parasitology, Center of Infectious Diseases, Leiden University Medical Center (LUMC), Leiden 2333ZA, the Netherlands
| | - Jai Ramesar
- Leiden Malaria Research Group, Parasitology, Center of Infectious Diseases, Leiden University Medical Center (LUMC), Leiden 2333ZA, the Netherlands
| | - Tom Metcalf
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Colin Herd
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Paul-Christian Burda
- Institute of Cell Biology, University of Bern, Bern 3012, Switzerland; Bernhard Nocht Institute for Tropical Medicine, Hamburg 20359, Germany
| | - Julian C Rayner
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK; Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge CB2, 0XY, UK
| | - Dominique Soldati-Favre
- Department of Microbiology & Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva 1211, Switzerland
| | - Chris J Janse
- Leiden Malaria Research Group, Parasitology, Center of Infectious Diseases, Leiden University Medical Center (LUMC), Leiden 2333ZA, the Netherlands
| | - Vassily Hatzimanikatis
- Laboratory of Computational Systems Biotechnology, École Polytechnique Fédérale de Lausanne, EPFL, Lausanne 1015, Switzerland
| | - Oliver Billker
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK; Molecular Infection Medicine Sweden (MIMS), Department of Molecular Biology, Umeå University, Umeå 901 87, Sweden.
| | - Volker T Heussler
- Institute of Cell Biology, University of Bern, Bern 3012, Switzerland.
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43
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Ranford-Cartwright L, Gómez-Díaz E. Plasmodium comparative genomics. Brief Funct Genomics 2020; 18:267-269. [PMID: 31696202 DOI: 10.1093/bfgp/elz020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Lisa Ranford-Cartwright
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Scotland, UK
| | - Elena Gómez-Díaz
- Institute of Parasitology and Biomedicine López-Neyra, Spanish National Research Council (CSIC), Spain
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44
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Vještica A, Marek M, Nkosi PJ, Merlini L, Liu G, Bérard M, Billault-Chaumartin I, Martin SG. A toolbox of stable integration vectors in the fission yeast Schizosaccharomyces pombe. J Cell Sci 2020; 133:jcs.240754. [PMID: 31801797 DOI: 10.1242/jcs.240754] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Accepted: 11/24/2019] [Indexed: 12/14/2022] Open
Abstract
Schizosaccharomyces pombe is a widely used model organism to study many aspects of eukaryotic cell physiology. Its popularity as an experimental system partially stems from the ease of genetic manipulations, where the innate homology-targeted repair is exploited to precisely edit the genome. While vectors to incorporate exogenous sequences into the chromosomes are available, most are poorly characterized. Here, we show that commonly used fission yeast vectors, which upon integration produce repetitive genomic regions, give rise to unstable genomic loci. We overcome this problem by designing a new series of stable integration vectors (SIVs) that target four different prototrophy genes. SIVs produce non-repetitive, stable genomic loci and integrate predominantly as single copy. Additionally, we develop a set of complementary auxotrophic alleles that preclude false-positive integration events. We expand the vector series to include antibiotic resistance markers, promoters, fluorescent tags and terminators, and build a highly modular toolbox to introduce heterologous sequences. Finally, as proof of concept, we generate a large set of ready-to-use, fluorescent probes to mark organelles and cellular processes with a wide range of applications in fission yeast research.This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Aleksandar Vještica
- Department of Fundamental Microbiology, University of Lausanne, Biophore building, CH-1015 Lausanne, Switzerland
| | - Magdalena Marek
- Department of Fundamental Microbiology, University of Lausanne, Biophore building, CH-1015 Lausanne, Switzerland
| | - Pedro Junior Nkosi
- Department of Fundamental Microbiology, University of Lausanne, Biophore building, CH-1015 Lausanne, Switzerland
| | - Laura Merlini
- Department of Fundamental Microbiology, University of Lausanne, Biophore building, CH-1015 Lausanne, Switzerland
| | - Gaowen Liu
- Department of Fundamental Microbiology, University of Lausanne, Biophore building, CH-1015 Lausanne, Switzerland
| | - Melvin Bérard
- Department of Fundamental Microbiology, University of Lausanne, Biophore building, CH-1015 Lausanne, Switzerland
| | - Ingrid Billault-Chaumartin
- Department of Fundamental Microbiology, University of Lausanne, Biophore building, CH-1015 Lausanne, Switzerland
| | - Sophie G Martin
- Department of Fundamental Microbiology, University of Lausanne, Biophore building, CH-1015 Lausanne, Switzerland
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45
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Abstract
Intensified treatment and control efforts since the early 2000s have dramatically reduced the burden of Plasmodium falciparum malaria. However, drug resistance threatens to derail this progress. In this review, we present four antimalarial resistance case studies that differ in timeline, technical approaches, mechanisms of action, and categories of resistance: chloroquine, sulfadoxine-pyrimethamine, artemisinin, and piperaquine. Lessons learned from prior losses of treatment efficacy, drug combinations, and control strategies will help advance mechanistic research into how P. falciparum parasites acquire resistance to current first-line artemisinin-based combination therapies. Understanding resistance in the clinic and laboratory is essential to prolong the effectiveness of current antimalarial drugs and to optimize the pipeline of future medicines.
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Affiliation(s)
- Leila S Ross
- Department of Microbiology & Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - David A Fidock
- Department of Microbiology & Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA; Division of Infectious Diseases, Department of Medicine, Columbia University Irving Medical Center, New York, NY 10032, USA.
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46
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Lee MCS, Lindner SE, Lopez-Rubio JJ, Llinás M. Cutting back malaria: CRISPR/Cas9 genome editing of Plasmodium. Brief Funct Genomics 2019; 18:281-289. [PMID: 31365053 PMCID: PMC6859820 DOI: 10.1093/bfgp/elz012] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 04/15/2019] [Accepted: 05/20/2019] [Indexed: 12/15/2022] Open
Abstract
CRISPR/Cas9 approaches are revolutionizing our ability to perform functional genomics across a wide range of organisms, including the Plasmodium parasites that cause malaria. The ability to deliver single point mutations, epitope tags and gene deletions at increased speed and scale is enabling our understanding of the biology of these complex parasites, and pointing to potential new therapeutic targets. In this review, we describe some of the biological and technical considerations for designing CRISPR-based experiments, and discuss potential future developments that broaden the applications for CRISPR/Cas9 interrogation of the malaria parasite genome.
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Affiliation(s)
- Marcus C S Lee
- Parasites and Microbes Programme, Wellcome Sanger Institute, Hinxton, UK
| | - Scott E Lindner
- Department of Biochemistry and Molecular Biology, Huck Center for Malaria Research, The Pennsylvania State University, Pennsylvania, USA
| | - Jose-Juan Lopez-Rubio
- Dynamique des Interactions Membranaires Normales et Pathologiques, UMR5235 CNRS, INSERM, Université Montpellier, Montpellier, France
| | - Manuel Llinás
- Department of Biochemistry and Molecular Biology, Huck Center for Malaria Research, The Pennsylvania State University, Pennsylvania, USA
- Department of Chemistry, The Pennsylvania State University, Pennsylvania, USA
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47
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Huckaby AC, Granum CS, Carey MA, Szlachta K, Al-Barghouthi B, Wang YH, Guler JL. Complex DNA structures trigger copy number variation across the Plasmodium falciparum genome. Nucleic Acids Res 2019; 47:1615-1627. [PMID: 30576466 PMCID: PMC6393310 DOI: 10.1093/nar/gky1268] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 12/04/2018] [Accepted: 12/07/2018] [Indexed: 02/06/2023] Open
Abstract
Antimalarial resistance is a major obstacle in the eradication of the human malaria parasite, Plasmodium falciparum. Genome amplifications, a type of DNA copy number variation (CNV), facilitate overexpression of drug targets and contribute to parasite survival. Long monomeric A/T tracks are found at the breakpoints of many Plasmodium resistance-conferring CNVs. We hypothesize that other proximal sequence features, such as DNA hairpins, act with A/T tracks to trigger CNV formation. By adapting a sequence analysis pipeline to investigate previously reported CNVs, we identified breakpoints in 35 parasite clones with near single base-pair resolution. Using parental genome sequence, we predicted the formation of stable hairpins within close proximity to all future breakpoint locations. Especially stable hairpins were predicted to form near five shared breakpoints, establishing that the initiating event could have occurred at these sites. Further in-depth analyses defined characteristics of these 'trigger sites' across the genome and detected signatures of error-prone repair pathways at the breakpoints. We propose that these two genomic signals form the initial lesion (hairpins) and facilitate microhomology-mediated repair (A/T tracks) that lead to CNV formation across this highly repetitive genome. Targeting these repair pathways in P. falciparum may be used to block adaptation to antimalarial drugs.
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Affiliation(s)
- Adam C Huckaby
- Department of Biology, University of Virginia, Charlottesville, VA 22908, USA
| | - Claire S Granum
- Department of Biology, University of Virginia, Charlottesville, VA 22908, USA
| | - Maureen A Carey
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia Health System, Charlottesville, VA 22908, USA.,Division of Infectious Diseases and International Health, University of Virginia Health System, Charlottesville, VA 22908, USA
| | - Karol Szlachta
- Department of Biochemistry and Molecular Genetics, University of Virginia Health System, Charlottesville, VA 22908, USA
| | - Basel Al-Barghouthi
- Department of Biochemistry and Molecular Genetics, University of Virginia Health System, Charlottesville, VA 22908, USA.,Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908, USA
| | - Yuh-Hwa Wang
- Department of Biochemistry and Molecular Genetics, University of Virginia Health System, Charlottesville, VA 22908, USA
| | - Jennifer L Guler
- Department of Biology, University of Virginia, Charlottesville, VA 22908, USA.,Division of Infectious Diseases and International Health, University of Virginia Health System, Charlottesville, VA 22908, USA
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48
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Tiwari A, Kuldeep J, Siddiqi MI, Habib S. Plasmodium falciparumApn1 homolog is a mitochondrial base excision repair protein with restricted enzymatic functions. FEBS J 2019; 287:589-606. [DOI: 10.1111/febs.15032] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 06/18/2019] [Accepted: 08/02/2019] [Indexed: 01/14/2023]
Affiliation(s)
- Anupama Tiwari
- Division of Molecular and Structural Biology CSIR‐Central Drug Research Institute Lucknow India
| | - Jitendra Kuldeep
- Division of Molecular and Structural Biology CSIR‐Central Drug Research Institute Lucknow India
| | - Mohammad Imran Siddiqi
- 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
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49
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Xu R, Liu Y, Fan R, Liang R, Yue L, Liu S, Su XZ, Li J. Generation and functional characterisation of Plasmodium yoelii csp deletion mutants using a microhomology-based CRISPR/Cas9 method. Int J Parasitol 2019; 49:705-714. [PMID: 31202685 PMCID: PMC10993195 DOI: 10.1016/j.ijpara.2019.04.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 04/01/2019] [Accepted: 04/05/2019] [Indexed: 11/24/2022]
Abstract
CRISPR/Cas9 is a powerful genome editing method that has greatly facilitated functional studies in many eukaryotic organisms including malaria parasites. Due to the lack of genes encoding enzymes necessary for the non-homologous end joining DNA repair pathway, genetic manipulation of malaria parasite genomes is generally accomplished through homologous recombination requiring the presence of DNA templates. Recently, an alternative double-strand break repair pathway, microhomology-mediated end joining, was found in the Plasmodium falciparum parasite. Taking advantage of the MMEJ pathway, we developed a MMEJ-based CRISPR/Cas9 (mCRISPR) strategy to efficiently generate multiple mutant parasites simultaneously in genes with repetitive sequences. As a proof of principle, we successfully produced various size mutants in the central repeat region of the Plasmodium yoelii circumsporozoite surface protein without the use of template DNA. Monitoring mixed parasite populations and individual parasites with different sizes of CSP-CRR showed that the CSP-CRR plays a role in the development of mosquito stages, with severe developmental defects in parasites with large deletions in the repeat region. However, the majority of the csp mutant parasite clones grew similarly to the wild type P. yoelii 17XL parasite in mice. This study develops a useful technique to efficiently generate mutant parasites with deletions or insertions, and shows that the CSP-CRR plays a role in parasite development in mosquito.
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Affiliation(s)
- Ruixue Xu
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, Fujian 361102, China
| | - Yanjing Liu
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, Fujian 361102, China
| | - Ruoxi Fan
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, Fujian 361102, China
| | - Rui Liang
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, Fujian 361102, China
| | - Lixia Yue
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, Fujian 361102, China
| | - Shengfa Liu
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, Fujian 361102, China
| | - Xin-Zhuan Su
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Jian Li
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, Fujian 361102, China.
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50
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Nenarokova A, Záhonová K, Krasilnikova M, Gahura O, McCulloch R, Zíková A, Yurchenko V, Lukeš J. Causes and Effects of Loss of Classical Nonhomologous End Joining Pathway in Parasitic Eukaryotes. mBio 2019; 10:e01541-19. [PMID: 31311886 PMCID: PMC6635534 DOI: 10.1128/mbio.01541-19] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 06/18/2019] [Indexed: 01/22/2023] Open
Abstract
We report frequent losses of components of the classical nonhomologous end joining pathway (C-NHEJ), one of the main eukaryotic tools for end joining repair of DNA double-strand breaks, in several lineages of parasitic protists. Moreover, we have identified a single lineage among trypanosomatid flagellates that has lost Ku70 and Ku80, the core C-NHEJ components, and accumulated numerous insertions in many protein-coding genes. We propose a correlation between these two phenomena and discuss the possible impact of the C-NHEJ loss on genome evolution and transition to the parasitic lifestyle.IMPORTANCE Parasites tend to evolve small and compact genomes, generally endowed with a high mutation rate, compared with those of their free-living relatives. However, the mechanisms by which they achieve these features, independently in unrelated lineages, remain largely unknown. We argue that the loss of the classical nonhomologous end joining pathway components may be one of the crucial steps responsible for characteristic features of parasite genomes.
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Affiliation(s)
- Anna Nenarokova
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Kristína Záhonová
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Prague, Czech Republic
| | - Marija Krasilnikova
- Wellcome Centre for Molecular Parasitology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, Scotland
| | - Ondřej Gahura
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Richard McCulloch
- Wellcome Centre for Molecular Parasitology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, Scotland
| | - Alena Zíková
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Vyacheslav Yurchenko
- Martsinovsky Institute of Medical Parasitology, Sechenov University, Moscow, Russia
- Life Science Research Centre and Institute of Environmental Technologies, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Julius Lukeš
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
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