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Lou J, Rezvani Y, Arriojas A, Wu Y, Shankar N, Degras D, Keroack CD, Duraisingh MT, Zarringhalam K, Gubbels MJ. Single cell expression and chromatin accessibility of the Toxoplasma gondii lytic cycle identifies AP2XII-8 as an essential ribosome regulon driver. Nat Commun 2024; 15:7419. [PMID: 39198388 PMCID: PMC11358496 DOI: 10.1038/s41467-024-51011-7] [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: 12/21/2023] [Accepted: 07/22/2024] [Indexed: 09/01/2024] Open
Abstract
Sequential lytic cycles driven by cascading transcriptional waves underlie pathogenesis in the apicomplexan parasite Toxoplasma gondii. This parasite's unique division by internal budding, short cell cycle, and jumbled up classically defined cell cycle stages have restrained in-depth transcriptional program analysis. Here, unbiased transcriptome and chromatin accessibility maps throughout the lytic cell cycle are established at the single-cell level. Correlated pseudo-timeline assemblies of expression and chromatin profiles maps transcriptional versus chromatin level transition points promoting the cell division cycle. Sequential clustering analysis identifies functionally related gene groups promoting cell cycle progression. Promoter DNA motif mapping reveals patterns of combinatorial regulation. Pseudo-time trajectory analysis reveals transcriptional bursts at different cell cycle points. The dominant burst in G1 is driven largely by transcription factor AP2XII-8, which engages a conserved DNA motif, and promotes the expression of 44 ribosomal proteins encoding regulon. Overall, the study provides integrated, multi-level insights into apicomplexan transcriptional regulation.
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Affiliation(s)
- Jingjing Lou
- Department of Biology, Boston College, Chestnut Hill, MA, USA
| | - Yasaman Rezvani
- Department of Mathematics, University of Massachusetts Boston, Boston, MA, USA
- Center for Personalized Cancer Therapy, University of Massachusetts Boston, Boston, MA, USA
| | - Argenis Arriojas
- Center for Personalized Cancer Therapy, University of Massachusetts Boston, Boston, MA, USA
| | - Yihan Wu
- Department of Biology, Boston College, Chestnut Hill, MA, USA
| | - Nachiket Shankar
- Center for Personalized Cancer Therapy, University of Massachusetts Boston, Boston, MA, USA
| | - David Degras
- Department of Mathematics, University of Massachusetts Boston, Boston, MA, USA
| | - Caroline D Keroack
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Harvard University, Boston, MA, USA
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI, USA
| | - Manoj T Duraisingh
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Harvard University, Boston, MA, USA
| | - Kourosh Zarringhalam
- Department of Mathematics, University of Massachusetts Boston, Boston, MA, USA.
- Center for Personalized Cancer Therapy, University of Massachusetts Boston, Boston, MA, USA.
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Functional dissection of proliferating-cell nuclear antigens (1 and 2) in human malarial parasite Plasmodium falciparum: possible involvement in DNA replication and DNA damage response. Biochem J 2015; 470:115-29. [PMID: 26251451 DOI: 10.1042/bj20150452] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Accepted: 06/22/2015] [Indexed: 11/17/2022]
Abstract
Eukaryotic PCNAs (proliferating-cell nuclear antigens) play diverse roles in nucleic acid metabolism in addition to DNA replication. Plasmodium falciparum, which causes human malaria, harbours two PCNA homologues: PfPCNA1 and PfPCNA2. The functional role of two distinct PCNAs in the parasite still eludes us. In the present study, we show that, whereas both PfPCNAs share structural and biochemical properties, only PfPCNA1 functionally complements the ScPCNA mutant and forms distinct replication foci in the parasite, which PfPCNA2 fails to do. Although PfPCNA1 appears to be the primary replicative PCNA, both PfPCNA1 and PfPCNA2 participate in an active DDR (DNA-damage-response) pathway with significant accumulation in the parasite upon DNA damage induction. Interestingly, PfPCNA genes were found to be regulated not at the transcription level, but presumably at the protein stability level upon DNA damage. Such regulation of PCNA has not been shown in eukaryotes before. Moreover, overexpression of PfPCNA1 and PfPCNA2 in the parasite confers a survival edge on the parasite in a genotoxic environment. This is the first evidence of a PfPCNA-mediated DDR in the parasite and gives new insights and rationale for the presence of two PCNAs as a parasite survival strategy and its probable success.
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Nuclear actin-related protein is required for chromosome segregation in Toxoplasma gondii. Mol Biochem Parasitol 2011; 181:7-16. [PMID: 21963440 DOI: 10.1016/j.molbiopara.2011.09.006] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2011] [Revised: 09/10/2011] [Accepted: 09/15/2011] [Indexed: 12/30/2022]
Abstract
Apicomplexa parasites use complex cell cycles to replicate that are not well understood mechanistically. We have established a robust forward genetic strategy to identify the essential components of parasite cell division. Here we describe a novel temperature sensitive Toxoplasma strain, mutant 13-20C2, which growth arrests due to a defect in mitosis. The primary phenotype is the mis-segregation of duplicated chromosomes with chromosome loss during nuclear division. This defect is conditional-lethal with respect to temperature, although relatively mild in regard to the preservation of the major microtubule organizing centers. Despite severe DNA loss many of the physical structures associated with daughter budding and the assembly of invasion structures formed and operated normally at the non-permissive temperature before completely arresting. These results suggest there are coordinating mechanisms that govern the timing of these events in the parasite cell cycle. The defect in mutant 13-20C2 was mapped by genetic complementation to Toxoplasma chromosome III and to a specific mutation in the gene encoding an ortholog of nuclear actin-related protein 4. A change in a conserved isoleucine to threonine in the helical structure of this nuclear actin related protein leads to protein instability and cellular mis-localization at the higher temperature. Given the age of this protist family, the results indicate a key role for nuclear actin-related proteins in chromosome segregation was established very early in the evolution of eukaryotes.
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Cardona-Felix CS, Lara-Gonzalez S, Brieba LG. Structure and biochemical characterization of proliferating cellular nuclear antigen from a parasitic protozoon. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2011; 67:497-505. [PMID: 21636889 DOI: 10.1107/s0907444911010547] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2011] [Accepted: 03/21/2011] [Indexed: 11/10/2022]
Abstract
Proliferating cellular nuclear antigen (PCNA) is a toroidal-shaped protein that is involved in cell-cycle control, DNA replication and DNA repair. Parasitic protozoa are early-diverged eukaryotes that are responsible for neglected diseases. In this work, a PCNA from a parasitic protozoon was identified, cloned and biochemically characterized and its crystal structure was determined. Structural and biochemical studies demonstrate that PCNA from Entamoeba histolytica assembles as a homotrimer that is able to interact with and stimulate the activity of a PCNA-interacting peptide-motif protein from E. histolytica, EhDNAligI. The data indicate a conservation of the biochemical mechanisms of PCNA-mediated interactions between metazoa, yeast and parasitic protozoa.
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Affiliation(s)
- Cesar S Cardona-Felix
- Grupo de Bioquímica Estructural, Laboratorio Nacional de Genomica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Km 9.6 Libramiento Norte, Carretera Irapuato-León, 36821 Irapuato, Guanajuato, México
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Strzalka W, Ziemienowicz A. Proliferating cell nuclear antigen (PCNA): a key factor in DNA replication and cell cycle regulation. ANNALS OF BOTANY 2011; 107:1127-40. [PMID: 21169293 PMCID: PMC3091797 DOI: 10.1093/aob/mcq243] [Citation(s) in RCA: 516] [Impact Index Per Article: 36.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
BACKGROUND PCNA (proliferating cell nuclear antigen) has been found in the nuclei of yeast, plant and animal cells that undergo cell division, suggesting a function in cell cycle regulation and/or DNA replication. It subsequently became clear that PCNA also played a role in other processes involving the cell genome. SCOPE This review discusses eukaryotic PCNA, with an emphasis on plant PCNA, in terms of the protein structure and its biochemical properties as well as gene structure, organization, expression and function. PCNA exerts a tripartite function by operating as (1) a sliding clamp during DNA synthesis, (2) a polymerase switch factor and (3) a recruitment factor. Most of its functions are mediated by its interactions with various proteins involved in DNA synthesis, repair and recombination as well as in regulation of the cell cycle and chromatid cohesion. Moreover, post-translational modifications of PCNA play a key role in regulation of its functions. Finally, a phylogenetic comparison of PCNA genes suggests that the multi-functionality observed in most species is a product of evolution. CONCLUSIONS Most plant PCNAs exhibit features similar to those found for PCNAs of other eukaryotes. Similarities include: (1) a trimeric ring structure of the PCNA sliding clamp, (2) the involvement of PCNA in DNA replication and repair, (3) the ability to stimulate the activity of DNA polymerase δ and (4) the ability to interact with p21, a regulator of the cell cycle. However, many plant genomes seem to contain the second, probably functional, copy of the PCNA gene, in contrast to PCNA pseudogenes that are found in mammalian genomes.
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Affiliation(s)
- Wojciech Strzalka
- Department of Plant Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Krakow, Poland
| | - Alicja Ziemienowicz
- Department of Biological Sciences, University of Lethbridge, 4401 University Drive, Lethbridge, AB T1K 3M4, Canada
- For correspondence. E-mail
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Behnke MS, Wootton JC, Lehmann MM, Radke JB, Lucas O, Nawas J, Sibley LD, White MW. Coordinated progression through two subtranscriptomes underlies the tachyzoite cycle of Toxoplasma gondii. PLoS One 2010; 5:e12354. [PMID: 20865045 PMCID: PMC2928733 DOI: 10.1371/journal.pone.0012354] [Citation(s) in RCA: 212] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2010] [Accepted: 06/12/2010] [Indexed: 01/29/2023] Open
Abstract
BACKGROUND Apicomplexan parasites replicate by varied and unusual processes where the typically eukaryotic expansion of cellular components and chromosome cycle are coordinated with the biosynthesis of parasite-specific structures essential for transmission. METHODOLOGY/PRINCIPAL FINDINGS Here we describe the global cell cycle transcriptome of the tachyzoite stage of Toxoplasma gondii. In dividing tachyzoites, more than a third of the mRNAs exhibit significant cyclical profiles whose timing correlates with biosynthetic events that unfold during daughter parasite formation. These 2,833 mRNAs have a bimodal organization with peak expression occurring in one of two transcriptional waves that are bounded by the transition into S phase and cell cycle exit following cytokinesis. The G1-subtranscriptome is enriched for genes required for basal biosynthetic and metabolic functions, similar to most eukaryotes, while the S/M-subtranscriptome is characterized by the uniquely apicomplexan requirements of parasite maturation, development of specialized organelles, and egress of infectious daughter cells. Two dozen AP2 transcription factors form a series through the tachyzoite cycle with successive sharp peaks of protein expression in the same timeframes as their mRNA patterns, indicating that the mechanisms responsible for the timing of protein delivery might be mediated by AP2 domains with different promoter recognition specificities. CONCLUSION/SIGNIFICANCE Underlying each of the major events in apicomplexan cell cycles, and many more subordinate actions, are dynamic changes in parasite gene expression. The mechanisms responsible for cyclical gene expression timing are likely crucial to the efficiency of parasite replication and may provide new avenues for interfering with parasite growth.
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Affiliation(s)
- Michael S. Behnke
- Department of Veterinary Molecular Biology, Montana State University, Bozeman, Montana, United States of America
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - John C. Wootton
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Margaret M. Lehmann
- Department of Veterinary Molecular Biology, Montana State University, Bozeman, Montana, United States of America
| | - Josh B. Radke
- Department of Veterinary Molecular Biology, Montana State University, Bozeman, Montana, United States of America
- Departments of Molecular Medicine and Global Health, University of South Florida, Tampa, Florida, United States of America
| | - Olivier Lucas
- Departments of Molecular Medicine and Global Health, University of South Florida, Tampa, Florida, United States of America
| | - Julie Nawas
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - L. David Sibley
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Michael W. White
- Department of Veterinary Molecular Biology, Montana State University, Bozeman, Montana, United States of America
- Departments of Molecular Medicine and Global Health, University of South Florida, Tampa, Florida, United States of America
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Strzalka W, Kaczmarek A, Naganowska B, Ziemienowicz A. Identification and functional analysis of PCNA1 and PCNA-like1 genes of Phaseolus coccineus. JOURNAL OF EXPERIMENTAL BOTANY 2010; 61:873-88. [PMID: 20007687 PMCID: PMC2814116 DOI: 10.1093/jxb/erp354] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2009] [Revised: 11/07/2009] [Accepted: 11/10/2009] [Indexed: 05/21/2023]
Abstract
Proliferating cell nuclear antigen (PCNA) is an essential factor in DNA replication and in many other processes in eukaryotic cells. Genetic analysis of Phaseolus coccineus showed the presence of at least two PCNA-like genes in the runner bean genome. Two PCNA genes have previously been found in a few plant species including Arabidopsis, tobacco, and maize. In these species, genes were nearly identical. Two cDNAs of P. coccineus PCNA (PcPCNA1 and PcPCNA-like1) have been identified that differ distinctly from each other. Interestingly, both the genetic organization of PcPCNA1 and PcPCNA-like1 genes and their expression patterns were similar, but these were the only similarities between these genes and their products. The identity between PcPCNA1 and PcPCNA-like1 at the amino acid level was only 54%, with PcPCNA-like1 lacking motifs that are crucial for the activity typical of PCNA. Consequently, these two proteins showed different properties. PcPCNA1 behaved like a typical PCNA protein: it formed a homotrimer and stimulated the activity of human DNA polymerase delta. In addition, PcPCNA1 interacted with a p21 peptide and was recognized by an anti-human PCNA monoclonal antibody PC10. By contrast, PcPCNA-like1 was detected as a monomer and was unable to stimulate the DNA polymerase delta activity. PcPCNA-like1 also could not interact with p21 and was not recognized by the PC10 antibody. Our results suggest that PcPCNA-like1 either is unable to function alone and therefore might be a component of the heterotrimeric PCNA ring or may have other, yet unknown functions. Alternatively, the PcPCNA-like1 gene may represent a pseudogene.
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Affiliation(s)
- Wojciech Strzalka
- Department of Molecular Genetics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Krakow, Poland
| | - Anna Kaczmarek
- Institute of Plant Genetics, Polish Academy of Science, Strzeszynska 34, 60-479 Poznan, Poland
| | - Barbara Naganowska
- Institute of Plant Genetics, Polish Academy of Science, Strzeszynska 34, 60-479 Poznan, Poland
| | - Alicja Ziemienowicz
- Department of Molecular Genetics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Krakow, Poland
- Department of Biological Sciences, University of Lethbridge, 4401 University Drive, Lethbridge, AB, T1K 3M4 Canada
- To whom correspondence should be addressed: E-mail:
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Kumar D, Minocha N, Rajanala K, Saha S. The distribution pattern of proliferating cell nuclear antigen in the nuclei of Leishmania donovani. MICROBIOLOGY-SGM 2009; 155:3748-3757. [PMID: 19729406 DOI: 10.1099/mic.0.033217-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
DNA replication in eukaryotes is a highly conserved process marked by the licensing of multiple origins, with pre-replication complex assembly in G1 phase, followed by the onset of replication at these origins in S phase. The two strands replicate by different mechanisms, and DNA synthesis is brought about by the activity of the replicative DNA polymerases Pol delta and Pol epsilon. Proliferating cell nuclear antigen (PCNA) augments the processivity of these polymerases by serving as a DNA sliding clamp protein. This study reports the cloning of PCNA from the protozoan Leishmania donovani, which is the causative agent of the systemic disease visceral leishmaniasis. PCNA was demonstrated to be robustly expressed in actively proliferating L. donovani promastigotes. We found that the protein was present primarily in the nucleus throughout the cell cycle, and it was found in both proliferating procyclic and metacyclic promastigotes. However, levels of expression of PCNA varied through cell cycle progression, with maximum expression evident in G1 and S phases. The subnuclear pattern of expression of PCNA differed in different stages of the cell cycle; it formed distinct subnuclear foci in S phase, while it was distributed in a more diffuse pattern in G2/M phase and post-mitotic phase cells. These subnuclear foci are the sites of active DNA replication, suggesting that replication factories exist in Leishmania, as they do in higher eukaryotes, thus opening avenues for investigating other Leishmania proteins that are involved in DNA replication as part of these replication factories.
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Affiliation(s)
- Devanand Kumar
- Department of Microbiology, University of Delhi South Campus, Benito Juarez Road, New Delhi 110021, India
| | - Neha Minocha
- Department of Microbiology, University of Delhi South Campus, Benito Juarez Road, New Delhi 110021, India
| | - Kalpana Rajanala
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Swati Saha
- Department of Microbiology, University of Delhi South Campus, Benito Juarez Road, New Delhi 110021, India
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Gupta A, Mehra P, Dhar SK. Plasmodium falciparum origin recognition complex subunit 5: functional characterization and role in DNA replication foci formation. Mol Microbiol 2008; 69:646-65. [PMID: 18554328 PMCID: PMC2610387 DOI: 10.1111/j.1365-2958.2008.06316.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/20/2008] [Indexed: 12/24/2022]
Abstract
The mechanism of DNA replication initiation and progression is poorly understood in the parasites, including human malaria parasite Plasmodium falciparum. Using bioinformatics tools and yeast complementation assay, we identified a putative homologue of Saccharomyces cerevisiaeorigin recognition complex subunit 5 in P. falciparum (PfORC5). PfORC5 forms distinct nuclear foci colocalized with the replication foci marker proliferating cell nuclear antigen (PfPCNA) and co-immunoprecipitates with PCNA during early-to-mid trophozoite stage replicating parasites. Interestingly, these proteins separate from each other at the non-replicating late schizont stage, citing the evidence of the presence of both PCNA and ORC components in replication foci during eukaryotic DNA replication. PfORC1, another ORC subunit, colocalizes with PfPCNA and PfORC5 at the beginning of DNA replication, but gets degraded at the late schizont stage, ensuring the regulation of DNA replication in the parasites. Further, we have identified putative PCNA-interacting protein box in PfORC1 that may explain in part the colocalization of PfORC and PfPCNA. Additionally, use of specific DNA replication inhibitor hydroxyurea affects ORC5/PCNA foci formation and parasitic growth. These results strongly favour replication factory model in the parasites and confer great potential to understand the co-ordination between ORC and PCNA during eukaryotic DNA replication in general.
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Affiliation(s)
| | | | - Suman Kumar Dhar
- Special Centre for Molecular Medicine, Jawaharlal Nehru UniversityNew Delhi 110067, India
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The cell cycle and Toxoplasma gondii cell division: tightly knit or loosely stitched? Int J Parasitol 2008; 38:1343-58. [PMID: 18703066 DOI: 10.1016/j.ijpara.2008.06.004] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2008] [Revised: 06/10/2008] [Accepted: 06/13/2008] [Indexed: 01/20/2023]
Abstract
The flexibility displayed by apicomplexan parasites to vary their mode of replication has intrigued biologists since their discovery by electron microscopy in the 1960s and 1970s. Starting in the 1990s we began to understand the cell biology of the cytoskeleton elements driving cytokinesis. By contrast, the molecular mechanisms that regulate the various division modes and how they translate into the budding process that uniquely characterizes this parasite family are much less understood. Although growth mechanisms are a neglected area of study, it is an important pathogenic parameter as fast division rounds are associated with fulminant infection whereas slower growth attenuates virulence, as is exploited in some vaccine strains. In this review we summarize a recent body of cell biological experiments that are rapidly leading to an understanding of the events that yield successful mitosis and cytokinesis in Toxoplasma. We place these observations within a cell cycle context with comments on how these events may be regulated by known eukaryotic checkpoints active in fission and budding yeasts as well as mammalian cells. The presence of cell cycle control mechanisms in the Apicomplexa is supported by our findings that identify several cell cycle checkpoints in Toxoplasma. The progress of the cell cycle is ultimately controlled by cyclin-Cdk pair activities, which are present throughout the Apicomplexa. Although many of the known controllers of cyclin-Cdk activity are present, several key controls cannot readily be identified, suggesting that apicomplexan parasites deviate at these points from the higher eukaryotic models. Altogether, new insights in Toxoplasma replication are reciprocally applied to hypothesize how other division modes in the Toxoplasma life cycle and in other Apicomplexa species could be controlled in terms of cell cycle checkpoint regulation.
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Gubbels MJ, Lehmann M, Muthalagi M, Jerome ME, Brooks CF, Szatanek T, Flynn J, Parrot B, Radke J, Striepen B, White MW. Forward genetic analysis of the apicomplexan cell division cycle in Toxoplasma gondii. PLoS Pathog 2008; 4:e36. [PMID: 18282098 PMCID: PMC2242837 DOI: 10.1371/journal.ppat.0040036] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2007] [Accepted: 01/07/2008] [Indexed: 11/18/2022] Open
Abstract
Apicomplexa are obligate intracellular pathogens that have fine-tuned their proliferative strategies to match a large variety of host cells. A critical aspect of this adaptation is a flexible cell cycle that remains poorly understood at the mechanistic level. Here we describe a forward genetic dissection of the apicomplexan cell cycle using the Toxoplasma model. By high-throughput screening, we have isolated 165 temperature sensitive parasite growth mutants. Phenotypic analysis of these mutants suggests regulated progression through the parasite cell cycle with defined phases and checkpoints. These analyses also highlight the critical importance of the peculiar intranuclear spindle as the physical hub of cell cycle regulation. To link these phenotypes to parasite genes, we have developed a robust complementation system based on a genomic cosmid library. Using this approach, we have so far complemented 22 temperature sensitive mutants and identified 18 candidate loci, eight of which were independently confirmed using a set of sequenced and arrayed cosmids. For three of these loci we have identified the mutant allele. The genes identified include regulators of spindle formation, nuclear trafficking, and protein degradation. The genetic approach described here should be widely applicable to numerous essential aspects of parasite biology.
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Affiliation(s)
- Marc-Jan Gubbels
- Center for Tropical and Emerging Global Diseases and Department of Cellular Biology, University of Georgia, Athens, Georgia, United States of America
- Department of Biology, Boston College, Chestnut Hill, Massachusetts, United States of America
| | - Margaret Lehmann
- Department of Veterinary Molecular Biology, Montana State University, Bozeman, Montana, United States of America
| | - Mani Muthalagi
- Center for Tropical and Emerging Global Diseases and Department of Cellular Biology, University of Georgia, Athens, Georgia, United States of America
| | - Maria E Jerome
- Department of Veterinary Molecular Biology, Montana State University, Bozeman, Montana, United States of America
| | - Carrie F Brooks
- Department of Veterinary Molecular Biology, Montana State University, Bozeman, Montana, United States of America
| | - Tomasz Szatanek
- Department of Biology, Boston College, Chestnut Hill, Massachusetts, United States of America
| | - Jayme Flynn
- Department of Biology, Boston College, Chestnut Hill, Massachusetts, United States of America
| | - Ben Parrot
- Center for Tropical and Emerging Global Diseases and Department of Cellular Biology, University of Georgia, Athens, Georgia, United States of America
| | - Josh Radke
- Department of Veterinary Molecular Biology, Montana State University, Bozeman, Montana, United States of America
| | - Boris Striepen
- Center for Tropical and Emerging Global Diseases and Department of Cellular Biology, University of Georgia, Athens, Georgia, United States of America
- * To whom correspondence should be addressed. E-mail: (BS); (MWW)
| | - Michael W White
- Department of Veterinary Molecular Biology, Montana State University, Bozeman, Montana, United States of America
- * To whom correspondence should be addressed. E-mail: (BS); (MWW)
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Casta LJ, Buguliskis JS, Matsumoto Y, Taraschi TF. Expression and biochemical characterization of the Plasmodium falciparum DNA repair enzyme, flap endonuclease-1 (PfFEN-1). Mol Biochem Parasitol 2008; 157:1-12. [PMID: 17928073 PMCID: PMC2699572 DOI: 10.1016/j.molbiopara.2007.08.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2007] [Revised: 08/24/2007] [Accepted: 08/27/2007] [Indexed: 11/29/2022]
Abstract
Flap endonuclease-1 (FEN-1) is a structure-specific endonuclease that is critical for the resolution of single-stranded DNA flap intermediates that form during long patch DNA base excision repair (BER). This investigation reports that Plasmodium species encode FEN-1 homologs. Protein sequence analysis revealed the N and I domains of Plasmodium falciparum (PfFEN-1) and Plasmodium yoelii (PyFEN-1) to be homologous to FEN-1 from other species. However, each possessed an extended C domain which had limited homology to apicomplexan FEN-1s and no homology to eukaryotic FEN-1s. A conserved proliferating cell nuclear antigen (PCNA)-binding site was identified at an internal location rather than the extreme C-terminal location typically seen in FEN-1 from other organisms. The endonuclease and exonuclease activities of PfFEN-1 and PyFEN-1 were investigated using recombinant protein produced in Escherichia coli. Pf and PyFEN-1 possessed DNA structure-specific flap endonuclease and 5'-->3' exonuclease activities, similar to FEN-1s from other species. Endonuclease activity was stimulated by Mg(2+) or Mn(2+) and inhibited by monovalent ions (>20.0 mM). A PfFEN-1 C-terminal truncation mutant lacking the terminal 250 amino acids (PfFEN-1DeltaC) had endonuclease activity that was approximately 130-fold greater (k(cat)=1.2x10(-1)) than full-length PfFEN-1 (k(cat)=9.1x10(-4)) or approximately 240-fold greater than PyFEN-1 (k(cat)=4.9x10(-4)) in vitro. PfFEN-1 generated a nicked DNA substrate that was ligated by recombinant Pf DNA Ligase I (PfLigI) using an in vitro DNA repair assay. Plasmodium FEN-1s have enzymatic activities similar to other species but contain extended C-termini and a more internally located PCNA-binding site.
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Affiliation(s)
- Louis J. Casta
- Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson University, Philadelphia, Pennsylvania 19107
| | - Jeffery S. Buguliskis
- Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson University, Philadelphia, Pennsylvania 19107
| | - Yoshihiro Matsumoto
- Medical Science Division, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, Pennsylvania 19111
| | - Theodore F. Taraschi
- Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson University, Philadelphia, Pennsylvania 19107
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Radke JR, Behnke MS, Mackey AJ, Radke JB, Roos DS, White MW. The transcriptome of Toxoplasma gondii. BMC Biol 2005; 3:26. [PMID: 16324218 PMCID: PMC1325263 DOI: 10.1186/1741-7007-3-26] [Citation(s) in RCA: 131] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2005] [Accepted: 12/02/2005] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Toxoplasma gondii gives rise to toxoplasmosis, among the most prevalent parasitic diseases of animals and man. Transformation of the tachzyoite stage into the latent bradyzoite-cyst form underlies chronic disease and leads to a lifetime risk of recrudescence in individuals whose immune system becomes compromised. Given the importance of tissue cyst formation, there has been intensive focus on the development of methods to study bradyzoite differentiation, although the molecular basis for the developmental switch is still largely unknown. RESULTS We have used serial analysis of gene expression (SAGE) to define the Toxoplasma gondii transcriptome of the intermediate-host life cycle that leads to the formation of the bradyzoite/tissue cyst. A broad view of gene expression is provided by >4-fold coverage from nine distinct libraries (approximately 300,000 SAGE tags) representing key developmental transitions in primary parasite populations and in laboratory strains representing the three canonical genotypes. SAGE tags, and their corresponding mRNAs, were analyzed with respect to abundance, uniqueness, and antisense/sense polarity and chromosome distribution and developmental specificity. CONCLUSION This study demonstrates that phenotypic transitions during parasite development were marked by unique stage-specific mRNAs that accounted for 18% of the total SAGE tags and varied from 1-5% of the tags in each developmental stage. We have also found that Toxoplasma mRNA pools have a unique parasite-specific composition with 1 in 5 transcripts encoding Apicomplexa-specific genes functioning in parasite invasion and transmission. Developmentally co-regulated genes were dispersed across all Toxoplasma chromosomes, as were tags representing each abundance class, and a variety of biochemical pathways indicating that trans-acting mechanisms likely control gene expression in this parasite. We observed distinct similarities in the specificity and expression levels of mRNAs in primary populations (Day-6 post-sporozoite infection) that occur prior to the onset of bradyzoite development that were uniquely shared with the virulent Type I-RH laboratory strain suggesting that development of RH may be arrested. By contrast, strains from Type II-Me49B7 and Type III-VEGmsj contain SAGE tags corresponding to bradyzoite genes, which suggests that priming of developmental expression likely plays a role in the greater capacity of these strains to complete bradyzoite development.
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Affiliation(s)
- Jay R Radke
- Department of Veterinary Molecular Biology, Montana State University Bozeman, MT 59717, USA
| | - Michael S Behnke
- Department of Veterinary Molecular Biology, Montana State University Bozeman, MT 59717, USA
| | - Aaron J Mackey
- Department of Biology and Penn Genomics Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Josh B Radke
- Department of Veterinary Molecular Biology, Montana State University Bozeman, MT 59717, USA
| | - David S Roos
- Department of Biology and Penn Genomics Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Michael W White
- Department of Veterinary Molecular Biology, Montana State University Bozeman, MT 59717, USA
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Guerini MN, Behnke MS, White MW. Biochemical and genetic analysis of the distinct proliferating cell nuclear antigens of Toxoplasma gondii. Mol Biochem Parasitol 2005; 142:56-65. [PMID: 15878790 DOI: 10.1016/j.molbiopara.2005.03.020] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2004] [Revised: 03/05/2005] [Accepted: 03/07/2005] [Indexed: 11/27/2022]
Abstract
The apicomplexa parasite Toxoplasma gondii expresses two distinct proliferating cell nuclear antigens (PCNA) that exhibit distinct patterns of subcellular localization during tachyzoite growth. In all cell cycle phases, TgPCNA1 is concentrated in the nucleus, while TgPCNA2 is only concentrated in the nucleus during S-phase and uniformly distributed throughout the cell during mitosis and early G1-phase. TgPCNA1-GFP and native TgPCNA2 display a punctate staining pattern that is consistent with assembly into replication foci during S-phase; however, TgPCNA2 disassociates from replication foci before TgPCNA1-GFP. Consistent with the distinct pattern of TgPCNA2 cellular localization, homotypic TgPCNA2 interactions were primarily observed by yeast two-hybrid or co-immunoprecipitation analysis. Transgenic parasites in which the TgPCNA2 gene was disrupted displayed a slower growth rate in vitro; however, no difference in DNA polymerase activity, response to chemical mutagens, or recombinational frequency was observed in these mutant clones demonstrating that TgPCNA2 is non-essential in the tachyzoite developmental stage. Heterologous expression of TgPCNA1, but not TgPCNA2, was able to complement a POL30 cold-sensitive yeast strain suggesting that this isoform may serve as a major replisomal factor in T. gondii and is consistent with the failure to disrupt this gene in tachyzoites.
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Affiliation(s)
- Michael N Guerini
- Department of Veterinary Molecular Biology, 960 Technology Blvd, Montana State University, Bozeman, MT 59717-3610, USA
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15
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Radke JR, Guerini MN, Jerome M, White MW. A change in the premitotic period of the cell cycle is associated with bradyzoite differentiation in Toxoplasma gondii. Mol Biochem Parasitol 2004; 131:119-27. [PMID: 14511810 DOI: 10.1016/s0166-6851(03)00198-1] [Citation(s) in RCA: 83] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We have demonstrated that bradyzoites return to the tissue-cyst stage by a developmental pathway that is indistinguishable from that initiated by sporozoites. Mature bradyzoites, like sporozoites from oocysts, were non-proliferative as they contained uniform 1N DNA contents, and replication occurred only in parasites that de-differentiated back into tachyzoites. Moreover, tachyzoites emergent from the bradyzoite-initiated pathway underwent a spontaneous growth shift prior to the onset of tissue cyst formation in a timeframe that was identical to cultures infected with sporozoites. In sporozoite-infected cultures, a novel premitotic, near-diploid subpopulation was detected during bradyzoite differentiation that co-expressed tachyzoite and bradyzoite markers. These observations suggest that activation of a G2-related cell cycle mechanism is required during bradyzoite development, and indicates that equivalent cell cycle mechanisms may govern development in the intermediate life cycle regardless of the origin of infection.
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Affiliation(s)
- Jay R Radke
- Department of Veterinary Molecular Biology, Montana State University, Bozeman, MT 59717-3610, USA.
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Li JL, Warren AV, Cox LS. Identification of a second proliferating cell nuclear antigen in the human malarial pathogen Plasmodium falciparum. Int J Parasitol 2002; 32:1683-92. [PMID: 12464414 DOI: 10.1016/s0020-7519(02)00162-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Proliferating cell nuclear antigen seems to exist as a single form in higher eukaryotic cells and plays multiple roles in nucleic acid metabolism. We have identified a second additional proliferating cell nuclear antigen (PfPCNA2) in Plasmodium falciparum on the basis of several lines of evidence. (1) PfPCNA2, consisting of 264 amino acid residues with a predicted molecular mass of 30.2kDa, shares only 29% identity and 53% similarity with PfPCNA1 at the amino acid level. (2) Southern blot analyses revealed that the hybridisation pattern of the Pfpcna2 gene is completely different from that of the Pfpcna1 gene. (3) Chromosomal localisation studies showed that Pfpcna2 is located on chromosome 12 while Pfpcna1 is located on chromosome 13. Northern blot analyses revealed two different transcripts of Pfpcna2, one expressed in both asexual and sexual erythrocytic stages, while the other existed only in the sexual stage, implying that PfPCNA2 may play multiple roles in DNA metabolism in different stages of the parasite. Recombinant protein of PfPCNA2, overexpressed in Escherichia coli, has been purified to near homogeneity and shown to form an oligomer, probably a trimer, as revealed by a size-exclusion chromatography and a native gel electrophoresis, suggesting that PfPCNA2, like its higher eukaryotic counterparts, may serve as a sliding platform which is capable of interaction with diverse proteins and regulation of their activities.
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Affiliation(s)
- Ji-Liang Li
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK.
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Patterson S, Whittle C, Robert C, Chakrabarti D. Molecular characterization and expression of an alternate proliferating cell nuclear antigen homologue, PfPCNA2, in Plasmodium falciparum. Biochem Biophys Res Commun 2002; 298:371-6. [PMID: 12413950 DOI: 10.1016/s0006-291x(02)02436-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The malaria parasite Plasmodium falciparum genome sequencing has revealed the existence of a second gene for proliferating cell nuclear antigen (PCNA), a key factor in a variety of DNA metabolic events. The alternate copy of PCNA (PfPCNA2) shows only 23% identity to an earlier reported P. falciparum PCNA homologue (PfPCNA1). Our analysis indicated structural conservation of PfPCNA2 compared to eukaryotic PCNAs. PfPCNA1 and 2 polypeptides showed differential expression in the intraerythrocytic cell cycle of the malaria parasite. PfPCNA1 expression slowly increases about threefold from the ring to the late schizont stage. In contrast PfPCNA2 showed robust expression in trophozoites and early schizonts with a sudden drop in expression in the late schizont stage, suggesting that the two PfPCNAs may function under different physiological conditions. Chemical cross-linking indicated the presence of a trimeric PfPCNA2 protein, indicating the possible existence of a functional ring-like PfPCNA2 structure.
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Affiliation(s)
- Shelley Patterson
- Department of Molecular Biology and Microbiology, University of Central Florida, Orlando, FL 32826, USA
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Kvaal CA, Radke JR, Guerini MN, White MW. Isolation of a Toxoplasma gondii cyclin by yeast two-hybrid interactive screen. Mol Biochem Parasitol 2002; 120:187-94. [PMID: 11897124 DOI: 10.1016/s0166-6851(01)00454-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
GAL4-based yeast two-hybrid cDNA libraries from Toxoplasma gondii RH strain were constructed and screened for interactors of a putative T. gondii cdc2-related kinase, TgCRK2. A screen of 3.2 million transformants yielded a single yeast clone that harbored a protein fusion capable of specifically interacting with TgCRK2. Sequencing revealed the cDNA insert (TgCYC1) had homology to the cyclin class of proteins. The TgCYC1 cDNA fragment was used to probe a conventional T. gondii cDNA library and a 2.65 kb cDNA coding for a predicted protein of 582 amino acids was obtained. Based on comparison with a 5'-RACE product from tachyzoite mRNA, the 2.65 kb cDNA for TgCYC1 appeared to be complete. TgCYC1 had the highest similarity to Plasmodium falciparum CYC1 and displayed sequence characteristics that place it in the cyclin H class of eukaryotic cyclins. In synchronous tachyzoite populations the level of TgCYC1 mRNA was unchanged indicating it is not cell cycle regulated at the mRNA level. TgCYC1 rescues the G(1)/S cyclin cell cycle defect in S. cerevisiae strain DL1 demonstrating that this apicomplexan cyclin can function in an established heterologous model system.
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Affiliation(s)
- Christopher A Kvaal
- Department of Veterinary Molecular Biology, Marsh Laboratory, Montana State University, Bozeman, MT 59717-3610, USA
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Striepen B, Crawford MJ, Shaw MK, Tilney LG, Seeber F, Roos DS. The plastid of Toxoplasma gondii is divided by association with the centrosomes. J Cell Biol 2000; 151:1423-34. [PMID: 11134072 PMCID: PMC2150670 DOI: 10.1083/jcb.151.7.1423] [Citation(s) in RCA: 176] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Apicomplexan parasites harbor a single nonphotosynthetic plastid, the apicoplast, which is essential for parasite survival. Exploiting Toxoplasma gondii as an accessible system for cell biological analysis and molecular genetic manipulation, we have studied how these parasites ensure that the plastid and its 35-kb circular genome are faithfully segregated during cell division. Parasite organelles were labeled by recombinant expression of fluorescent proteins targeted to the plastid and the nucleus, and time-lapse video microscopy was used to image labeled organelles throughout the cell cycle. Apicoplast division is tightly associated with nuclear and cell division and is characterized by an elongated, dumbbell-shaped intermediate. The plastid genome is divided early in this process, associating with the ends of the elongated organelle. A centrin-specific antibody demonstrates that the ends of dividing apicoplast are closely linked to the centrosomes. Treatment with dinitroaniline herbicides (which disrupt microtubule organization) leads to the formation of multiple spindles and large reticulate plastids studded with centrosomes. The mitotic spindle and the pellicle of the forming daughter cells appear to generate the force required for apicoplast division in Toxoplasma gondii. These observations are discussed in the context of autonomous and FtsZ-dependent division of plastids in plants and algae.
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Affiliation(s)
- B Striepen
- Department of Cellular Biology and Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, Georgia 30602, USA.
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