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Bonnell VA, Zhang Y, Brown AS, Horton J, Josling GA, Chiu TP, Rohs R, Mahony S, Gordân R, Llinás M. DNA sequence and chromatin differentiate sequence-specific transcription factor binding in the human malaria parasite Plasmodium falciparum. Nucleic Acids Res 2024:gkae585. [PMID: 38966997 DOI: 10.1093/nar/gkae585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 05/30/2024] [Accepted: 06/27/2024] [Indexed: 07/06/2024] Open
Abstract
Development of the malaria parasite, Plasmodium falciparum, is regulated by a limited number of sequence-specific transcription factors (TFs). However, the mechanisms by which these TFs recognize genome-wide binding sites is largely unknown. To address TF specificity, we investigated the binding of two TF subsets that either bind CACACA or GTGCAC DNA sequence motifs and further characterized two additional ApiAP2 TFs, PfAP2-G and PfAP2-EXP, which bind unique DNA motifs (GTAC and TGCATGCA). We also interrogated the impact of DNA sequence and chromatin context on P. falciparum TF binding by integrating high-throughput in vitro and in vivo binding assays, DNA shape predictions, epigenetic post-translational modifications, and chromatin accessibility. We found that DNA sequence context minimally impacts binding site selection for paralogous CACACA-binding TFs, while chromatin accessibility, epigenetic patterns, co-factor recruitment, and dimerization correlate with differential binding. In contrast, GTGCAC-binding TFs prefer different DNA sequence context in addition to chromatin dynamics. Finally, we determined that TFs that preferentially bind divergent DNA motifs may bind overlapping genomic regions due to low-affinity binding to other sequence motifs. Our results demonstrate that TF binding site selection relies on a combination of DNA sequence and chromatin features, thereby contributing to the complexity of P. falciparum gene regulatory mechanisms.
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Affiliation(s)
- Victoria A Bonnell
- Department of Biochemistry and Molecular Biology, University of Southern California, Los Angeles, CA 90089, USA
- Huck Institutes Center for Eukaryotic Gene Regulation, University of Southern California, Los Angeles, CA 90089, USA
- Huck Institutes Center for Malaria Research, University of Southern California, Los Angeles, CA 90089, USA
| | - Yuning Zhang
- Center for Genomic and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA
- Department of Biostatistics and Bioinformatics, University of Southern California, Los Angeles, CA 90089, USA
- Program in Computational Biology and Bioinformatics, University of Southern California, Los Angeles, CA 90089, USA
| | - Alan S Brown
- Department of Biochemistry and Molecular Biology, University of Southern California, Los Angeles, CA 90089, USA
- Huck Institutes Center for Eukaryotic Gene Regulation, University of Southern California, Los Angeles, CA 90089, USA
- Huck Institutes Center for Malaria Research, University of Southern California, Los Angeles, CA 90089, USA
| | - John Horton
- Center for Genomic and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA
- Department of Biostatistics and Bioinformatics, University of Southern California, Los Angeles, CA 90089, USA
| | - Gabrielle A Josling
- Department of Biochemistry and Molecular Biology, University of Southern California, Los Angeles, CA 90089, USA
- Huck Institutes Center for Eukaryotic Gene Regulation, University of Southern California, Los Angeles, CA 90089, USA
- Huck Institutes Center for Malaria Research, University of Southern California, Los Angeles, CA 90089, USA
| | - Tsu-Pei Chiu
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA
| | - Remo Rohs
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA
- Department of Physics and Astronomy, University of Southern California, Los Angeles, CA 90089, USA
- Thomas Lord Department of Computer Science, University of Southern California, Los Angeles, CA 90089, USA
| | - Shaun Mahony
- Department of Biochemistry and Molecular Biology, University of Southern California, Los Angeles, CA 90089, USA
- Huck Institutes Center for Eukaryotic Gene Regulation, University of Southern California, Los Angeles, CA 90089, USA
| | - Raluca Gordân
- Center for Genomic and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA
- Department of Biostatistics and Bioinformatics, University of Southern California, Los Angeles, CA 90089, USA
- Department of Computer Science, Durham, NC 27708, USA
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC 27708, USA
| | - Manuel Llinás
- Department of Biochemistry and Molecular Biology, University of Southern California, Los Angeles, CA 90089, USA
- Huck Institutes Center for Eukaryotic Gene Regulation, University of Southern California, Los Angeles, CA 90089, USA
- Huck Institutes Center for Malaria Research, University of Southern California, Los Angeles, CA 90089, USA
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA
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2
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Liu C, Tang J, Liang K, Liu P, Li Z. Ready for renascence in mosquito: The regulation of gene expression in Plasmodium sexual development. Acta Trop 2024; 254:107191. [PMID: 38554994 DOI: 10.1016/j.actatropica.2024.107191] [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] [Received: 12/21/2023] [Revised: 02/21/2024] [Accepted: 03/18/2024] [Indexed: 04/02/2024]
Abstract
Malaria remains one of the most perilous vector-borne infectious diseases for humans globally. Sexual gametocyte represents the exclusive stage at which malaria parasites are transmitted from the vertebrate to the Anopheles host. The feasible and effective approach to prevent malaria transmission is by addressing the sexual developmental processes, that is, gametocytogenesis and gametogenesis. Thus, this review will comprehensively cover advances in the regulation of gene expression surrounding the transmissible stages, including epigenetic, transcriptional, and post-transcriptional control.
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Affiliation(s)
- Cong Liu
- Institute of Pathogenic Biology and Key Laboratory of Special Pathogen Prevention and Control of Hunan Province, School of Basic Medical Sciences, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China; School of Public Health, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
| | - Jingjing Tang
- Institute of Pathogenic Biology and Key Laboratory of Special Pathogen Prevention and Control of Hunan Province, School of Basic Medical Sciences, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
| | - Kejia Liang
- Institute of Pathogenic Biology and Key Laboratory of Special Pathogen Prevention and Control of Hunan Province, School of Basic Medical Sciences, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
| | - Peng Liu
- Institute of Pathogenic Biology and Key Laboratory of Special Pathogen Prevention and Control of Hunan Province, School of Basic Medical Sciences, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
| | - Zhenkui Li
- Institute of Pathogenic Biology and Key Laboratory of Special Pathogen Prevention and Control of Hunan Province, School of Basic Medical Sciences, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China.
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3
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Abstract
Plasmodium falciparum, the human malaria parasite, infects two hosts and various cell types, inducing distinct morphological and physiological changes in the parasite in response to different environmental conditions. These variations required the parasite to adapt and develop elaborate molecular mechanisms to ensure its spread and transmission. Recent findings have significantly improved our understanding of the regulation of gene expression in P. falciparum. Here, we provide an up-to-date overview of technologies used to highlight the transcriptomic adjustments occurring in the parasite throughout its life cycle. We also emphasize the complementary and complex epigenetic mechanisms regulating gene expression in malaria parasites. This review concludes with an outlook on the chromatin architecture, the remodeling systems, and how this 3D genome organization is critical in various biological processes.
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Affiliation(s)
- Thomas Hollin
- Department of Molecular, Cell and Systems Biology, University of California, Riverside, California, USA;
| | - Zeinab Chahine
- Department of Molecular, Cell and Systems Biology, University of California, Riverside, California, USA;
| | - Karine G Le Roch
- Department of Molecular, Cell and Systems Biology, University of California, Riverside, California, USA;
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4
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Ouologuem DT, Dara A, Kone A, Ouattara A, Djimde AA. Plasmodium falciparum Development from Gametocyte to Oocyst: Insight from Functional Studies. Microorganisms 2023; 11:1966. [PMID: 37630530 PMCID: PMC10460021 DOI: 10.3390/microorganisms11081966] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 07/06/2023] [Accepted: 07/14/2023] [Indexed: 08/27/2023] Open
Abstract
Malaria elimination may never succeed without the implementation of transmission-blocking strategies. The transmission of Plasmodium spp. parasites from the human host to the mosquito vector depends on circulating gametocytes in the peripheral blood of the vertebrate host. Once ingested by the mosquito during blood meals, these sexual forms undergo a series of radical morphological and metabolic changes to survive and progress from the gut to the salivary glands, where they will be waiting to be injected into the vertebrate host. The design of effective transmission-blocking strategies requires a thorough understanding of all the mechanisms that drive the development of gametocytes, gametes, sexual reproduction, and subsequent differentiation within the mosquito. The drastic changes in Plasmodium falciparum shape and function throughout its life cycle rely on the tight regulation of stage-specific gene expression. This review outlines the mechanisms involved in Plasmodium falciparum sexual stage development in both the human and mosquito vector, and zygote to oocyst differentiation. Functional studies unravel mechanisms employed by P. falciparum to orchestrate the expression of stage-specific functional products required to succeed in its complex life cycle, thus providing us with potential targets for developing new therapeutics. These mechanisms are based on studies conducted with various Plasmodium species, including predominantly P. falciparum and the rodent malaria parasites P. berghei. However, the great potential of epigenetics, genomics, transcriptomics, proteomics, and functional genetic studies to improve the understanding of malaria as a disease remains partly untapped because of limitations in studies using human malaria parasites and field isolates.
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Affiliation(s)
- Dinkorma T. Ouologuem
- Malaria Research and Training Center, Faculty of Pharmacy, Faculty of Medicine and Dentistry, University of Sciences, Techniques, and Technologies of Bamako, Bamako 1805, Mali
| | - Antoine Dara
- Malaria Research and Training Center, Faculty of Pharmacy, Faculty of Medicine and Dentistry, University of Sciences, Techniques, and Technologies of Bamako, Bamako 1805, Mali
| | - Aminatou Kone
- Malaria Research and Training Center, Faculty of Pharmacy, Faculty of Medicine and Dentistry, University of Sciences, Techniques, and Technologies of Bamako, Bamako 1805, Mali
| | - Amed Ouattara
- Malaria Research Program, Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Abdoulaye A. Djimde
- Malaria Research and Training Center, Faculty of Pharmacy, Faculty of Medicine and Dentistry, University of Sciences, Techniques, and Technologies of Bamako, Bamako 1805, Mali
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5
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Godin MJ, Sebastian A, Albert I, Lindner SE. Long-Read Genome Assembly and Gene Model Annotations for the Rodent Malaria Parasite Plasmodium yoelii 17XNL. J Biol Chem 2023:104871. [PMID: 37247760 PMCID: PMC10320607 DOI: 10.1016/j.jbc.2023.104871] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 05/20/2023] [Accepted: 05/22/2023] [Indexed: 05/31/2023] Open
Abstract
Malaria causes over 600 thousand fatalities each year, with most cases attributed to the human-infectious Plasmodium falciparum species. Many rodent-infectious Plasmodium species, like Plasmodium berghei and Plasmodium yoelii, have been used as model species that can expedite studies of this pathogen. P. yoelii is an especially good model for investigating the mosquito and liver stages of parasite development because key attributes closely resemble those of P. falciparum. Because of its importance, in 2002 the 17XNL strain of P. yoelii was the first rodent malaria parasite to be sequenced. While a breakthrough effort, the assembly consisted of >5000 contiguous sequences that adversely impacted the annotated gene models. While other rodent malaria parasite genomes have been sequenced and annotated since then, including the related P. yoelii 17X strain, the 17XNL strain has not. As a result, genomic data for 17X has become the de facto reference genome for the 17XNL strain while leaving open questions surrounding possible differences between the 17XNL and 17X genomes. In this work, we present a high-quality genome assembly for P. yoelii 17XNL using PacBio DNA sequencing. In addition, we use Nanopore and Illumina RNA sequencing of mixed blood stages to create complete gene models that include coding sequences, alternate isoforms, and UTR designations. A comparison of the 17X and this new 17XNL assembly revealed biologically meaningful differences between the strains due to the presence of coding sequence variants. Taken together, our work provides a new genomic framework for studies with this commonly used rodent malaria model species.
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Affiliation(s)
- Mitchell J Godin
- Department of Biochemistry and Molecular Biology, The Huck Center for Malaria Research, The Center for Eukaryotic Gene Regulation, Pennsylvania State University, University Park, PA, 16802
| | - Aswathy Sebastian
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, 16802
| | - Istvan Albert
- Department of Biochemistry and Molecular Biology, The Huck Center for Malaria Research, The Center for Eukaryotic Gene Regulation, Pennsylvania State University, University Park, PA, 16802; Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, 16802.
| | - Scott E Lindner
- Department of Biochemistry and Molecular Biology, The Huck Center for Malaria Research, The Center for Eukaryotic Gene Regulation, Pennsylvania State University, University Park, PA, 16802.
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6
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Kazan MM, Asmare MM, Mahapatra RK. Identification of Potential Drug Targets in Erythrocyte Invasion Pathway of Plasmodium falciparum. Curr Microbiol 2023; 80:165. [PMID: 37020052 DOI: 10.1007/s00284-023-03282-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 03/21/2023] [Indexed: 04/07/2023]
Abstract
The erythrocyte invasion phase plays a critical role in multiplication, sexual determination, and drug resistance in Plasmodium falciparum. In order to identify the critical genes and pathways in the erythrocyte invasion phase, the gene set (GSE129949) and the RNA-Seq count data for the W2mef strain were used for further analysis. An integrative bioinformatics study was performed to scrutinize genes as potential drug targets. 487 differentially expressed genes (DEGs) with an adjusted P value < 0.001 enriched 47 Gene Ontology (GO) terms that were over-represented based on hyper-geometric analysis P value < 0.01. Protein-Protein interaction network analysis was done using DEGs with higher confidence interactions (PPI score threshold = 0.7). MCODE and cytoHubba apps were utilized to define the hub proteins and rank them based on multiple topological analyses and MCODE scores. Furthermore, Gene Set Enrichment Analysis (GSEA) was carried out by using 322 gene sets from the MPMP database. The genes involved in multiple significant gene sets were determined by leading-edge analysis. Our study identified six genes encoding proteins that could be potential drug targets involved in the erythrocyte invasion phase related to merozoites motility, cell-cycle regulation, G-dependent protein kinase phosphorylation in schizonts, control of microtubule assembly, and sexual commitment. The druggability of those proteins was calculated based on the DCI (Drug Confidence Index) and predicted binding pockets' values. The protein that showed the best binding pocket value was subjected to deep learning-based virtual screening. The study identified the best small molecule inhibitors in terms of drug-binding score against the proteins for inhibitor identification.
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Affiliation(s)
- Mohammad Mustafa Kazan
- School of Biotechnology, KIIT Deemed to be University, Bhubaneswar, Odisha, 751024, India
| | | | - Rajani Kanta Mahapatra
- School of Biotechnology, KIIT Deemed to be University, Bhubaneswar, Odisha, 751024, India.
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7
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Xu SJ, Shen HM, Cui YB, Chen SB, Xu B, Chen JH. Genetic diversity and natural selection of rif gene (PF3D7_1254800) in the Plasmodium falciparum global populations. Mol Biochem Parasitol 2023; 254:111558. [PMID: 36918126 DOI: 10.1016/j.molbiopara.2023.111558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 02/10/2023] [Accepted: 03/08/2023] [Indexed: 03/14/2023]
Abstract
To reveal the genetic characteristics of one member of the Plasmodium falciparum repetitive interspersed family (rif), we sequenced the rif gene (PF3D7_1254800) in 53 field isolates collected from Ghana-imported cases into China and compared them with 350 publicly available P. falciparum rif sequences from global populations. In the Ghana-imported population, the nucleotide diversities were 0.05714 and 0.06616 for the full length and variable region of rif gene, respectively. Meanwhile, 22 and 20 haplotypes were identified for the full length and variable region of rif gene (Hd = 0.843 and 0.838, respectively). Diversity of rif gene in Ghana-imported population was higher than that observed in Cambodia, Thailand, Vietnam, Myanmar, Mali, Ghana, and Senegal populations. In this analysis, we found high genetic diversity of rif gene in global P. falciparum populations and identified 158 haplotypes. Tajima's D-test shows that there are large differences in the direction of selection between the conserved and variable region of rif gene. Tajima's D value for the variable region was 0.20074, indicating that balancing selection existed in this region. We found that the variable region was the main target of selection for positive diversification, and most mutation sites were located in this region. The population structure suggested optimized cluster values of K = 6. The five groups in Ghana-imported population included a unique subpopulation. Our results reveal the dynamics of the rif gene (PF3D7_1254800) in P. falciparum populations, which can aid in the rational design of P. falciparum rif-based vaccines.
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Affiliation(s)
- Shao-Jie Xu
- National Institute of Parasitic Diseases, Chinese Center for Diseases Control and Prevention, (Chinese Center for Tropical Diseases Research), Shanghai 200025, PR China; National Health Commission of the People's Republic of China (NHC) Key Laboratory of Parasite and Vector Biology, Shanghai 200025, PR China; World Health Organization (WHO) Collaborating Center for Tropical Diseases, Shanghai 200025, PR China; National Centre for International Research on Tropical Diseases, Shanghai 200025, PR China
| | - Hai-Mo Shen
- National Institute of Parasitic Diseases, Chinese Center for Diseases Control and Prevention, (Chinese Center for Tropical Diseases Research), Shanghai 200025, PR China; National Health Commission of the People's Republic of China (NHC) Key Laboratory of Parasite and Vector Biology, Shanghai 200025, PR China; World Health Organization (WHO) Collaborating Center for Tropical Diseases, Shanghai 200025, PR China; National Centre for International Research on Tropical Diseases, Shanghai 200025, PR China
| | - Yan-Bing Cui
- National Institute of Parasitic Diseases, Chinese Center for Diseases Control and Prevention, (Chinese Center for Tropical Diseases Research), Shanghai 200025, PR China; National Health Commission of the People's Republic of China (NHC) Key Laboratory of Parasite and Vector Biology, Shanghai 200025, PR China; World Health Organization (WHO) Collaborating Center for Tropical Diseases, Shanghai 200025, PR China; National Centre for International Research on Tropical Diseases, Shanghai 200025, PR China
| | - Shen-Bo Chen
- National Institute of Parasitic Diseases, Chinese Center for Diseases Control and Prevention, (Chinese Center for Tropical Diseases Research), Shanghai 200025, PR China; National Health Commission of the People's Republic of China (NHC) Key Laboratory of Parasite and Vector Biology, Shanghai 200025, PR China; World Health Organization (WHO) Collaborating Center for Tropical Diseases, Shanghai 200025, PR China; National Centre for International Research on Tropical Diseases, Shanghai 200025, PR China
| | - Bin Xu
- National Institute of Parasitic Diseases, Chinese Center for Diseases Control and Prevention, (Chinese Center for Tropical Diseases Research), Shanghai 200025, PR China; National Health Commission of the People's Republic of China (NHC) Key Laboratory of Parasite and Vector Biology, Shanghai 200025, PR China; World Health Organization (WHO) Collaborating Center for Tropical Diseases, Shanghai 200025, PR China; National Centre for International Research on Tropical Diseases, Shanghai 200025, PR China
| | - Jun-Hu Chen
- National Institute of Parasitic Diseases, Chinese Center for Diseases Control and Prevention, (Chinese Center for Tropical Diseases Research), Shanghai 200025, PR China; National Health Commission of the People's Republic of China (NHC) Key Laboratory of Parasite and Vector Biology, Shanghai 200025, PR China; World Health Organization (WHO) Collaborating Center for Tropical Diseases, Shanghai 200025, PR China; National Centre for International Research on Tropical Diseases, Shanghai 200025, PR China; School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, PR China; School of Basic Medical Sciences and Forensic Medicine, Hangzhou Medical College, Hangzhou 310013, PR China.
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8
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Godin MJ, Sebastian A, Albert I, Lindner SE. Long-Read Genome Assembly and Gene Model Annotations for the Rodent Malaria Parasite Plasmodium yoelii 17XNL. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.06.523040. [PMID: 36711553 PMCID: PMC9882011 DOI: 10.1101/2023.01.06.523040] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Malaria causes over 200 million infections and over 600 thousand fatalities each year, with most cases attributed to a human-infectious Plasmodium species, Plasmodium falciparum . Many rodent-infectious Plasmodium species, like Plasmodium berghei, Plasmodium chabaudi , and Plasmodium yoelii , have been used as genetically tractable model species that can expedite studies of this pathogen. In particular, P. yoelii is an especially good model for investigating the mosquito and liver stages of parasite development because key attributes closely resemble those of P. falciparum . Because of its importance to malaria research, in 2002 the 17XNL strain of P. yoelii was the first rodent malaria parasite to be sequenced. While sequencing and assembling this genome was a breakthrough effort, the final assembly consisted of >5000 contiguous sequences that impacted the creation of annotated gene models. While other important rodent malaria parasite genomes have been sequenced and annotated since then, including the related P. yoelii 17X strain, the 17XNL strain has not. As a result, genomic data for 17X has become the de facto reference genome for the 17XNL strain while leaving open questions surrounding possible differences between the 17XNL and 17X genomes. In this work, we present a high-quality genome assembly for P. yoelii 17XNL using HiFi PacBio long-read DNA sequencing. In addition, we use Nanopore long-read direct RNA-seq and Illumina short-read sequencing of mixed blood stages to create complete gene models that include not only coding sequences but also alternate transcript isoforms, and 5' and 3' UTR designations. A comparison of the 17X and this new 17XNL assembly revealed biologically meaningful differences between the strains due to the presence of coding sequence variants. Taken together, our work provides a new genomic and gene expression framework for studies with this commonly used rodent malaria model species.
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Affiliation(s)
- Mitchell J. Godin
- Department of Biochemistry and Molecular Biology, The Huck Center for Malaria Research, The Center for Eukaryotic Gene Regulation, Pennsylvania State University, University Park, PA, 16802
| | - Aswathy Sebastian
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, 16802
| | - Istvan Albert
- Department of Biochemistry and Molecular Biology, The Huck Center for Malaria Research, The Center for Eukaryotic Gene Regulation, Pennsylvania State University, University Park, PA, 16802
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, 16802
| | - Scott E. Lindner
- Department of Biochemistry and Molecular Biology, The Huck Center for Malaria Research, The Center for Eukaryotic Gene Regulation, Pennsylvania State University, University Park, PA, 16802
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9
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Diffendall GM, Barcons-Simon A, Baumgarten S, Dingli F, Loew D, Scherf A. Discovery of RUF6 ncRNA-interacting proteins involved in P. falciparum immune evasion. Life Sci Alliance 2022; 6:6/1/e202201577. [PMID: 36379669 PMCID: PMC9670795 DOI: 10.26508/lsa.202201577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 10/25/2022] [Accepted: 10/26/2022] [Indexed: 11/16/2022] Open
Abstract
Non-coding RNAs (ncRNAs) are emerging regulators of immune evasion and transmission of Plasmodium falciparum RUF6 is an ncRNA gene family that is transcribed by RNA polymerase III but actively regulates the Pol II-transcribed var virulence gene family. Understanding how RUF6 ncRNA connects to downstream effectors is lacking. We developed an RNA-directed proteomic discovery (ChIRP-MS) protocol to identify in vivo RUF6 ncRNA-protein interactions. The RUF6 ncRNA interactome was purified with biotinylated antisense oligonucleotides. Quantitative label-free mass spectrometry identified several unique proteins linked to gene transcription including RNA Pol II subunits, nucleosome assembly proteins, and a homologue of DEAD box helicase 5 (DDX5). Affinity purification of Pf-DDX5 identified proteins originally found by our RUF6-ChIRP protocol, validating the technique's robustness for identifying ncRNA interactomes in P. falciparum Inducible displacement of nuclear Pf-DDX5 resulted in significant down-regulation of the active var gene. Our work identifies a RUF6 ncRNA-protein complex that interacts with RNA Pol II to sustain the var gene expression, including a helicase that may resolve G-quadruplex secondary structures in var genes to facilitate transcriptional activation and progression.
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Affiliation(s)
- Gretchen M Diffendall
- Universite Paris Cité, Institut Pasteur, Biology of Host-Parasite Interactions Unit, INSERM U1201, CNRS EMR9195, Paris, France,Sorbonne Université Ecole doctorale Complexité du Vivant ED515, Paris, France
| | - Anna Barcons-Simon
- Universite Paris Cité, Institut Pasteur, Biology of Host-Parasite Interactions Unit, INSERM U1201, CNRS EMR9195, Paris, France,Sorbonne Université Ecole doctorale Complexité du Vivant ED515, Paris, France,Biomedical Center, Division of Physiological Chemistry, Faculty of Medicine, Ludwig-Maximilians-Universität München, Munich, Germany
| | | | - Florent Dingli
- Institut Curie, PSL Research University, Centre de Recherche, CurieCoreTech Mass Spectrometry Proteomics, Paris, France
| | - Damarys Loew
- Institut Curie, PSL Research University, Centre de Recherche, CurieCoreTech Mass Spectrometry Proteomics, Paris, France
| | - Artur Scherf
- Universite Paris Cité, Institut Pasteur, Biology of Host-Parasite Interactions Unit, INSERM U1201, CNRS EMR9195, Paris, France
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10
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Inhibitors of ApiAP2 protein DNA binding exhibit multistage activity against Plasmodium parasites. PLoS Pathog 2022; 18:e1010887. [PMID: 36223427 PMCID: PMC9591056 DOI: 10.1371/journal.ppat.1010887] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 10/24/2022] [Accepted: 09/17/2022] [Indexed: 11/06/2022] Open
Abstract
Plasmodium parasites are reliant on the Apicomplexan AP2 (ApiAP2) transcription factor family to regulate gene expression programs. AP2 DNA binding domains have no homologs in the human or mosquito host genomes, making them potential antimalarial drug targets. Using an in-silico screen to dock thousands of small molecules into the crystal structure of the AP2-EXP (Pf3D7_1466400) AP2 domain (PDB:3IGM), we identified putative AP2-EXP interacting compounds. Four compounds were found to block DNA binding by AP2-EXP and at least one additional ApiAP2 protein. Our top ApiAP2 competitor compound perturbs the transcriptome of P. falciparum trophozoites and results in a decrease in abundance of log2 fold change > 2 for 50% (46/93) of AP2-EXP target genes. Additionally, two ApiAP2 competitor compounds have multi-stage anti-Plasmodium activity against blood and mosquito stage parasites. In summary, we describe a novel set of antimalarial compounds that interact with AP2 DNA binding domains. These compounds may be used for future chemical genetic interrogation of ApiAP2 proteins or serve as starting points for a new class of antimalarial therapeutics. Plasmodium parasites are the causative agent of malaria, which resulted in over 600,000 deaths in 2021. Due to resistance arising for every antimalarial therapeutic deployed to date, new drug targets and druggable pathways must be explored. To address this concern, we used a molecular docking screen to predict competitors of DNA binding by the parasite specific family of Apicomplexan AP2 (ApiAP2) transcription factor proteins for testing in vitro and in vivo. We find that ApiAP2 competing compounds have antimalarial activity consistent with the disruption of gene regulation. This work will further our understanding of both the biological role and targetability of parasite transcriptional regulation.
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11
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Theileria annulata histone deacetylase 1 (TaHDAC1) initiates schizont to merozoite stage conversion. Sci Rep 2022; 12:12710. [PMID: 35882887 PMCID: PMC9325746 DOI: 10.1038/s41598-022-15518-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 06/24/2022] [Indexed: 11/24/2022] Open
Abstract
A fungal metabolite, FR235222, specifically inhibits a histone deacetylase of the apicomplexan parasite Toxoplasma gondii and TgHDAC3 has emerged as a key factor regulating developmental stage transition in this species. Here, we exploited FR235222 to ask if changes in histone acetylation regulate developmental stage transition of Theileria annulata, another apicomplexan species. We found that FR235222 treatment of T. annulata-infected transformed leukocytes induced a proliferation arrest. The blockade in proliferation was due to drug-induced conversion of intracellular schizonts to merozoites that lack the ability to maintain host leukocyte cell division. Induction of merogony by FR235222 leads to an increase in expression of merozoite-marker (rhoptry) proteins. RNA-seq of FR235222-treated T. annulata-infected B cells identified deregulated expression of 468 parasite genes including a number encoding parasite ApiAP2 transcription factors. Thus, similar to T. gondii, FR235222 inhibits T. annulata HDAC (TaHDAC1) activity and places parasite histone acetylation as a major regulatory event of the transition from schizonts to merozoites.
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12
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ApiAP2 Gene-Network Regulates Gametocytogenesis in Plasmodium Parasites. Cell Microbiol 2022. [DOI: 10.1155/2022/5796578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Malaria is a mosquito-borne infectious disease, caused by unicellular Apicomplexan protozoa of the genus Plasmodium. The sexual stage of Plasmodium is one of the most fascinating aspects of the Plasmodium life cycle, yet relatively less explored until now. The production of sexually fit gametocytes through gametocytogenesis is essential to the transmission of the Plasmodium parasite into an anopheline mosquito vector. Understanding how gametocytogenesis is regulated promotes the identification of novel drug targets and also the development of transmission-blocking vaccines that would help reduce the disease burden in endemic areas. Transcriptional regulation in Plasmodium parasites is primarily controlled by a family of twenty-seven Apicomplexan Apetela 2 (ApiAP2) genes which act in a cascade to enable the parasite to progress through its asexual replication as well as gametocytogenesis. Here, we review the latest progress made on members of the ApiAP2 family characterized as key players of the transcriptional machinery of gametocytes. Further, we will highlight the transcriptional regulation network of ApiAP2 genes at each stage of gametocytogenesis.
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13
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Plasmodium falciparum S-Adenosylmethionine Synthetase Is Essential for Parasite Survival through a Complex Interaction Network with Cytoplasmic and Nuclear Proteins. Microorganisms 2022; 10:microorganisms10071419. [PMID: 35889137 PMCID: PMC9320499 DOI: 10.3390/microorganisms10071419] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 07/01/2022] [Accepted: 07/11/2022] [Indexed: 11/16/2022] Open
Abstract
S-adenosylmethionine synthetase (SAMS) is a key enzyme for the synthesis of the lone methyl donor S-adenosyl methionine (SAM), which is involved in transmethylation reactions and hence required for cellular processes such as DNA, RNA, and histone methylation, but also polyamine biosynthesis and proteostasis. In the human malaria parasite Plasmodium falciparum, PfSAMS is encoded by a single gene and has been suggested to be crucial for malaria pathogenesis and transmission; however, to date, PfSAMS has not been fully characterized. To gain deeper insight into the function of PfSAMS, we generated a conditional gene knockdown (KD) using the glmS ribozyme system. We show that PfSAMS localizes to the cytoplasm and the nucleus of blood-stage parasites. PfSAMS-KD results in reduced histone methylation and leads to impaired intraerythrocytic growth and gametocyte development. To further determine the interaction network of PfSAMS, we performed a proximity-dependent biotin identification analysis. We identified a complex network of 1114 proteins involved in biological processes such as cell cycle control and DNA replication, or transcription, but also in phosphatidylcholine and polyamine biosynthesis and proteasome regulation. Our findings highlight the diverse roles of PfSAMS during intraerythrocytic growth and sexual stage development and emphasize that PfSAMS is a potential drug target.
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14
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Quinn JE, Jeninga MD, Limm K, Pareek K, Meißgeier T, Bachmann A, Duffy MF, Petter M. The Putative Bromodomain Protein PfBDP7 of the Human Malaria Parasite Plasmodium Falciparum Cooperates With PfBDP1 in the Silencing of Variant Surface Antigen Expression. Front Cell Dev Biol 2022; 10:816558. [PMID: 35493110 PMCID: PMC9039026 DOI: 10.3389/fcell.2022.816558] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 03/18/2022] [Indexed: 01/08/2023] Open
Abstract
Epigenetic regulation is a critical mechanism in controlling virulence, differentiation, and survival of the human malaria parasite Plasmodium (P.) falciparum. Bromodomain proteins contribute to this process by binding to acetylated lysine residues of histones and thereby targeting the gene regulatory machinery to gene promoters. A protein complex containing the P. falciparum bromodomain proteins (PfBDP) 1 and PfBDP2 (BDP1/BDP2 core complex) was previously shown to play an essential role for the correct transcription of invasion related genes. Here, we performed a functional characterization of a third component of this complex, which we dubbed PfBDP7, because structural modelling predicted a typical bromodomain fold. We confirmed that PfBDP7 is a nuclear protein that interacts with PfBDP1 at invasion gene promoters in mature schizont stage parasites and contributes to their transcription. Although partial depletion of PfBDP7 showed no significant effect on parasite viability, conditional knock down of either PfBDP7 or PfBDP1 resulted in the de-repression of variant surface antigens (VSA), which are important pathogenicity factors. This de-repression was evident both on mRNA and protein level. To understand the underlying mechanism, we mapped the genome wide binding sites of PfBDP7 by ChIPseq and showed that in early schizonts, PfBDP7 and PfBDP1 are commonly enriched in heterochromatic regions across the gene body of all VSA families, including genes coding for PfEMP1, RIFIN, STEVOR, and PfMC-2TM. This suggests that PfBDP7 and PfBDP1 contribute to the silencing of VSAs by associating with heterochromatin. In conclusion, we identified PfBDP7 as a chromatin binding protein that is a constitutive part of the P. falciparum BDP1/BDP2 core complex and established PfBDP1 and PfBDP7 as novel players in the silencing of heterochromatin regulated virulence gene families of the malaria parasite P. falciparum.
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Affiliation(s)
- Jennifer E. Quinn
- Mikrobiologisches Institut—Klinische Mikrobiologie, Immunologie und Hygiene, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Erlangen, Germany
| | - Myriam D. Jeninga
- Mikrobiologisches Institut—Klinische Mikrobiologie, Immunologie und Hygiene, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Erlangen, Germany
| | - Katharina Limm
- Institute of Functional Genomics, University of Regensburg, Regensburg, Germany
| | - Kapil Pareek
- Mikrobiologisches Institut—Klinische Mikrobiologie, Immunologie und Hygiene, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Erlangen, Germany
| | - Tina Meißgeier
- Mikrobiologisches Institut—Klinische Mikrobiologie, Immunologie und Hygiene, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Erlangen, Germany
| | - Anna Bachmann
- Department of Cellular Parasitology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
- Centre for Structural Systems Biology (CSSB), Hamburg, Germany
- Biology Department, University of Hamburg, Hamburg, Germany
| | - Michael F. Duffy
- Department of Microbiology and Immunology, The University of Melbourne, Bio21 Institute, Parkville, VIC, Australia
| | - Michaela Petter
- Mikrobiologisches Institut—Klinische Mikrobiologie, Immunologie und Hygiene, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Erlangen, Germany
- Department of Medicine, The University of Melbourne, Royal Melbourne Hospital, Parkville, VIC, Australia
- *Correspondence: Michaela Petter,
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15
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Turnbull LB, Button-Simons KA, Agbayani N, Ferdig MT. Sources of transcription variation in Plasmodium falciparum. J Genet Genomics 2022; 49:965-974. [PMID: 35395422 DOI: 10.1016/j.jgg.2022.03.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 03/21/2022] [Accepted: 03/22/2022] [Indexed: 12/20/2022]
Abstract
Variation in transcript abundance can contribute to both short-term environmental response and long-term evolutionary adaptation. Most studies are designed to assess differences in mean transcription levels and do not consider other potentially important and confounding sources of transcriptional variation. Detailed quantification of variation sources will improve our ability to detect and identify the mechanisms that contribute to genome-wide transcription changes that underpin adaptive responses. To quantify innate levels of expression variation, we measured mRNA levels for more than 5000 genes in the malaria parasite, Plasmodium falciparum, among clones derived from two parasite strains across biologically and experimentally replicated batches. Using a mixed effects model, we partitioned the total variation among four sources - between strain, within strain, environmental batch effects, and stochastic noise. We found 646 genes with significant variation attributable to at least one of these sources. These genes were categorized by their predominant variation source and further examined using gene ontology enrichment analysis to associate function with each source of variation. Genes with environmental batch effect and within strain transcript variation may contribute to phenotypic plasticity, while genes with between strain variation may contribute to adaptive responses and processes that lead to parasite strain-specific survival under varied conditions.
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Affiliation(s)
- Lindsey B Turnbull
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Katrina A Button-Simons
- Department of Biological Sciences, Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Nestor Agbayani
- Department of Biological Sciences, Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN, 46556, USA; Rush School of Medicine, Chicago, IL, 60612, USA
| | - Michael T Ferdig
- Department of Biological Sciences, Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN, 46556, USA.
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16
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Shang X, Wang C, Shen L, Sheng F, He X, Wang F, Fan Y, He X, Jiang M. PfAP2-EXP2, an Essential Transcription Factor for the Intraerythrocytic Development of Plasmodium falciparum. Front Cell Dev Biol 2022; 9:782293. [PMID: 35083215 PMCID: PMC8785209 DOI: 10.3389/fcell.2021.782293] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 12/09/2021] [Indexed: 12/13/2022] Open
Abstract
Plasmodium falciparum undergoes a series of asexual replications in human erythrocytes after infection, which are effective targets for combatting malaria. Here, we report roles of an ApiAP2 transcription factor PfAP2-EXP2 (PF3D7_0611200) in the intraerythrocytic developmental cycle of P. falciparum. PfAP2-EXP2 conditional knockdown resulted in an asexual growth defect but without an appreciable effect on parasite morphology. Further ChIP-seq analysis revealed that PfAP2-EXP2 targeted genes related to virulence and interaction between erythrocytes and parasites. Especially, PfAP2-EXP2 regulation of euchromatic genes does not depend on recognizing specific DNA sequences, while a CCCTAAACCC motif is found in its heterochromatic binding sites. Combined with transcriptome profiling, we suggest that PfAP2-EXP2 is participated in the intraerythrocytic development by affecting the expression of genes related to cell remodeling at the schizont stage. In summary, this study explores an ApiAP2 member plays an important role for the P. falciparum blood-stage replication, which suggests a new perspective for malaria elimination.
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Affiliation(s)
- Xiaomin Shang
- Department of Medical Genetics, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, China.,Department of Parasitology, Xiangya School of Medicine, Central South University, Changsha, China
| | - Changhong Wang
- Department of Medical Genetics, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Li Shen
- Department of Medical Genetics, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Fei Sheng
- Department of Medical Genetics, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Xiaohui He
- Department of Medical Genetics, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, China.,National Health Commission Key Laboratory of Parasitic Disease Control and Prevention, Jiangsu Provincial Key Laboratory on Parasite and Vector Control Technology, Jiangsu Institute of Parasitic Diseases, Wuxi, China
| | - Fei Wang
- Department of Medical Genetics, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Yanting Fan
- Department of Medical Genetics, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Xiaoqin He
- National Health Commission Key Laboratory of Parasitic Disease Control and Prevention, Jiangsu Provincial Key Laboratory on Parasite and Vector Control Technology, Jiangsu Institute of Parasitic Diseases, Wuxi, China
| | - Mei Jiang
- Department of Medical Genetics, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, China
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17
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Shang X, Wang C, Fan Y, Guo G, Wang F, Zhao Y, Sheng F, Tang J, He X, Yu X, Zhang M, Zhu G, Yin S, Mu J, Culleton R, Cao J, Jiang M, Zhang Q. OUP accepted manuscript. Nucleic Acids Res 2022; 50:3413-3431. [PMID: 35288749 PMCID: PMC8989538 DOI: 10.1093/nar/gkac176] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 03/03/2022] [Accepted: 03/05/2022] [Indexed: 11/13/2022] Open
Abstract
Heterochromatin-associated gene silencing controls multiple physiological processes in malaria parasites, however, little is known concerning the regulatory network and cis-acting sequences involved in the organization of heterochromatin and how they modulate heterochromatic gene expression. Based on systematic profiling of genome-wide occupancy of eighteen Apicomplexan AP2 transcription factors by ChIP-seq analysis, we identify and characterize eight heterochromatin-associated factors (PfAP2-HFs), which exhibit preferential enrichment within heterochromatic regions but with differential coverage profiles. Although these ApiAP2s target euchromatic gene loci via specific DNA motifs, they are likely integral components of heterochromatin independent of DNA motif recognition. Systematic knockout screenings of ApiAP2 factors coupled with RNA-seq transcriptomic profiling revealed three activators and three repressors of heterochromatic gene expression including four PfAP2-HFs. Notably, expression of virulence genes is either completely silenced or significantly reduced upon the depletion of PfAP2-HC. Integrated multi-omics analyses reveal autoregulation and feed-forward loops to be common features of the ApiAP2 regulatory network, in addition to the occurrence of dynamic interplay between local chromatin structure and ApiAP2s in transcriptional control. Collectively, this study provides a valuable resource describing the genome-wide landscape of the ApiAP2 family and insights into functional divergence and cooperation within this family during the blood-stage development of malaria parasites.
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Affiliation(s)
| | | | | | | | - Fei Wang
- Laboratory of Molecular Parasitology, Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Tongji Hospital; Clinical Center for Brain and Spinal Cord Research, School of Medicine, Tongji University, Shanghai 200092, China
| | - Yuemeng Zhao
- Laboratory of Molecular Parasitology, Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Tongji Hospital; Clinical Center for Brain and Spinal Cord Research, School of Medicine, Tongji University, Shanghai 200092, China
| | - Fei Sheng
- Laboratory of Molecular Parasitology, Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Tongji Hospital; Clinical Center for Brain and Spinal Cord Research, School of Medicine, Tongji University, Shanghai 200092, China
| | - Jianxia Tang
- National Health Commission Key Laboratory of Parasitic Disease Control and Prevention, Jiangsu Provincial Key Laboratory on Parasite and Vector Control Technology, Jiangsu Institute of Parasitic Diseases, Wuxi, 214064, China
| | - Xiaoqin He
- National Health Commission Key Laboratory of Parasitic Disease Control and Prevention, Jiangsu Provincial Key Laboratory on Parasite and Vector Control Technology, Jiangsu Institute of Parasitic Diseases, Wuxi, 214064, China
| | - Xinyu Yu
- National Health Commission Key Laboratory of Parasitic Disease Control and Prevention, Jiangsu Provincial Key Laboratory on Parasite and Vector Control Technology, Jiangsu Institute of Parasitic Diseases, Wuxi, 214064, China
| | - Meihua Zhang
- National Health Commission Key Laboratory of Parasitic Disease Control and Prevention, Jiangsu Provincial Key Laboratory on Parasite and Vector Control Technology, Jiangsu Institute of Parasitic Diseases, Wuxi, 214064, China
| | - Guoding Zhu
- National Health Commission Key Laboratory of Parasitic Disease Control and Prevention, Jiangsu Provincial Key Laboratory on Parasite and Vector Control Technology, Jiangsu Institute of Parasitic Diseases, Wuxi, 214064, China
| | - Shigang Yin
- Laboratory of Neurological Diseases and Brain Function, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Jianbing Mu
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20892-8132, USA
| | - Richard Culleton
- Division of Molecular Parasitology, Proteo-Science Centre, Ehime University, Matsuyama, Ehime 790-8577, Japan
| | - Jun Cao
- Correspondence may also be addressed to Jun Cao. Tel: +05 10 6878 1007;
| | - Mei Jiang
- Correspondence may also be addressed to Mei Jiang. Tel: +86 21 6598 5138;
| | - Qingfeng Zhang
- To whom correspondence should be addressed. Tel: +86 21 6598 5138;
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18
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Rawat M, Srivastava A, Johri S, Gupta I, Karmodiya K. Single-Cell RNA Sequencing Reveals Cellular Heterogeneity and Stage Transition under Temperature Stress in Synchronized Plasmodium falciparum Cells. Microbiol Spectr 2021; 9:e0000821. [PMID: 34232098 PMCID: PMC8552519 DOI: 10.1128/spectrum.00008-21] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 05/26/2021] [Indexed: 12/12/2022] Open
Abstract
The malaria parasite has a complex life cycle exhibiting phenotypic and morphogenic variations in two different hosts by existing in heterogeneous developmental states. To investigate this cellular heterogeneity of the parasite within the human host, we performed single-cell RNA sequencing of synchronized Plasmodium cells under control and temperature treatment conditions. Using the Malaria Cell Atlas (https://www.sanger.ac.uk/science/tools/mca) as a guide, we identified 9 subtypes of the parasite distributed across known intraerythrocytic stages. Interestingly, temperature treatment results in the upregulation of the AP2-G gene, the master regulator of sexual development in a small subpopulation of the parasites. Moreover, we identified a heterogeneous stress-responsive subpopulation (clusters 5, 6, and 7 [∼10% of the total population]) that exhibits upregulation of stress response pathways under normal growth conditions. We also developed an online exploratory tool that will provide new insights into gene function under normal and temperature stress conditions. Thus, our study reveals important insights into cell-to-cell heterogeneity in the parasite population under temperature treatment that will be instrumental toward a mechanistic understanding of cellular adaptation and population dynamics in Plasmodium falciparum. IMPORTANCE The malaria parasite has a complex life cycle exhibiting phenotypic variations in two different hosts accompanied by cell-to-cell variability that is important for stress tolerance, immune evasion, and drug resistance. To investigate cellular heterogeneity determined by gene expression, we performed single-cell RNA sequencing (scRNA-seq) of about 12,000 synchronized Plasmodium cells under physiologically relevant normal (37°C) and temperature stress (40°C) conditions phenocopying the cyclic bouts of fever experienced during malarial infection. In this study, we found that parasites exhibit transcriptional heterogeneity in an otherwise morphologically synchronized culture. Also, a subset of parasites is continually committed to gametocytogenesis and stress-responsive pathways. These observations have important implications for understanding the mechanisms of drug resistance generation and vaccine development against the malaria parasite.
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Affiliation(s)
- Mukul Rawat
- Department of Biology, Indian Institute of Science Education and Research, Pashan, Pune, Maharashtra, India
| | - Ashish Srivastava
- Department of Biology, Indian Institute of Science Education and Research, Pashan, Pune, Maharashtra, India
| | - Shreya Johri
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi, India
| | - Ishaan Gupta
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi, India
| | - Krishanpal Karmodiya
- Department of Biology, Indian Institute of Science Education and Research, Pashan, Pune, Maharashtra, India
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19
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Shang X, Shen S, Tang J, He X, Zhao Y, Wang C, He X, Guo G, Liu M, Wang L, Zhu Q, Yang G, Jiang C, Zhang M, Yu X, Han J, Culleton R, Jiang L, Cao J, Gu L, Zhang Q. A cascade of transcriptional repression determines sexual commitment and development in Plasmodium falciparum. Nucleic Acids Res 2021; 49:9264-9279. [PMID: 34365503 PMCID: PMC8450074 DOI: 10.1093/nar/gkab683] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 07/25/2021] [Accepted: 07/28/2021] [Indexed: 11/12/2022] Open
Abstract
Gametocytogenesis, the process by which malaria parasites produce sexual forms that can infect mosquitoes, is essential for the transmission of malaria. A transcriptional switch of the pfap2-g gene triggers sexual commitment, but how the complex multi-step process is precisely programed remains largely unknown. Here, by systematic functional screening of a panel of ApiAP2 transcription factors, we identify six new ApiAP2 members associated with gametocytogenesis in Plasmodium falciparum. Among these, PfAP2-G5 (PF3D7_1139300) was found to be indispensable for gametocytogenesis. This factor suppresses the transcriptional activity of the pfap2-g gene via binding to both the upstream region and exonic gene body, the latter is linked to the maintenance of local heterochromatin structure, thereby preventing initiation of sexual commitment. Removal of this repressive effect through pfap2-g5 knockout disrupts the asexual replication cycle and promotes sexual commitment accompanied by upregulation of pfap2-g expression. However, the gametocytes produced fail to mature fully. Further analyses show that PfAP2-G5 is essential for gametocyte maturation, and causes the down-regulation of pfap2-g and a set of early gametocyte genes activated by PfAP2-G prior to gametocyte development. Collectively, our findings reveal a regulation cascade of gametocyte production in malaria parasites, and provide a new target for transmission blocking interventions.
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Affiliation(s)
- Xiaomin Shang
- Laboratory of Molecular Parasitology, Research Center for Translational Medicine, Key Laboratory of Arrhythmias of the Ministry of Education of China, East Hospital, School of Medicine, Tongji University, Shanghai 200120, China
| | - Shijun Shen
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Orthopaedic Department of Tongji Hospital, Shanghai Key Laboratory of Signaling and Disease Research, the School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Jianxia Tang
- National Health Commission Key Laboratory of Parasitic Disease Control and Prevention, Jiangsu Provincial Key Laboratory on Parasite and Vector Control Technology, Jiangsu Institute of Parasitic Diseases, Wuxi 214064, China
| | - Xiaoqin He
- National Health Commission Key Laboratory of Parasitic Disease Control and Prevention, Jiangsu Provincial Key Laboratory on Parasite and Vector Control Technology, Jiangsu Institute of Parasitic Diseases, Wuxi 214064, China
| | - Yuemeng Zhao
- Laboratory of Molecular Parasitology, Research Center for Translational Medicine, Key Laboratory of Arrhythmias of the Ministry of Education of China, East Hospital, School of Medicine, Tongji University, Shanghai 200120, China.,Unit of Human Parasite Molecular and Cell Biology, Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Changhong Wang
- Laboratory of Molecular Parasitology, Research Center for Translational Medicine, Key Laboratory of Arrhythmias of the Ministry of Education of China, East Hospital, School of Medicine, Tongji University, Shanghai 200120, China
| | - Xiaohui He
- Laboratory of Molecular Parasitology, Research Center for Translational Medicine, Key Laboratory of Arrhythmias of the Ministry of Education of China, East Hospital, School of Medicine, Tongji University, Shanghai 200120, China
| | - Gangqiang Guo
- Laboratory of Molecular Parasitology, Research Center for Translational Medicine, Key Laboratory of Arrhythmias of the Ministry of Education of China, East Hospital, School of Medicine, Tongji University, Shanghai 200120, China.,Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Orthopaedic Department of Tongji Hospital, Shanghai Key Laboratory of Signaling and Disease Research, the School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Meng Liu
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Orthopaedic Department of Tongji Hospital, Shanghai Key Laboratory of Signaling and Disease Research, the School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Liping Wang
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Orthopaedic Department of Tongji Hospital, Shanghai Key Laboratory of Signaling and Disease Research, the School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Qianshu Zhu
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Orthopaedic Department of Tongji Hospital, Shanghai Key Laboratory of Signaling and Disease Research, the School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Guang Yang
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Orthopaedic Department of Tongji Hospital, Shanghai Key Laboratory of Signaling and Disease Research, the School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Cizhong Jiang
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Orthopaedic Department of Tongji Hospital, Shanghai Key Laboratory of Signaling and Disease Research, the School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Meihua Zhang
- National Health Commission Key Laboratory of Parasitic Disease Control and Prevention, Jiangsu Provincial Key Laboratory on Parasite and Vector Control Technology, Jiangsu Institute of Parasitic Diseases, Wuxi 214064, China
| | - Xinyu Yu
- National Health Commission Key Laboratory of Parasitic Disease Control and Prevention, Jiangsu Provincial Key Laboratory on Parasite and Vector Control Technology, Jiangsu Institute of Parasitic Diseases, Wuxi 214064, China
| | - Jiping Han
- Unit of Human Parasite Molecular and Cell Biology, Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Richard Culleton
- Division of Molecular Parasitology, Proteo-Science Centre, Ehime University, Matsuyama, Ehime 790-8577, Japan.,Department of Protozoology, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan
| | - Lubin Jiang
- Unit of Human Parasite Molecular and Cell Biology, Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Jun Cao
- National Health Commission Key Laboratory of Parasitic Disease Control and Prevention, Jiangsu Provincial Key Laboratory on Parasite and Vector Control Technology, Jiangsu Institute of Parasitic Diseases, Wuxi 214064, China.,Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, China.,Public Health Research Center, Jiangnan University, Wuxi 214122, China
| | - Liang Gu
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Orthopaedic Department of Tongji Hospital, Shanghai Key Laboratory of Signaling and Disease Research, the School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Qingfeng Zhang
- Laboratory of Molecular Parasitology, Research Center for Translational Medicine, Key Laboratory of Arrhythmias of the Ministry of Education of China, East Hospital, School of Medicine, Tongji University, Shanghai 200120, China
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20
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Walters HA, Temesvari LA. Target acquired: transcriptional regulators as drug targets for protozoan parasites. Int J Parasitol 2021; 51:599-611. [PMID: 33722681 PMCID: PMC8169582 DOI: 10.1016/j.ijpara.2020.12.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 12/09/2020] [Accepted: 12/17/2020] [Indexed: 11/22/2022]
Abstract
Protozoan parasites are single-celled eukaryotic organisms that cause significant human disease and pose a substantial health and socioeconomic burden worldwide. They are responsible for at least 1 million deaths annually. The treatment of such diseases is hindered by the ability of parasites to form latent cysts, develop drug resistance, or be transmitted by insect vectors. Additionally, these pathogens have developed complex mechanisms to alter host gene expression. The prevalence of these diseases is predicted to increase as climate change leads to the augmentation of ambient temperatures, insect ranges, and warm water reservoirs. Therefore, the discovery of novel treatments is necessary. Transcription factors lie at the junction of multiple signalling pathways in eukaryotes and aberrant transcription factor function contributes to the progression of numerous human diseases including cancer, diabetes, inflammatory disorders and cardiovascular disease. Transcription factors were previously thought to be undruggable. However, due to recent advances, transcription factors now represent appealing drug targets. It is conceivable that transcription factors, and the pathways they regulate, may also serve as targets for anti-parasitic drug design. Here, we review transcription factors and transcriptional modulators of protozoan parasites, and discuss how they may be useful in drug discovery. We also provide information on transcription factors that play a role in stage conversion of parasites, TATA box-binding proteins, and transcription factors and cofactors that participate with RNA polymerases I, II and III. We also highlight a significant gap in knowledge in that the transcription factors of some of parasites have been under-investigated. Understanding parasite transcriptional pathways and how parasites alter host gene expression will be essential in discovering innovative drug targets.
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Affiliation(s)
- H A Walters
- Department of Biological Sciences, Clemson University, Clemson, SC 29634, United States; Eukaryotic Pathogens Innovation Center, Clemson University, Clemson, SC 29634, United States
| | - L A Temesvari
- Department of Biological Sciences, Clemson University, Clemson, SC 29634, United States; Eukaryotic Pathogens Innovation Center, Clemson University, Clemson, SC 29634, United States.
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21
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Cubillos EFG, Prata IO, Fotoran WL, Ranford-Cartwright L, Wunderlich G. The Transcription Factor PfAP2-O Influences Virulence Gene Transcription and Sexual Development in Plasmodium falciparum. Front Cell Infect Microbiol 2021; 11:669088. [PMID: 34268135 PMCID: PMC8275450 DOI: 10.3389/fcimb.2021.669088] [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: 02/17/2021] [Accepted: 04/23/2021] [Indexed: 12/02/2022] Open
Abstract
The human malaria parasite Plasmodium falciparum expresses variant PfEMP1 proteins on the infected erythrocyte, which function as ligands for endothelial receptors in capillary vessels, leading to erythrocyte sequestration and severe malaria. The factors that orchestrate the mono-allelic expression of the 45–90 PfEMP1-encoding var genes within each parasite genome are still not fully identified. Here, we show that the transcription factor PfAP2-O influences the transcription of var genes. The temporary knockdown of PfAP2-O leads to a complete loss of var transcriptional memory and a decrease in cytoadherence in CD36 adherent parasites. AP2-O-knocked-down parasites exhibited also significant reductions in transmission through Anopheles mosquitoes. We propose that PfAP2-O is, beside its role in transmission stages, also one of the virulence gene transcriptional regulators and may therefore be exploited as an important target to disrupt severe malaria and block parasite transmission.
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Affiliation(s)
- Eliana F G Cubillos
- Department of Parasitology, Institute for Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Isadora Oliveira Prata
- Department of Parasitology, Institute for Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Wesley Luzetti Fotoran
- Department of Parasitology, Institute for Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Lisa Ranford-Cartwright
- Institute of Biodiversity, Animal Health & Comparative Medicine, College of Medical, Veterinary and Life Science, University of Glasgow, Glasgow, United Kingdom
| | - Gerhard Wunderlich
- Department of Parasitology, Institute for Biomedical Sciences, University of São Paulo, São Paulo, Brazil
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22
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Sekar V, Rivero A, Pigeault R, Gandon S, Drews A, Ahren D, Hellgren O. Gene regulation of the avian malaria parasite Plasmodium relictum, during the different stages within the mosquito vector. Genomics 2021; 113:2327-2337. [PMID: 34023365 DOI: 10.1016/j.ygeno.2021.05.021] [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: 01/18/2021] [Revised: 04/26/2021] [Accepted: 05/18/2021] [Indexed: 10/21/2022]
Abstract
The malaria parasite Plasmodium relictum is one of the most widespread species of avian malaria. As in the case of its human counterparts, bird Plasmodium undergoes a complex life cycle infecting two hosts: the arthropod vector and the vertebrate host. In this study, we examined transcriptomes of P. relictum (SGS1) during crucial timepoints within its vector, Culex pipiens quinquefasciatus. Differential gene-expression analyses identified genes linked to the parasites life-stages at: i) a few minutes after the blood meal is ingested, ii) during peak oocyst production phase, iii) during peak sporozoite phase and iv) during the late-stages of the infection. A large amount of genes coding for functions linked to host-immune invasion and multifunctional genes was active throughout the infection cycle. One gene associated with a conserved Plasmodium membrane protein with unknown function was upregulated throughout the parasite development in the vector, suggesting an important role in the successful completion of the sporogonic cycle. Gene expression analysis further identified genes, with unknown functions to be significantly differentially expressed during the infection in the vector as well as upregulation of reticulocyte-binding proteins, which raises the possibility of the multifunctionality of these RBPs. We establish the existence of highly stage-specific pathways being overexpressed during the infection. This first study of gene-expression of a non-human Plasmodium species in its vector provides a comprehensive insight into the molecular mechanisms of the common avian malaria parasite P. relictum and provides essential information on the evolutionary diversity in gene regulation of the Plasmodium's vector stages.
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Affiliation(s)
| | - Ana Rivero
- MIVEGEC (CNRS - Université de Montpellier - IRD), 34394 Montpellier, France; CREES (Centre de Recherche en Ecologie et Evolution de la Santé), 34394 Montpellier, France
| | - Romain Pigeault
- Department of Biology, Lund University, Sweden; Department of Ecology and Evolution, CH-1015 Lausanne, Switzerland
| | - Sylvain Gandon
- CEFE (CNRS - Université de Montpellier - Université Paul-Valéry - EPHE - IRD), Montpellier, France
| | - Anna Drews
- MEMEG, Department of Biology, Lund University, Sweden
| | - Dag Ahren
- National Bioinformatics Infrastructure Sweden (NBIS), SciLifeLab, Department of Biology, Lund, Sweden
| | - Olof Hellgren
- MEMEG, Department of Biology, Lund University, Sweden.
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23
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The Architectural Factor HMGB1 Is Involved in Genome Organization in the Human Malaria Parasite Plasmodium falciparum. mBio 2021; 12:mBio.00148-21. [PMID: 33906919 PMCID: PMC8092211 DOI: 10.1128/mbio.00148-21] [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] [Indexed: 12/16/2022] Open
Abstract
The three-dimensional (3D) genome organization plays a critical role in the regulation of gene expression in eukaryotic organisms. In the unicellular malaria parasite Plasmodium falciparum, the high-order chromosome organization has emerged as an important epigenetic pathway mediating gene expression, particularly for virulence genes, but the related architectural factors and underlying mechanism remain elusive. Herein, we have identified the high-mobility-group protein HMGB1 as a critical architectural factor for maintenance of genome organization in P. falciparum Genome-wide occupancy analysis (chromatin immunoprecipitation sequencing [ChIP-seq]) shows that the HMGB1 protein is recruited mainly to centromeric regions likely via a DNA-binding-independent pathway. Chromosome conformation capture coupled with next-generation sequencing (Hi-C-seq) and 3D modeling analysis show that the loss of HMGB1 disrupts the integrity of centromere/telomere-based chromosome organization accompanied with diminished interaction frequency among centromere clusters. This triggers local chromatin alteration and dysregulated gene expression. Notably, the entire repertoire of the primary virulence genes (var) was completely silenced in the absence of P. falciparum HMGB1 (PfHMGB1). Furthermore, the disrupted nuclear organization was reconstituted by complementation of HMGB1, thereby rescuing the mutually exclusive expression of the var gene family. Collectively, these data demonstrate that the architectural factor HMGB1 is associated with gene expression via mediating the high-order structure of genome organization. This finding not only contributes better understanding of the epigenetic regulation of gene expression but may also provide novel targets for antimalarial strategies.IMPORTANCE Malaria remains a major public health and economic burden currently. The mutually exclusive expression of the virulence genes is associated with the pathogenesis and immune evasion of human malaria parasites in the host. The nuclear architecture provides a well-organized environment for differential gene expression in the nucleus, but the underlying mechanism remains largely unknown. In this study, we have identified the highly conserved high-mobility-group protein HMGB1 as a key architecture regulator involved in virulence gene expression by establishing high-order genome organization in the nucleus of P. falciparum Mechanistic investigation revealed that the specific interaction of HMGB1 and centromeres constructed the precisely organized nuclear architecture, which coordinated with local chromatin structure to control the singular expression of virulence genes. Hence, this protein appears to be a critical architectural regulator for the pathogenesis of malaria infection and may be a new target for the development of an intervention strategy against malaria.
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24
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Carrington E, Cooijmans RHM, Keller D, Toenhake CG, Bártfai R, Voss TS. The ApiAP2 factor PfAP2-HC is an integral component of heterochromatin in the malaria parasite Plasmodium falciparum. iScience 2021; 24:102444. [PMID: 33997710 PMCID: PMC8105651 DOI: 10.1016/j.isci.2021.102444] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 03/10/2021] [Accepted: 04/14/2021] [Indexed: 12/18/2022] Open
Abstract
Malaria parasites undergo a complex life cycle in the human host and the mosquito vector. The ApiAP2 family of DNA-binding proteins plays a dominant role in parasite development and life cycle progression. Most ApiAP2 factors studied to date act as transcription factors regulating stage-specific gene expression. Here, we characterized an ApiAP2 factor in Plasmodium falciparum that we termed PfAP2-HC. We demonstrate that PfAP2-HC specifically binds to heterochromatin throughout the genome. Intriguingly, PfAP2-HC does not bind DNA in vivo and recruitment of PfAP2-HC to heterochromatin is independent of its DNA-binding domain but strictly dependent on heterochromatin protein 1. Furthermore, our results suggest that PfAP2-HC functions neither in the regulation of gene expression nor in heterochromatin formation or maintenance. In summary, our findings reveal PfAP2-HC as a core component of heterochromatin in malaria parasites and identify unexpected properties and substantial functional divergence among the members of the ApiAP2 family of regulatory proteins. The ApiAP2 factor AP2-HC is a core component of heterochromatin in malaria parasites Binding of AP2-HC to heterochromatin strictly depends on heterochromatin protein 1 The AP2 DNA-binding domain of AP2-HC is dispensable for heterochromatin association
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Affiliation(s)
- Eilidh Carrington
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, 4051 Basel, Switzerland.,University of Basel, 4001 Basel, Switzerland
| | | | - Dominique Keller
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, 4051 Basel, Switzerland.,University of Basel, 4001 Basel, Switzerland
| | | | - Richárd Bártfai
- Department of Molecular Biology, Radboud University, 6525GA Nijmegen, The Netherlands
| | - Till Steffen Voss
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, 4051 Basel, Switzerland.,University of Basel, 4001 Basel, Switzerland
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25
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Xu Y, Qiao D, Wen Y, Bi Y, Chen Y, Huang Z, Cui L, Guo J, Cao Y. PfAP2-G2 Is Associated to Production and Maturation of Gametocytes in Plasmodium falciparum via Regulating the Expression of PfMDV-1. Front Microbiol 2021; 11:631444. [PMID: 33537025 PMCID: PMC7848025 DOI: 10.3389/fmicb.2020.631444] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 12/21/2020] [Indexed: 11/13/2022] Open
Abstract
Gametocyte is the sole form of the Plasmodium falciparum which is transmissible to the mosquito vector. Here, we report that an Apicomplexan Apetala2 (ApiAP2) family transcription factor, PfAP2-G2 (Pf3D7_1408200), plays a role in the development of gametocytes in P. falciparum by regulating the expression of PfMDV-1 (Pf3D7_1216500). Reverse transcriptase-quantitative PCR (RT-qPCR) analysis showed that PfAP2-G2 was highly expressed in the ring stage. Indirect immunofluorescence assay showed nuclear localization of PfAP2-G2 in asexual stages. The knockout of PfAP2-G2 led to a ~95% decrease in the number of mature gametocytes with a more substantial influence on the production and maturation of the male gametocytes, resulting in a higher female/male gametocyte ratio. To test the mechanism of this phenotype, RNA-seq and RT-qPCR showed that disruption of PfAP2-G2 led to the down-regulation of male development gene-1 (PfMDV-1) in asexual stages. We further found that PfAP2-G2 was enriched at the transcriptional start site (TSS) of PfMDV-1 by chromatin immunoprecipitation and qPCR assay in both ring stage and schizont stage, which demonstrated that PfMDV-1 is one of the targets of PfAP2-G2. In addition, RT-qPCR also showed that PfAP2-G (Pf3D7_1222600), the master regulator for sexual commitment, was also down-regulated in the PfAP2-G2 knockout parasites in the schizont stage, but no change in the ring stage. This phenomenon suggested that PfAP2-G2 played a role at the asexual stage for the development of parasite gametocytes and warrants further investigations in regulatory pathways of PfAP2-G2.
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Affiliation(s)
- Yaozheng Xu
- Department of Immunology, College of Basic Medical Sciences, China Medical University, Shenyang, China
| | - Dan Qiao
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yuhao Wen
- Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China
| | - Yifei Bi
- Philosophy, Politics and Economics Department, University College London, London, United Kingdom
| | - Yuxi Chen
- Department of Immunology, College of Basic Medical Sciences, China Medical University, Shenyang, China
| | - Zhenghui Huang
- Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China
| | - Liwang Cui
- Department of Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, United States
| | - Jian Guo
- Department of Laboratory Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Yaming Cao
- Department of Immunology, College of Basic Medical Sciences, China Medical University, Shenyang, China
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26
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Hollin T, Le Roch KG. From Genes to Transcripts, a Tightly Regulated Journey in Plasmodium. Front Cell Infect Microbiol 2020; 10:618454. [PMID: 33425787 PMCID: PMC7793691 DOI: 10.3389/fcimb.2020.618454] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Accepted: 11/19/2020] [Indexed: 12/17/2022] Open
Abstract
Over the past decade, we have witnessed significant progresses in understanding gene regulation in Apicomplexa including the human malaria parasite, Plasmodium falciparum. This parasite possesses the ability to convert in multiple stages in various hosts, cell types, and environments. Recent findings indicate that P. falciparum is talented at using efficient and complementary molecular mechanisms to ensure a tight control of gene expression at each stage of its life cycle. Here, we review the current understanding on the contribution of the epigenome, atypical transcription factors, and chromatin organization to regulate stage conversion in P. falciparum. The adjustment of these regulatory mechanisms occurring during the progression of the life cycle will be extensively discussed.
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Affiliation(s)
- Thomas Hollin
- Department of Molecular, Cell and Systems Biology, University of California Riverside, CA, United States
| | - Karine G Le Roch
- Department of Molecular, Cell and Systems Biology, University of California Riverside, CA, United States
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27
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Dynamic Chromatin Structure and Epigenetics Control the Fate of Malaria Parasites. Trends Genet 2020; 37:73-85. [PMID: 32988634 DOI: 10.1016/j.tig.2020.09.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 08/27/2020] [Accepted: 09/02/2020] [Indexed: 12/11/2022]
Abstract
Multiple hosts and various life cycle stages prompt the human malaria parasite, Plasmodium falciparum, to acquire sophisticated molecular mechanisms to ensure its survival, spread, and transmission to its next host. To face these environmental challenges, increasing evidence suggests that the parasite has developed complex and complementary layers of regulatory mechanisms controlling gene expression. Here, we discuss the recent developments in the discovery of molecular components that contribute to cell replication and differentiation and highlight the major contributions of epigenetics, transcription factors, and nuclear architecture in controlling gene regulation and life cycle progression in Plasmodium spp.
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28
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Bryant JM, Baumgarten S, Dingli F, Loew D, Sinha A, Claës A, Preiser PR, Dedon PC, Scherf A. Exploring the virulence gene interactome with CRISPR/dCas9 in the human malaria parasite. Mol Syst Biol 2020; 16:e9569. [PMID: 32816370 PMCID: PMC7440042 DOI: 10.15252/msb.20209569] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 07/17/2020] [Accepted: 07/22/2020] [Indexed: 12/13/2022] Open
Abstract
Mutually exclusive expression of the var multigene family is key to immune evasion and pathogenesis in Plasmodium falciparum, but few factors have been shown to play a direct role. We adapted a CRISPR-based proteomics approach to identify novel factors associated with var genes in their natural chromatin context. Catalytically inactive Cas9 ("dCas9") was targeted to var gene regulatory elements, immunoprecipitated, and analyzed with mass spectrometry. Known and novel factors were enriched including structural proteins, DNA helicases, and chromatin remodelers. Functional characterization of PfISWI, an evolutionarily divergent putative chromatin remodeler enriched at the var gene promoter, revealed a role in transcriptional activation. Proteomics of PfISWI identified several proteins enriched at the var gene promoter such as acetyl-CoA synthetase, a putative MORC protein, and an ApiAP2 transcription factor. These findings validate the CRISPR/dCas9 proteomics method and define a new var gene-associated chromatin complex. This study establishes a tool for targeted chromatin purification of unaltered genomic loci and identifies novel chromatin-associated factors potentially involved in transcriptional control and/or chromatin organization of virulence genes in the human malaria parasite.
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Affiliation(s)
- Jessica M Bryant
- Biology of Host‐Parasite Interactions UnitInstitut PasteurParisFrance
- INSERM U1201ParisFrance
- CNRS ERL9195ParisFrance
| | - Sebastian Baumgarten
- Biology of Host‐Parasite Interactions UnitInstitut PasteurParisFrance
- INSERM U1201ParisFrance
- CNRS ERL9195ParisFrance
| | - Florent Dingli
- Institut CuriePSL Research UniversityCentre de RechercheMass Spectrometry and Proteomics FacilityParisFrance
| | - Damarys Loew
- Institut CuriePSL Research UniversityCentre de RechercheMass Spectrometry and Proteomics FacilityParisFrance
| | - Ameya Sinha
- School of Biological SciencesNanyang Technological UniversitySingaporeSingapore
- Antimicrobial Resistance Interdisciplinary Research GroupSingapore‐MIT Alliance for Research and TechnologySingaporeSingapore
| | - Aurélie Claës
- Biology of Host‐Parasite Interactions UnitInstitut PasteurParisFrance
- INSERM U1201ParisFrance
- CNRS ERL9195ParisFrance
| | - Peter R Preiser
- School of Biological SciencesNanyang Technological UniversitySingaporeSingapore
- Antimicrobial Resistance Interdisciplinary Research GroupSingapore‐MIT Alliance for Research and TechnologySingaporeSingapore
| | - Peter C Dedon
- Antimicrobial Resistance Interdisciplinary Research GroupSingapore‐MIT Alliance for Research and TechnologySingaporeSingapore
- Department of Biological EngineeringMassachusetts Institute of TechnologyCambridgeMAUSA
| | - Artur Scherf
- Biology of Host‐Parasite Interactions UnitInstitut PasteurParisFrance
- INSERM U1201ParisFrance
- CNRS ERL9195ParisFrance
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29
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Ruiz JL, Gómez-Díaz E. The second life of Plasmodium in the mosquito host: gene regulation on the move. Brief Funct Genomics 2020; 18:313-357. [PMID: 31058281 DOI: 10.1093/bfgp/elz007] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 03/08/2019] [Accepted: 03/26/2019] [Indexed: 01/08/2023] Open
Abstract
Malaria parasites face dynamically changing environments and strong selective constraints within human and mosquito hosts. To survive such hostile and shifting conditions, Plasmodium switches transcriptional programs during development and has evolved mechanisms to adjust its phenotype through heterogeneous patterns of gene expression. In vitro studies on culture-adapted isolates have served to set the link between chromatin structure and functional gene expression. Yet, experimental evidence is limited to certain stages of the parasite in the vertebrate, i.e. blood, while the precise mechanisms underlying the dynamic regulatory landscapes during development and in the adaptation to within-host conditions remain poorly understood. In this review, we discuss available data on transcriptional and epigenetic regulation in Plasmodium mosquito stages in the context of sporogonic development and phenotypic variation, including both bet-hedging and environmentally triggered direct transcriptional responses. With this, we advocate the mosquito offers an in vivo biological model to investigate the regulatory networks, transcription factors and chromatin-modifying enzymes and their modes of interaction with regulatory sequences, which might be responsible for the plasticity of the Plasmodium genome that dictates stage- and cell type-specific blueprints of gene expression.
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Affiliation(s)
- José L Ruiz
- Instituto de Parasitología y Biomedicina López-Neyra (IPBLN), Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Elena Gómez-Díaz
- Instituto de Parasitología y Biomedicina López-Neyra (IPBLN), Consejo Superior de Investigaciones Científicas, Granada, Spain
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30
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Investigating a Plasmodium falciparum erythrocyte invasion phenotype switch at the whole transcriptome level. Sci Rep 2020; 10:245. [PMID: 31937828 PMCID: PMC6959351 DOI: 10.1038/s41598-019-56386-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 12/11/2019] [Indexed: 12/14/2022] Open
Abstract
The central role that erythrocyte invasion plays in Plasmodium falciparum survival and reproduction makes this process an attractive target for therapeutic or vaccine development. However, multiple invasion-related genes with complementary and overlapping functions afford the parasite the plasticity to vary ligands used for invasion, leading to phenotypic variation and immune evasion. Overcoming the challenge posed by redundant ligands requires a deeper understanding of conditions that select for variant phenotypes and the molecular mediators. While host factors including receptor heterogeneity and acquired immune responses may drive parasite phenotypic variation, we have previously shown that host-independent changes in invasion phenotype can be achieved by continuous culturing of the W2mef and Dd2 P. falciparum strains in moving suspension as opposed to static conditions. Here, we have used a highly biologically replicated whole transcriptome sequencing approach to identify the molecular signatures of variation associated with the phenotype switch. The data show increased expression of particular invasion-related genes in switched parasites, as well as a large number of genes encoding proteins that are either exported or form part of the export machinery. The genes with most markedly increased expression included members of the erythrocyte binding antigens (EBA), reticulocyte binding homologues (RH), surface associated interspersed proteins (SURFIN), exported protein family 1 (EPF1) and Plasmodium Helical Interspersed Sub-Telomeric (PHIST) gene families. The data indicate changes in expression of a repertoire of genes not previously associated with erythrocyte invasion phenotypes, suggesting the possibility that moving suspension culture may also select for other traits.
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31
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Hoo R, Bruske E, Dimonte S, Zhu L, Mordmüller B, Sim BKL, Kremsner PG, Hoffman SL, Bozdech Z, Frank M, Preiser PR. Transcriptome profiling reveals functional variation in Plasmodium falciparum parasites from controlled human malaria infection studies. EBioMedicine 2019; 48:442-452. [PMID: 31521613 PMCID: PMC6838377 DOI: 10.1016/j.ebiom.2019.09.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 08/29/2019] [Accepted: 09/01/2019] [Indexed: 11/03/2022] Open
Abstract
BACKGROUND The transcriptome of Plasmodium falciparum clinical isolates varies according to strain, mosquito bites, disease severity and clinical history. Therefore, it remains a challenge to directly interpret the parasite's transcriptomic information into a more general biological signature in a natural human malaria infection. These confounding variations can be potentially overcome with parasites derived from controlled-human malaria infection (CHMI) studies. METHODS We performed CHMI studies in healthy and immunologically naïve volunteers receiving the same P. falciparum strain ((Sanaria® PfSPZ Challenge (NF54)), but with different sporozoite dosage and route of infection. Parasites isolated from these volunteers at the day of patency were subjected to in vitro culture for several generations and synchronized ring-stage parasites were subjected to transcriptome profiling. FINDINGS We observed clear deviations between CHMI-derived parasites from volunteer groups receiving different PfSPZ dose and route. CHMI-derived parasites and the pre-mosquito strain used for PfSPZ generation showed significant transcriptional variability for gene clusters associated with malaria pathogenesis, immune evasion and transmission. These transcriptional variation signature clusters were also observed in the transcriptome of P. falciparum isolates from acute clinical infections. INTERPRETATION Our work identifies a previously unrecognized transcriptional pattern in malaria infections in a non-immune background. Significant transcriptome heterogeneity exits between parasites derived from human infections and the pre-mosquito strain, implying that the malaria parasites undergo a change in functional state to adapt to its host environment. Our work also highlights the potential use of transcriptomics data from CHMI study advance our understanding of malaria parasite adaptation and transmission in humans. FUND: This work is supported by German Israeli Foundation, German ministry for education and research, MOE Tier 1 from the Singapore Ministry of Education Academic Research Fund, Singapore Ministry of Health's National Medical Research Council, National Institute of Allergy and Infectious Diseases, National Institutes of Health, USA and the German Centre for Infection Research (Deutsches Zentrum für Infektionsforschung-DZIF).
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Affiliation(s)
- Regina Hoo
- School of Biological Sciences, Nanyang Technological University, Singapore
| | - Ellen Bruske
- Institute of Tropical Medicine, Wilhelmstr. 27, University of Tübingen, 72074 Tübingen, Germany
| | - Sandra Dimonte
- Institute of Tropical Medicine, Wilhelmstr. 27, University of Tübingen, 72074 Tübingen, Germany
| | - Lei Zhu
- School of Biological Sciences, Nanyang Technological University, Singapore
| | - Benjamin Mordmüller
- Institute of Tropical Medicine, Wilhelmstr. 27, University of Tübingen, 72074 Tübingen, Germany; German Center for Infection Research, partner site Tübingen, Germany
| | - B Kim Lee Sim
- Sanaria Inc, 9800 Medical Center Dr A209, Rockville, MD 20850, USA
| | - Peter G Kremsner
- Institute of Tropical Medicine, Wilhelmstr. 27, University of Tübingen, 72074 Tübingen, Germany; Centre de Recherches Médicales de Lambaréné, BP 242 Lambaréné, Gabon
| | | | - Zbynek Bozdech
- School of Biological Sciences, Nanyang Technological University, Singapore
| | - Matthias Frank
- Institute of Tropical Medicine, Wilhelmstr. 27, University of Tübingen, 72074 Tübingen, Germany.
| | - Peter R Preiser
- School of Biological Sciences, Nanyang Technological University, Singapore.
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32
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Toenhake CG, Bártfai R. What functional genomics has taught us about transcriptional regulation in malaria parasites. Brief Funct Genomics 2019; 18:290-301. [PMID: 31220867 PMCID: PMC6859821 DOI: 10.1093/bfgp/elz004] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 02/08/2019] [Accepted: 03/14/2019] [Indexed: 12/16/2022] Open
Abstract
Malaria parasites are characterized by a complex life cycle that is accompanied by dynamic gene expression patterns. The factors and mechanisms that regulate gene expression in these parasites have been searched for even before the advent of next generation sequencing technologies. Functional genomics approaches have substantially boosted this area of research and have yielded significant insights into the interplay between epigenetic, transcriptional and post-transcriptional mechanisms. Recently, considerable progress has been made in identifying sequence-specific transcription factors and DNA-encoded regulatory elements. Here, we review the insights obtained from these efforts including the characterization of core promoters, the involvement of sequence-specific transcription factors in life cycle progression and the mapping of gene regulatory elements. Furthermore, we discuss recent developments in the field of functional genomics and how they might contribute to further characterization of this complex gene regulatory network.
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Affiliation(s)
- Christa G Toenhake
- Radboud University, Faculty of Science, Department of Molecular Biology, Nijmegen, the Netherlands
| | - Richárd Bártfai
- Radboud University, Faculty of Science, Department of Molecular Biology, Nijmegen, the Netherlands
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Ruiz JL, Tena JJ, Bancells C, Cortés A, Gómez-Skarmeta JL, Gómez-Díaz E. Characterization of the accessible genome in the human malaria parasite Plasmodium falciparum. Nucleic Acids Res 2019; 46:9414-9431. [PMID: 30016465 PMCID: PMC6182165 DOI: 10.1093/nar/gky643] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2018] [Accepted: 07/10/2018] [Indexed: 12/27/2022] Open
Abstract
Human malaria is a devastating disease and a major cause of poverty in resource-limited countries. To develop and adapt within hosts Plasmodium falciparum undergoes drastic switches in gene expression. To identify regulatory regions in the parasite genome, we performed genome-wide profiling of chromatin accessibility in two culture-adapted isogenic subclones at four developmental stages during the intraerythrocytic cycle by using the Assay for Transposase-Accessible Chromatin by sequencing (ATAC-seq). Tn5 transposase hypersensitivity sites (THSSs) localize preferentially at transcriptional start sites (TSSs). Chromatin accessibility by ATAC-seq is predictive of active transcription and of the levels of histone marks H3K9ac and H3K4me3. Our assay allows the identification of novel regulatory regions including TSS and enhancer-like elements. We show that the dynamics in the accessible chromatin profile matches temporal transcription during development. Motif analysis of stage-specific ATAC-seq sites predicts the in vivo binding sites and function of multiple ApiAP2 transcription factors. At last, the alternative expression states of some clonally variant genes (CVGs), including eba, phist, var and clag genes, associate with a differential ATAC-seq signal at their promoters. Altogether, this study identifies genome-wide regulatory regions likely to play an essential function in the developmental transitions and in CVG expression in P. falciparum.
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Affiliation(s)
- José Luis Ruiz
- Estación Biológica de Doñana (EBD), Consejo Superior de Investigaciones Científicas, Seville 41092, Spain
| | - Juan J Tena
- Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas-Universidad Pablo de Olavide-Junta de Andalucía, Seville 41013, Spain
| | - Cristina Bancells
- ISGlobal, Hospital Clínic - Universitat de Barcelona, Barcelona, Catalonia 08036, Spain
| | - Alfred Cortés
- ISGlobal, Hospital Clínic - Universitat de Barcelona, Barcelona, Catalonia 08036, Spain.,ICREA, Barcelona, Catalonia 08010, Spain
| | - José Luis Gómez-Skarmeta
- Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas-Universidad Pablo de Olavide-Junta de Andalucía, Seville 41013, Spain
| | - Elena Gómez-Díaz
- Estación Biológica de Doñana (EBD), Consejo Superior de Investigaciones Científicas, Seville 41092, Spain.,Instituto de Parasitología y Biomedicina 'López-Neyra' (IPBLN), Consejo Superior de Investigaciones Científicas, Granada 18016, Spain
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ApiAP2 Transcription Factors in Apicomplexan Parasites. Pathogens 2019; 8:pathogens8020047. [PMID: 30959972 PMCID: PMC6631176 DOI: 10.3390/pathogens8020047] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 03/26/2019] [Accepted: 03/28/2019] [Indexed: 12/26/2022] Open
Abstract
Apicomplexan parasites are protozoan organisms that are characterised by complex life cycles and they include medically important species, such as the malaria parasite Plasmodium and the causative agents of toxoplasmosis (Toxoplasma gondii) and cryptosporidiosis (Cryptosporidium spp.). Apicomplexan parasites can infect one or more hosts, in which they differentiate into several morphologically and metabolically distinct life cycle stages. These developmental transitions rely on changes in gene expression. In the last few years, the important roles of different members of the ApiAP2 transcription factor family in regulating life cycle transitions and other aspects of parasite biology have become apparent. Here, we review recent progress in our understanding of the different members of the ApiAP2 transcription factor family in apicomplexan parasites.
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Castillo AI, Nelson ADL, Lyons E. Tail Wags the Dog? Functional Gene Classes Driving Genome-Wide GC Content in Plasmodium spp. Genome Biol Evol 2019; 11:497-507. [PMID: 30689842 PMCID: PMC6385630 DOI: 10.1093/gbe/evz015] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/18/2019] [Indexed: 01/16/2023] Open
Abstract
Plasmodium parasites are valuable models to understand how nucleotide composition affects mutation, diversification, and adaptation. No other observed eukaryotes have undergone such large changes in genomic Guanine-Cytosine (GC) content as seen in the genus Plasmodium (∼30% within 35-40 Myr). Although mutational biases are known to influence GC content in the human-infective Plasmodium vivax and Plasmodium falciparum; no study has addressed how different gene functional classes contribute to genus-wide compositional changes, or if Plasmodium GC content variation is driven by natural selection. Here, we tested the hypothesis that certain gene processes and functions drive variation in global GC content between Plasmodium species. We performed a large-scale comparative genomic analysis using the genomes and predicted genes of 17 Plasmodium species encompassing a wide genomic GC content range. Genic GC content was sorted and divided into ten equally sized quantiles that were then assessed for functional enrichment classes. In agreement that selection on gene classes may drive genomic GC content, trans-membrane proteins were enriched within extreme GC content quantiles (Q1 and Q10). Specifically, variant surface antigens, which primarily interact with vertebrate immune systems, showed skewed GC content distributions compared with other trans-membrane proteins. Although a definitive causation linking GC content, expression, and positive selection within variant surface antigens from Plasmodium vivax, Plasmodium berghei, and Plasmodium falciparum could not be established, we found that regardless of genomic nucleotide composition, genic GC content and expression were positively correlated during trophozoite stages. Overall, these data suggest that, alongside mutational biases, functional protein classes drive Plasmodium GC content change.
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Affiliation(s)
- Andreina I Castillo
- School of Environmental Science, Policy, and Management, University of California, Berkeley
| | | | - Eric Lyons
- BIO5 Institute, School of Plant Sciences, University of Arizona
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Josling GA, Williamson KC, Llinás M. Regulation of Sexual Commitment and Gametocytogenesis in Malaria Parasites. Annu Rev Microbiol 2018; 72:501-519. [PMID: 29975590 DOI: 10.1146/annurev-micro-090817-062712] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Sexual differentiation of malaria parasites from the asexual blood stage into gametocytes is an essential part of the life cycle, as gametocytes are the form that is taken up by the mosquito host. Because of the essentiality of this process for transmission to the mosquito, gametocytogenesis is an extremely attractive target for therapeutic interventions. The subject of this review is the considerable progress that has been made in recent years in elucidating the molecular mechanisms governing this important differentiation process. In particular, a number of critical transcription factors and epigenetic regulators have emerged as crucial elements in the regulation of commitment. The identification of these factors has allowed us to understand better than ever before the events occurring prior to and during commitment to sexual development and offers potential for new therapeutic interventions.
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Affiliation(s)
- Gabrielle A Josling
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA; .,Huck Center for Malaria Research, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Kim C Williamson
- Microbiology and Immunology Department, Uniformed Services University of the Health Sciences, Bethesda, Maryland 20814, USA
| | - Manuel Llinás
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA; .,Huck Center for Malaria Research, Pennsylvania State University, University Park, Pennsylvania 16802, USA.,Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802, USA
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Araujo RBD, Silva TM, Kaiser CS, Leite GF, Alonso D, Ribolla PEM, Wunderlich G. Independent regulation of Plasmodium falciparum rif gene promoters. Sci Rep 2018; 8:9332. [PMID: 29921926 PMCID: PMC6008437 DOI: 10.1038/s41598-018-27646-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Accepted: 06/07/2018] [Indexed: 11/09/2022] Open
Abstract
All Plasmodium species express variant antigens which may mediate immune escape in the vertebrate host. In Plasmodium falciparum, the rif gene family encodes variant antigens which are partly exposed on the infected red blood cell surface and may function as virulence factors. Not all rif genes are expressed at the same time and it is unclear what controls rif gene expression. In this work, we addressed global rif transcription using plasmid vectors with two drug resistance markers, one controlled by a rif 5′ upstream region and the second by a constitutively active promoter. After spontaneous integration into the genome of one construct, we observed that the resistance marker controlled by the rif 5′ upstream region was expressed dependent on the applied drug pressure. Then, the global transcription of rif genes in these transfectants was compared in the presence or absence of drugs. The relative transcript quantities of all rif loci did not change profoundly between strains grown with or without drug. We conclude that either there is no crosstalk between rif loci or that the elusive system of allelic exclusion of rif gene transcription is not controlled by their 5′ upstream region alone.
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Affiliation(s)
- Rosana Beatriz Duque Araujo
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, Av. Prof. Lineu Prestes, 1374, São Paulo - SP, 05508000, Brazil
| | - Tatiane Macedo Silva
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, Av. Prof. Lineu Prestes, 1374, São Paulo - SP, 05508000, Brazil
| | - Charlotte Sophie Kaiser
- Institute of Animal Physiology, Schloßplatz 8, Westfälische Wilhelms Universität, Münster, Germany
| | - Gabriela Fernandes Leite
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, Av. Prof. Lineu Prestes, 1374, São Paulo - SP, 05508000, Brazil
| | - Diego Alonso
- Department of Parasitology, IBB/IBTEC, State University of São Paulo, Botucatu, São Paulo, Brazil
| | | | - Gerhard Wunderlich
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, Av. Prof. Lineu Prestes, 1374, São Paulo - SP, 05508000, Brazil.
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