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Min H, Liang X, Wang C, Qin J, Boonhok R, Muneer A, Brashear AM, Li X, Minns AM, Adapa SR, Jiang RHY, Ning G, Cao Y, Lindner SE, Miao J, Cui L. The DEAD-box RNA helicase PfDOZI imposes opposing actions on RNA metabolism in Plasmodium falciparum. Nat Commun 2024; 15:3747. [PMID: 38702310 PMCID: PMC11068891 DOI: 10.1038/s41467-024-48140-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 04/19/2024] [Indexed: 05/06/2024] Open
Abstract
In malaria parasites, the regulation of mRNA translation, storage and degradation during development and life-stage transitions remains largely unknown. Here, we functionally characterized the DEAD-box RNA helicase PfDOZI in P. falciparum. Disruption of pfdozi enhanced asexual proliferation but reduced sexual commitment and impaired gametocyte development. By quantitative transcriptomics, we show that PfDOZI is involved in the regulation of invasion-related genes and sexual stage-specific genes during different developmental stages. PfDOZI predominantly participates in processing body-like mRNPs in schizonts but germ cell granule-like mRNPs in gametocytes to impose opposing actions of degradation and protection on different mRNA targets. We further show the formation of stress granule-like mRNPs during nutritional deprivation, highlighting an essential role of PfDOZI-associated mRNPs in stress response. We demonstrate that PfDOZI participates in distinct mRNPs to maintain mRNA homeostasis in response to life-stage transition and environmental changes by differentially executing post-transcriptional regulation on the target mRNAs.
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Affiliation(s)
- Hui Min
- Department of Internal Medicine, Morsani College of Medicine, University of South Florida, 3720 Spectrum Boulevard, Tampa, FL, 33612, USA
- Department of Immunology, College of Basic Medical Sciences, China Medical University, Shenyang, Liaoning, China
| | - Xiaoying Liang
- Department of Internal Medicine, Morsani College of Medicine, University of South Florida, 3720 Spectrum Boulevard, Tampa, FL, 33612, USA
| | - Chengqi Wang
- Center for Global Health and Infectious Diseases, Department of Global Health, College of Public Health, University of South Florida, Tampa, FL, 33612, USA
| | - Junling Qin
- Department of Internal Medicine, Morsani College of Medicine, University of South Florida, 3720 Spectrum Boulevard, Tampa, FL, 33612, USA
| | - Rachasak Boonhok
- Department of Internal Medicine, Morsani College of Medicine, University of South Florida, 3720 Spectrum Boulevard, Tampa, FL, 33612, USA
- Department of Medical Technology, School of Allied Health Sciences, and Research Excellence Center for Innovation and Health Products (RECIHP), Walailak University, Nakhon Si Thammarat, 80160, Thailand
| | - Azhar Muneer
- Department of Internal Medicine, Morsani College of Medicine, University of South Florida, 3720 Spectrum Boulevard, Tampa, FL, 33612, USA
| | - Awtum M Brashear
- Department of Internal Medicine, Morsani College of Medicine, University of South Florida, 3720 Spectrum Boulevard, Tampa, FL, 33612, USA
| | - Xiaolian Li
- Department of Internal Medicine, Morsani College of Medicine, University of South Florida, 3720 Spectrum Boulevard, Tampa, FL, 33612, USA
| | - Allen M Minns
- Department of Biochemistry and Molecular Biology, Huck Center for Malaria Research, Pennsylvania State University, University Park, PA, 16802, USA
| | - Swamy Rakesh Adapa
- Center for Global Health and Infectious Diseases, Department of Global Health, College of Public Health, University of South Florida, Tampa, FL, 33612, USA
| | - Rays H Y Jiang
- Center for Global Health and Infectious Diseases, Department of Global Health, College of Public Health, University of South Florida, Tampa, FL, 33612, USA
| | - Gang Ning
- Electron Microscopy Facility, The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, 16802, USA
| | - Yaming Cao
- Department of Immunology, College of Basic Medical Sciences, China Medical University, Shenyang, Liaoning, China
| | - Scott E Lindner
- Department of Biochemistry and Molecular Biology, Huck Center for Malaria Research, Pennsylvania State University, University Park, PA, 16802, USA
| | - Jun Miao
- Department of Internal Medicine, Morsani College of Medicine, University of South Florida, 3720 Spectrum Boulevard, Tampa, FL, 33612, USA.
| | - Liwang Cui
- Department of Internal Medicine, Morsani College of Medicine, University of South Florida, 3720 Spectrum Boulevard, Tampa, FL, 33612, USA.
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2
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Wang C, Dong Y, Li C, Oberstaller J, Zhang M, Gibbons J, Pires CV, Xiao M, Zhu L, Jiang RHY, Kim K, Miao J, Otto TD, Cui L, Adams JH, Liu X. MalariaSED: a deep learning framework to decipher the regulatory contributions of noncoding variants in malaria parasites. Genome Biol 2023; 24:231. [PMID: 37845769 PMCID: PMC10577899 DOI: 10.1186/s13059-023-03063-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 09/19/2023] [Indexed: 10/18/2023] Open
Abstract
Malaria remains one of the deadliest infectious diseases. Transcriptional regulation effects of noncoding variants in this unusual genome of malaria parasites remain elusive. We developed a sequence-based, ab initio deep learning framework, MalariaSED, for predicting chromatin profiles in malaria parasites. The MalariaSED performance was validated by published ChIP-qPCR and TF motifs results. Applying MalariaSED to ~ 1.3 million variants shows that geographically differentiated noncoding variants are associated with parasite invasion and drug resistance. Further analysis reveals chromatin accessibility changes at Plasmodium falciparum rings are partly associated with artemisinin resistance. MalariaSED illuminates the potential functional roles of noncoding variants in malaria parasites.
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Affiliation(s)
- Chengqi Wang
- Center for Global Health and Infectious Diseases Research and USF Genomics Program, College of Public Health, University of South Florida, Tampa, FL, USA.
| | - Yibo Dong
- Center for Global Health and Infectious Diseases Research and USF Genomics Program, College of Public Health, University of South Florida, Tampa, FL, USA
- Present address: Florida Department of Health, Jacksonville, FL, USA
| | - Chang Li
- Center for Global Health and Infectious Diseases Research and USF Genomics Program, College of Public Health, University of South Florida, Tampa, FL, USA
| | - Jenna Oberstaller
- Center for Global Health and Infectious Diseases Research and USF Genomics Program, College of Public Health, University of South Florida, Tampa, FL, USA
| | - Min Zhang
- Center for Global Health and Infectious Diseases Research and USF Genomics Program, College of Public Health, University of South Florida, Tampa, FL, USA
| | - Justin Gibbons
- Center for Global Health and Infectious Diseases Research and USF Genomics Program, College of Public Health, University of South Florida, Tampa, FL, USA
| | - Camilla Valente Pires
- Center for Global Health and Infectious Diseases Research and USF Genomics Program, College of Public Health, University of South Florida, Tampa, FL, USA
| | - Mianli Xiao
- Center for Global Health and Infectious Diseases Research and USF Genomics Program, College of Public Health, University of South Florida, Tampa, FL, USA
- Department of Epidemiology and Biostatistics, College of Public Health, University of South Florida, Tampa, FL, USA
| | - Lei Zhu
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Rays H Y Jiang
- Center for Global Health and Infectious Diseases Research and USF Genomics Program, College of Public Health, University of South Florida, Tampa, FL, USA
| | - Kami Kim
- Department of Internal Medicine, Morsani College of Medicine, Tampa, FL, USA
| | - Jun Miao
- Department of Internal Medicine, Morsani College of Medicine, Tampa, FL, USA
| | - Thomas D Otto
- School of Infection & Immunity, MVLS, University of Glasgow, Glasgow, UK
| | - Liwang Cui
- Department of Internal Medicine, Morsani College of Medicine, Tampa, FL, USA
| | - John H Adams
- Center for Global Health and Infectious Diseases Research and USF Genomics Program, College of Public Health, University of South Florida, Tampa, FL, USA
| | - Xiaoming Liu
- Center for Global Health and Infectious Diseases Research and USF Genomics Program, College of Public Health, University of South Florida, Tampa, FL, USA
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Lucky AB, Wang C, Liu M, Liang X, Min H, Fan Q, Siddiqui FA, Adapa SR, Li X, Jiang RHY, Chen X, Cui L, Miao J. A type II protein arginine methyltransferase regulates merozoite invasion in Plasmodium falciparum. Commun Biol 2023; 6:659. [PMID: 37349497 PMCID: PMC10287762 DOI: 10.1038/s42003-023-05038-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 06/12/2023] [Indexed: 06/24/2023] Open
Abstract
Protein arginine methyltransferases (PRMTs) regulate many important cellular processes, such as transcription and RNA processing in model organisms but their functions in human malaria parasites are not elucidated. Here, we characterize PfPRMT5 in Plasmodium falciparum, which catalyzes symmetric dimethylation of histone H3 at R2 (H3R2me2s) and R8, and histone H4 at R3 in vitro. PfPRMT5 disruption results in asexual stage growth defects primarily due to lower invasion efficiency of the merozoites. Transcriptomic analysis reveals down-regulation of many transcripts related to invasion upon PfPRMT5 disruption, in agreement with H3R2me2s being an active chromatin mark. Genome-wide chromatin profiling detects extensive H3R2me2s marking of genes of different cellular processes, including invasion-related genes in wildtype parasites and PfPRMT5 disruption leads to the depletion of H3R2me2s. Interactome studies identify the association of PfPRMT5 with invasion-related transcriptional regulators such as AP2-I, BDP1, and GCN5. Furthermore, PfPRMT5 is associated with the RNA splicing machinery, and PfPRMT5 disruption caused substantial anomalies in RNA splicing events, including those for invasion-related genes. In summary, PfPRMT5 is critical for regulating parasite invasion and RNA splicing in this early-branching eukaryote.
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Affiliation(s)
- Amuza Byaruhanga Lucky
- Department of Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, USA
| | - Chengqi Wang
- Center for Global Health and Infectious Diseases, Department of Global Health, University of South Florida, Tampa, FL, 33612, USA
| | - Min Liu
- Department of Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, USA
- Department of Pathogen Biology, School of Public Health, Southern Medical University, Guangzhou, Guangdong, 510515, China
| | - Xiaoying Liang
- Department of Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, USA
| | - Hui Min
- Department of Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, USA
| | - Qi Fan
- Dalian Institute of Biotechnology, Dalian, Liaoning, China
| | - Faiza Amber Siddiqui
- Department of Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, USA
| | - Swamy Rakesh Adapa
- Center for Global Health and Infectious Diseases, Department of Global Health, University of South Florida, Tampa, FL, 33612, USA
| | - Xiaolian Li
- Department of Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, USA
| | - Rays H Y Jiang
- Center for Global Health and Infectious Diseases, Department of Global Health, University of South Florida, Tampa, FL, 33612, USA
| | - Xiaoguang Chen
- Department of Pathogen Biology, School of Public Health, Southern Medical University, Guangzhou, Guangdong, 510515, China
| | - Liwang Cui
- Department of Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, USA
| | - Jun Miao
- Department of Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, USA.
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Pires CV, Oberstaller J, Wang C, Casandra D, Zhang M, Chawla J, Adapa SR, Otto TD, Ferdig MT, Rayner JC, Jiang RHY, Adams JH. Chemogenomic Profiling of a Plasmodium falciparum Transposon Mutant Library Reveals Shared Effects of Dihydroartemisinin and Bortezomib on Lipid Metabolism and Exported Proteins. Microbiol Spectr 2023; 11:e0501422. [PMID: 37067430 PMCID: PMC10269874 DOI: 10.1128/spectrum.05014-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 03/21/2023] [Indexed: 04/18/2023] Open
Abstract
The antimalarial activity of the frontline drug artemisinin involves generation of reactive oxygen species (ROS) leading to oxidative damage of parasite proteins. To achieve homeostasis and maintain protein quality control in the overwhelmed parasite, the ubiquitin-proteasome system kicks in. Even though molecular markers for artemisinin resistance like pfkelch13 have been identified, the intricate network of mechanisms driving resistance remains to be elucidated. Here, we report a forward genetic screening strategy that enables a broader identification of genetic factors responsible for altering sensitivity to dihydroartemisinin (DHA) and a proteasome inhibitor, bortezomib (BTZ). Using a library of isogenic piggyBac mutants in P. falciparum, we defined phenotype-genotype associations influencing drug responses and highlighted shared mechanisms between the two processes, which mainly included proteasome-mediated degradation and the lipid metabolism genes. Additional transcriptomic analysis of a DHA/BTZ-sensitive piggyBac mutant showed it is possible to find differences between the two response mechanisms on the specific components for regulation of the exportome. Our results provide further insight into the molecular mechanisms of antimalarial drug resistance. IMPORTANCE Malaria control is seriously threatened by the emergence and spread of Plasmodium falciparum resistance to the leading antimalarial, artemisinin. The potent killing activity of artemisinin results from oxidative damage unleashed by free heme activation released by hemoglobin digestion. Although the ubiquitin-proteasome system is considered critical for parasite survival of this toxicity, the diverse genetic changes linked to artemisinin resistance are complex and, so far, have not included the ubiquitin-proteasome system. In this study, we use a systematic forward genetic approach by screening a library of P. falciparum random piggyBac mutants to decipher the genetic factors driving malaria parasite responses to the oxidative stress caused by antimalarial drugs. This study compares phenotype-genotype associations influencing dihydroartemisinin responses with the proteasome inhibitor bortezomib to delineate the role of ubiquitin-proteasome system. Our study highlights shared and unique pathways from the complex array of molecular processes critical for P. falciparum survival resulting from the oxidative damage of artemisinin.
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Affiliation(s)
- Camilla Valente Pires
- Center for Global Health and Infectious Diseases Research, College of Public Health, University of South Florida, Tampa, Florida, USA
- USF Genomics Program, College of Public Health, University of South Florida, Tampa, Florida, USA
| | - Jenna Oberstaller
- Center for Global Health and Infectious Diseases Research, College of Public Health, University of South Florida, Tampa, Florida, USA
- USF Genomics Program, College of Public Health, University of South Florida, Tampa, Florida, USA
| | - Chengqi Wang
- Center for Global Health and Infectious Diseases Research, College of Public Health, University of South Florida, Tampa, Florida, USA
- USF Genomics Program, College of Public Health, University of South Florida, Tampa, Florida, USA
| | - Debora Casandra
- Center for Global Health and Infectious Diseases Research, College of Public Health, University of South Florida, Tampa, Florida, USA
- USF Genomics Program, College of Public Health, University of South Florida, Tampa, Florida, USA
| | - Min Zhang
- Center for Global Health and Infectious Diseases Research, College of Public Health, University of South Florida, Tampa, Florida, USA
- USF Genomics Program, College of Public Health, University of South Florida, Tampa, Florida, USA
| | - Jyotsna Chawla
- Center for Global Health and Infectious Diseases Research, College of Public Health, University of South Florida, Tampa, Florida, USA
- USF Genomics Program, College of Public Health, University of South Florida, Tampa, Florida, USA
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, United States
| | - Swamy Rakesh Adapa
- Center for Global Health and Infectious Diseases Research, College of Public Health, University of South Florida, Tampa, Florida, USA
- USF Genomics Program, College of Public Health, University of South Florida, Tampa, Florida, USA
| | - Thomas D. Otto
- Institute of Infection, Immunity and Inflammation, MVLS, University of Glasgow, Glasgow, United Kingdom
| | - Michael T. Ferdig
- Eck Institute for Global Health, Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, USA
| | - Julian C. Rayner
- Cambridge Institute for Medical Research, Cambridge Biomedical Campus, University of Cambridge, Cambridge, United Kingdom
| | - Rays H. Y. Jiang
- Center for Global Health and Infectious Diseases Research, College of Public Health, University of South Florida, Tampa, Florida, USA
- USF Genomics Program, College of Public Health, University of South Florida, Tampa, Florida, USA
| | - John H. Adams
- Center for Global Health and Infectious Diseases Research, College of Public Health, University of South Florida, Tampa, Florida, USA
- USF Genomics Program, College of Public Health, University of South Florida, Tampa, Florida, USA
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5
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Downs CJ, Schoenle LA, Goolsby EW, Oakey SJ, Ball R, Jiang RHY, Martin LB. Large Mammals Have More Powerful Antibacterial Defenses Than Expected from Their Metabolic Rates. Am Nat 2023; 201:287-301. [PMID: 36724463 DOI: 10.1086/722504] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
AbstractTerrestrial mammals span seven orders of magnitude in body size, ranging from the <2-g Etruscan pygmy shrew (Suncus etruscus) to the >3,900-kg African elephant (Loxodonta africana). Although body size profoundly affects the behavior, physiology, ecology, and evolution of species, how investment in functional immune defenses changes with body size across species is unknown. Here, we (1) developed a novel 12-point dilution curve approach to describe and compare antibacterial capacity against three bacterial species among >160 terrestrial species of mammals and (2) tested published predictions about the scaling of immune defenses. Our study focused on the safety factor hypothesis, which predicts that broad, early-acting immune defenses should scale hypermetrically with body mass. However, our three statistical approaches demonstrated that antibacterial activity in sera across mammals exhibits isometry; killing capacity did not change with body size across species. Intriguingly, this result indicates that the serum of a large mammal is less hospitable to bacteria than would be predicted by its metabolic rates. In other words, if metabolic rates underlie the rates of physiological reactions as postulated by the metabolic theory of ecology, large species should have disproportionately lower antibacterial capacity than small species, but they do not. These results have direct implications for effectively modeling the evolution of immune defenses and identifying potential reservoir hosts of pathogens.
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Sacco MD, Wang S, Adapa SR, Zhang X, Lewandowski EM, Gongora MV, Keramisanou D, Atlas ZD, Townsend JA, Gatdula JR, Morgan RT, Hammond LR, Marty MT, Wang J, Eswara PJ, Gelis I, Jiang RHY, Sun X, Chen Y. A unique class of Zn 2+-binding serine-based PBPs underlies cephalosporin resistance and sporogenesis in Clostridioides difficile. Nat Commun 2022; 13:4370. [PMID: 35902581 PMCID: PMC9334274 DOI: 10.1038/s41467-022-32086-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 07/18/2022] [Indexed: 11/17/2022] Open
Abstract
Treatment with β-lactam antibiotics, particularly cephalosporins, is a major risk factor for Clostridioides difficile infection. These broad-spectrum antibiotics irreversibly inhibit penicillin-binding proteins (PBPs), which are serine-based enzymes that assemble the bacterial cell wall. However, C. difficile has four different PBPs (PBP1-3 and SpoVD) with various roles in growth and spore formation, and their specific links to β-lactam resistance in this pathogen are underexplored. Here, we show that PBP2 (known to be essential for vegetative growth) is the primary bactericidal target for β-lactams in C. difficile. PBP2 is insensitive to cephalosporin inhibition, and this appears to be the main basis for cephalosporin resistance in this organism. We determine crystal structures of C. difficile PBP2, alone and in complex with β-lactams, revealing unique features including ligand-induced conformational changes and an active site Zn2+-binding motif that influences β-lactam binding and protein stability. The Zn2+-binding motif is also present in C. difficile PBP3 and SpoVD (which are known to be essential for sporulation), as well as in other bacterial taxa including species living in extreme environments and the human gut. We speculate that this thiol-containing motif and its cognate Zn2+ might function as a redox sensor to regulate cell wall synthesis for survival in adverse or anaerobic environments.
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Affiliation(s)
- Michael D. Sacco
- grid.170693.a0000 0001 2353 285XDepartment of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612 USA
| | - Shaohui Wang
- grid.170693.a0000 0001 2353 285XDepartment of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612 USA
| | - Swamy R. Adapa
- grid.170693.a0000 0001 2353 285XDepartment of Global and Planetary Health, USF Genomics Program, Global Health and Infectious Disease Center, College of Public Health, University of South Florida, Tampa, FL 33620 USA
| | - Xiujun Zhang
- grid.170693.a0000 0001 2353 285XDepartment of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612 USA
| | - Eric M. Lewandowski
- grid.170693.a0000 0001 2353 285XDepartment of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612 USA
| | - Maura V. Gongora
- grid.170693.a0000 0001 2353 285XDepartment of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612 USA
| | - Dimitra Keramisanou
- grid.170693.a0000 0001 2353 285XDepartment of Chemistry, University of South Florida, Tampa, FL 33620 USA
| | - Zachary D. Atlas
- grid.170693.a0000 0001 2353 285XSchool of Geosciences, University of South Florida, Tampa, FL 33620 USA
| | - Julia A. Townsend
- grid.134563.60000 0001 2168 186XDepartment of Chemistry and Biochemistry, The University of Arizona, Tucson, AZ 85721 USA
| | - Jean R. Gatdula
- grid.170693.a0000 0001 2353 285XDepartment of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612 USA
| | - Ryan T. Morgan
- grid.170693.a0000 0001 2353 285XDepartment of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612 USA
| | - Lauren R. Hammond
- grid.170693.a0000 0001 2353 285XDepartment of Cell Biology, Microbiology, and Molecular Biology, University of South Florida, Tampa, FL 33620 USA
| | - Michael T. Marty
- grid.134563.60000 0001 2168 186XDepartment of Chemistry and Biochemistry, The University of Arizona, Tucson, AZ 85721 USA
| | - Jun Wang
- grid.430387.b0000 0004 1936 8796Department of Medicinal Chemistry, Ernest Mario School of Pharmacy, Rutgers, the State University of New Jersey, Piscataway, NJ 08854 USA
| | - Prahathees J. Eswara
- grid.170693.a0000 0001 2353 285XDepartment of Cell Biology, Microbiology, and Molecular Biology, University of South Florida, Tampa, FL 33620 USA
| | - Ioannis Gelis
- grid.170693.a0000 0001 2353 285XDepartment of Chemistry, University of South Florida, Tampa, FL 33620 USA
| | - Rays H. Y. Jiang
- grid.170693.a0000 0001 2353 285XDepartment of Global and Planetary Health, USF Genomics Program, Global Health and Infectious Disease Center, College of Public Health, University of South Florida, Tampa, FL 33620 USA
| | - Xingmin Sun
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, USA.
| | - Yu Chen
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, USA.
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7
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Maher SP, Vantaux A, Chaumeau V, Chua ACY, Cooper CA, Andolina C, Péneau J, Rouillier M, Rizopoulos Z, Phal S, Piv E, Vong C, Phen S, Chhin C, Tat B, Ouk S, Doeurk B, Kim S, Suriyakan S, Kittiphanakun P, Awuku NA, Conway AJ, Jiang RHY, Russell B, Bifani P, Campo B, Nosten F, Witkowski B, Kyle DE. Probing the distinct chemosensitivity of Plasmodium vivax liver stage parasites and demonstration of 8-aminoquinoline radical cure activity in vitro. Sci Rep 2021; 11:19905. [PMID: 34620901 PMCID: PMC8497498 DOI: 10.1038/s41598-021-99152-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 09/21/2021] [Indexed: 12/25/2022] Open
Abstract
Improved control of Plasmodium vivax malaria can be achieved with the discovery of new antimalarials with radical cure efficacy, including prevention of relapse caused by hypnozoites residing in the liver of patients. We screened several compound libraries against P. vivax liver stages, including 1565 compounds against mature hypnozoites, resulting in one drug-like and several probe-like hits useful for investigating hypnozoite biology. Primaquine and tafenoquine, administered in combination with chloroquine, are currently the only FDA-approved antimalarials for radical cure, yet their activity against mature P. vivax hypnozoites has not yet been demonstrated in vitro. By developing an extended assay, we show both drugs are individually hypnozonticidal and made more potent when partnered with chloroquine, similar to clinically relevant combinations. Post-hoc analyses of screening data revealed excellent performance of ionophore controls and the high quality of single point assays, demonstrating a platform able to support screening of greater compound numbers. A comparison of P. vivax liver stage activity data with that of the P. cynomolgi blood, P. falciparum blood, and P. berghei liver stages reveals overlap in schizonticidal but not hypnozonticidal activity, indicating that the delivery of new radical curative agents killing P. vivax hypnozoites requires an independent and focused drug development test cascade.
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Affiliation(s)
- Steven P Maher
- Center for Tropical and Emerging Global Diseases, University of Georgia, 500 DW Brooks Dr. Suite 370, Athens, GA, 30602, USA.
| | - Amélie Vantaux
- Malaria Molecular Epidemiology Unit, Institut Pasteur du Cambodge, 5 Boulevard Monivong, PO Box 983, Phnom Penh, 12201, Cambodia
| | - Victor Chaumeau
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, 68/30 Bantung Rd., Mae Sot, Tak, 63110, Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine Research Building, University of Oxford, Old Road Campus, Oxford, UK
| | - Adeline C Y Chua
- Infectious Diseases Laboratories (ID Labs), Agency for Science, Technology and Research (A*STAR), Immunos, Biopolis, Singapore, 138648, Singapore
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Caitlin A Cooper
- Center for Tropical and Emerging Global Diseases, University of Georgia, 500 DW Brooks Dr. Suite 370, Athens, GA, 30602, USA
| | - Chiara Andolina
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, 68/30 Bantung Rd., Mae Sot, Tak, 63110, Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine Research Building, University of Oxford, Old Road Campus, Oxford, UK
| | - Julie Péneau
- Malaria Molecular Epidemiology Unit, Institut Pasteur du Cambodge, 5 Boulevard Monivong, PO Box 983, Phnom Penh, 12201, Cambodia
| | - Mélanie Rouillier
- Medicines for Malaria Venture (MMV), Route de Pré-Bois 20, 1215, Geneva, Switzerland
| | - Zaira Rizopoulos
- Medicines for Malaria Venture (MMV), Route de Pré-Bois 20, 1215, Geneva, Switzerland
| | - Sivchheng Phal
- Malaria Molecular Epidemiology Unit, Institut Pasteur du Cambodge, 5 Boulevard Monivong, PO Box 983, Phnom Penh, 12201, Cambodia
| | - Eakpor Piv
- Malaria Molecular Epidemiology Unit, Institut Pasteur du Cambodge, 5 Boulevard Monivong, PO Box 983, Phnom Penh, 12201, Cambodia
| | - Chantrea Vong
- Malaria Molecular Epidemiology Unit, Institut Pasteur du Cambodge, 5 Boulevard Monivong, PO Box 983, Phnom Penh, 12201, Cambodia
| | - Sreyvouch Phen
- Malaria Molecular Epidemiology Unit, Institut Pasteur du Cambodge, 5 Boulevard Monivong, PO Box 983, Phnom Penh, 12201, Cambodia
| | - Chansophea Chhin
- Malaria Molecular Epidemiology Unit, Institut Pasteur du Cambodge, 5 Boulevard Monivong, PO Box 983, Phnom Penh, 12201, Cambodia
| | - Baura Tat
- Malaria Molecular Epidemiology Unit, Institut Pasteur du Cambodge, 5 Boulevard Monivong, PO Box 983, Phnom Penh, 12201, Cambodia
| | - Sivkeng Ouk
- Malaria Molecular Epidemiology Unit, Institut Pasteur du Cambodge, 5 Boulevard Monivong, PO Box 983, Phnom Penh, 12201, Cambodia
| | - Bros Doeurk
- Malaria Molecular Epidemiology Unit, Institut Pasteur du Cambodge, 5 Boulevard Monivong, PO Box 983, Phnom Penh, 12201, Cambodia
| | - Saorin Kim
- Malaria Molecular Epidemiology Unit, Institut Pasteur du Cambodge, 5 Boulevard Monivong, PO Box 983, Phnom Penh, 12201, Cambodia
| | - Sangrawee Suriyakan
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, 68/30 Bantung Rd., Mae Sot, Tak, 63110, Thailand
| | - Praphan Kittiphanakun
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, 68/30 Bantung Rd., Mae Sot, Tak, 63110, Thailand
| | - Nana Akua Awuku
- Center for Tropical and Emerging Global Diseases, University of Georgia, 500 DW Brooks Dr. Suite 370, Athens, GA, 30602, USA
| | - Amy J Conway
- Department of Global Health, College of Public Health, Center for Global Health and Infectious Disease Research, University of South Florida, 3720 Spectrum Blvd Suite 402, Tampa, FL, 33612, USA
| | - Rays H Y Jiang
- Department of Global Health, College of Public Health, Center for Global Health and Infectious Disease Research, University of South Florida, 3720 Spectrum Blvd Suite 402, Tampa, FL, 33612, USA
| | - Bruce Russell
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Pablo Bifani
- Infectious Diseases Laboratories (ID Labs), Agency for Science, Technology and Research (A*STAR), Immunos, Biopolis, Singapore, 138648, Singapore
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117545, Singapore
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
| | - Brice Campo
- Medicines for Malaria Venture (MMV), Route de Pré-Bois 20, 1215, Geneva, Switzerland
| | - François Nosten
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, 68/30 Bantung Rd., Mae Sot, Tak, 63110, Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine Research Building, University of Oxford, Old Road Campus, Oxford, UK
| | - Benoît Witkowski
- Malaria Molecular Epidemiology Unit, Institut Pasteur du Cambodge, 5 Boulevard Monivong, PO Box 983, Phnom Penh, 12201, Cambodia.
| | - Dennis E Kyle
- Center for Tropical and Emerging Global Diseases, University of Georgia, 500 DW Brooks Dr. Suite 370, Athens, GA, 30602, USA.
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8
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Kernbach ME, Martin LB, Unnasch TR, Hall RJ, Jiang RHY, Francis CD. Light pollution affects West Nile virus exposure risk across Florida. Proc Biol Sci 2021; 288:20210253. [PMID: 33757351 PMCID: PMC8059973 DOI: 10.1098/rspb.2021.0253] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 03/02/2021] [Indexed: 12/19/2022] Open
Abstract
Emerging infectious diseases (EIDs) present global health threats, and their emergences are often linked to anthropogenic change. Artificial light at night (ALAN) is one form of anthropogenic change that spans beyond urban boundaries and may be relevant to EIDs through its influence on the behaviour and physiology of hosts and/or vectors. Although West Nile virus (WNV) emergence has been described as peri-urban, we hypothesized that exposure risk could also be influenced by ALAN in particular, which is testable by comparing the effects of ALAN on prevalence while controlling for other aspects of urbanization. By modelling WNV exposure among sentinel chickens in Florida, we found strong support for a nonlinear relationship between ALAN and WNV exposure risk in chickens with peak WNV risk occurring at low ALAN levels. Although our goal was not to discern how ALAN affected WNV relative to other factors, effects of ALAN on WNV exposure were stronger than other known drivers of risk (i.e. impervious surface, human population density). Ambient temperature in the month prior to sampling, but no other considered variables, strongly influenced WNV risk. These results indicate that ALAN may contribute to spatio-temporal changes in WNV risk, justifying future investigations of ALAN on other vector-borne parasites.
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Affiliation(s)
- Meredith E. Kernbach
- Center for Global Health and Infectious Disease Research, College of Public Health, University of South Florida, 3720 Spectrum Blvd., Tampa, FL 33612, USA
| | - Lynn B. Martin
- Center for Global Health and Infectious Disease Research, College of Public Health, University of South Florida, 3720 Spectrum Blvd., Tampa, FL 33612, USA
| | - Thomas R. Unnasch
- Center for Global Health and Infectious Disease Research, College of Public Health, University of South Florida, 3720 Spectrum Blvd., Tampa, FL 33612, USA
| | - Richard J. Hall
- Odum School of Ecology and Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, 501 D.W. Brooks Dr., Athens, GA 30602, USA
| | - Rays H. Y. Jiang
- Center for Global Health and Infectious Disease Research, College of Public Health, University of South Florida, 3720 Spectrum Blvd., Tampa, FL 33612, USA
| | - Clinton D. Francis
- Department of Biological Sciences, California Polytechnic State University, 1 Grand Ave., San Luis Obispo, CA 93407, USA
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9
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Liu X, Cragun D, Pang J, Adapa SR, Fonseca R, Jiang RHY. False Alarms in Consumer Genomics Add to Public Fear and Potential Health Care Burden. J Pers Med 2020; 10:jpm10040187. [PMID: 33113957 PMCID: PMC7712761 DOI: 10.3390/jpm10040187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 10/03/2020] [Accepted: 10/19/2020] [Indexed: 11/16/2022] Open
Abstract
We have entered an era of direct-to-consumer (DTC) genomics. Patients have relayed many success stories of DTC genomics about finding causal mutations of genetic diseases before showing any symptoms and taking precautions. However, consumers may also take unnecessary medical actions based on false alarms of “pathogenic alleles”. The severity of this problem is not well known. Using publicly available data, we compared DTC microarray genotyping data with deep-sequencing data of 5 individuals and manually checked each inconsistently reported single nucleotide variants (SNVs). We estimated that, on average, a person would have ~5 “pathogenic” alleles reported due to wrongly reported genotypes if using a 23andMe genotyping microarray. We also found that the number of wrongly classified “pathogenic” alleles per person is at least as significant as those due to wrongly reported genotypes. We show that the scale of the false alarm problem could be large enough that the medical costs will become a burden to public health.
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Affiliation(s)
- Xiaoming Liu
- College of Public Health, University of South Florida, Tampa, FL 33612, USA; (D.C.); (J.P.); (S.R.A.); (R.H.Y.J.)
- Correspondence:
| | - Deborah Cragun
- College of Public Health, University of South Florida, Tampa, FL 33612, USA; (D.C.); (J.P.); (S.R.A.); (R.H.Y.J.)
| | - Jinyong Pang
- College of Public Health, University of South Florida, Tampa, FL 33612, USA; (D.C.); (J.P.); (S.R.A.); (R.H.Y.J.)
| | - Swamy R. Adapa
- College of Public Health, University of South Florida, Tampa, FL 33612, USA; (D.C.); (J.P.); (S.R.A.); (R.H.Y.J.)
| | - Renee Fonseca
- Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA;
| | - Rays H. Y. Jiang
- College of Public Health, University of South Florida, Tampa, FL 33612, USA; (D.C.); (J.P.); (S.R.A.); (R.H.Y.J.)
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10
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Wang C, Gibbons J, Adapa SR, Oberstaller J, Liao X, Zhang M, Adams JH, Jiang RHY. The human malaria parasite genome is configured into thousands of coexpressed linear regulatory units. J Genet Genomics 2020; 47:513-521. [PMID: 33272860 DOI: 10.1016/j.jgg.2020.08.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Revised: 08/07/2020] [Accepted: 08/28/2020] [Indexed: 12/27/2022]
Abstract
The human malaria parasite Plasmodium falciparum thrives in radically different host environments in mosquitoes and humans, with only a limited set of transcription factors. The nature of regulatory elements or their target genes in the P. falciparum genome remains elusive. Here, we found that this eukaryotic parasite uses an efficient way to maximally use genetic and epigenetic regulation to form regulatory units (RUs) during blood infections. Genes located in the same RU tend to have the same pattern of expression over time and are associated with open chromatin along regulatory elements. To precisely define and quantify these RUs, a novel hidden Markov model was developed to capture the regulatory structure in a genome-wide fashion by integrating expression and epigenetic evidence. We successfully identified thousands of RUs and cross-validated with previous findings. We found more genes involved in red blood cell (RBC) invasion located in the same RU as the PfAP2-I (AP2-I) transcription factor, demonstrating that AP2-I is responsible for regulating RBC invasion. Our study has provided a regulatory mechanism for a compact eukaryotic genome and offers new insights into the in vivo transcriptional regulation of the P. falciparum intraerythrocytic stage.
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Affiliation(s)
- Chengqi Wang
- Global and Planetary Health, USF Genomics, College of Public Health, University of South Florida, Tampa, FL 33612, USA
| | - Justin Gibbons
- Global and Planetary Health, USF Genomics, College of Public Health, University of South Florida, Tampa, FL 33612, USA
| | - Swamy R Adapa
- Global and Planetary Health, USF Genomics, College of Public Health, University of South Florida, Tampa, FL 33612, USA
| | - Jenna Oberstaller
- Global and Planetary Health, USF Genomics, College of Public Health, University of South Florida, Tampa, FL 33612, USA
| | - Xiangyun Liao
- Global and Planetary Health, USF Genomics, College of Public Health, University of South Florida, Tampa, FL 33612, USA
| | - Min Zhang
- Global and Planetary Health, USF Genomics, College of Public Health, University of South Florida, Tampa, FL 33612, USA
| | - John H Adams
- Global and Planetary Health, USF Genomics, College of Public Health, University of South Florida, Tampa, FL 33612, USA
| | - Rays H Y Jiang
- Global and Planetary Health, USF Genomics, College of Public Health, University of South Florida, Tampa, FL 33612, USA.
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11
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Maher SP, Conway AJ, Roth A, Adapa SR, Cualing P, Andolina C, Hsiao J, Turgeon J, Chaumeau V, Johnson M, Palmiotti C, Singh N, Barnes SJ, Patel R, Van Grod V, Carter R, Sun HCS, Sattabongkot J, Campo B, Nosten F, Saadi WM, Adams JH, Jiang RHY, Kyle DE. An adaptable soft-mold embossing process for fabricating optically-accessible, microfeature-based culture systems and application toward liver stage antimalarial compound testing. Lab Chip 2020; 20:1124-1139. [PMID: 32055808 DOI: 10.1039/c9lc00921c] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Advanced cell culture methods for modeling organ-level structure have been demonstrated to replicate in vivo conditions more accurately than traditional in vitro cell culture. Given that the liver is particularly important to human health, several advanced culture methods have been developed to experiment with liver disease states, including infection with Plasmodium parasites, the causative agent of malaria. These models have demonstrated that intrahepatic parasites require functionally stable hepatocytes to thrive and robust characterization of the parasite populations' response to investigational therapies is dependent on high-content and high-resolution imaging (HC/RI). We previously reported abiotic confinement extends the functional longevity of primary hepatocytes in a microfluidic platform and set out to instill confinement in a microtiter plate platform while maintaining optical accessibility for HC/RI; with an end-goal of producing an improved P. vivax liver stage culture model. We developed a novel fabrication process in which a PDMS soft mold embosses hepatocyte-confining microfeatures into polystyrene, resulting in microfeature-based hepatocyte confinement (μHEP) slides and plates. Our process was optimized to form both microfeatures and culture wells in a single embossing step, resulting in a 100 μm-thick bottom ideal for HC/RI, and was found inexpensively amendable to microfeature design changes. Microfeatures improved intrahepatic parasite infection rates and μHEP systems were used to reconfirm the activity of reference antimalarials in phenotypic dose-response assays. RNAseq of hepatocytes in μHEP systems demonstrated microfeatures sustain hepatic differentiation and function, suggesting broader utility for preclinical hepatic assays; while our tailorable embossing process could be repurposed for developing additional organ models.
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Affiliation(s)
- Steven P Maher
- Center for Global Health and Infectious Diseases Research, Department of Global Health, College of Public Health, University of South Florida, Tampa, Florida, USA. and Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA, USA
| | - Amy J Conway
- Center for Global Health and Infectious Diseases Research, Department of Global Health, College of Public Health, University of South Florida, Tampa, Florida, USA.
| | - Alison Roth
- Center for Global Health and Infectious Diseases Research, Department of Global Health, College of Public Health, University of South Florida, Tampa, Florida, USA.
| | - Swamy R Adapa
- Center for Global Health and Infectious Diseases Research, Department of Global Health, College of Public Health, University of South Florida, Tampa, Florida, USA.
| | - Phillip Cualing
- Center for Global Health and Infectious Diseases Research, Department of Global Health, College of Public Health, University of South Florida, Tampa, Florida, USA.
| | - Chiara Andolina
- Shoklo Malaria Research Unit, Mahidol Oxford Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand & Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - James Hsiao
- Charles Stark Draper Laboratory, Cambridge, MA, USA
| | - Jessica Turgeon
- Center for Global Health and Infectious Diseases Research, Department of Global Health, College of Public Health, University of South Florida, Tampa, Florida, USA.
| | - Victor Chaumeau
- Shoklo Malaria Research Unit, Mahidol Oxford Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand & Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Myles Johnson
- Center for Global Health and Infectious Diseases Research, Department of Global Health, College of Public Health, University of South Florida, Tampa, Florida, USA.
| | | | - Naresh Singh
- Center for Global Health and Infectious Diseases Research, Department of Global Health, College of Public Health, University of South Florida, Tampa, Florida, USA.
| | - Samantha J Barnes
- Center for Global Health and Infectious Diseases Research, Department of Global Health, College of Public Health, University of South Florida, Tampa, Florida, USA.
| | - Raahil Patel
- Center for Global Health and Infectious Diseases Research, Department of Global Health, College of Public Health, University of South Florida, Tampa, Florida, USA.
| | | | - Robert Carter
- Center for Global Health and Infectious Diseases Research, Department of Global Health, College of Public Health, University of South Florida, Tampa, Florida, USA.
| | | | - Jetsumon Sattabongkot
- Mahidol Vivax Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Brice Campo
- Medicines for Malaria Venture, Geneva, Switzerland
| | - François Nosten
- Shoklo Malaria Research Unit, Mahidol Oxford Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand & Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | - John H Adams
- Center for Global Health and Infectious Diseases Research, Department of Global Health, College of Public Health, University of South Florida, Tampa, Florida, USA.
| | - Rays H Y Jiang
- Center for Global Health and Infectious Diseases Research, Department of Global Health, College of Public Health, University of South Florida, Tampa, Florida, USA.
| | - Dennis E Kyle
- Center for Global Health and Infectious Diseases Research, Department of Global Health, College of Public Health, University of South Florida, Tampa, Florida, USA. and Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA, USA
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12
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Stojanovski BM, Hunter GA, Na I, Uversky VN, Jiang RHY, Ferreira GC. 5-Aminolevulinate synthase catalysis: The catcher in heme biosynthesis. Mol Genet Metab 2019; 128:178-189. [PMID: 31345668 PMCID: PMC6908770 DOI: 10.1016/j.ymgme.2019.06.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 05/27/2019] [Accepted: 06/07/2019] [Indexed: 01/26/2023]
Abstract
5-Aminolevulinate (ALA) synthase (ALAS), a homodimeric pyridoxal-5'-phosphate (PLP)-dependent enzyme, catalyzes the first step of heme biosynthesis in metazoa, fungi and α-proteobacteria. In this review, we focus on the advances made in unraveling the mechanism of the ALAS-catalyzed reaction during the past decade. The interplay between the PLP cofactor and the protein moiety determines and modulates the multi-intermediate reaction cycle of ALAS, which involves the decarboxylative condensation of two substrates, glycine and succinyl-CoA. Substrate binding and catalysis are rapid, and product (ALA) release dominates the overall ALAS kinetic mechanism. Interconversion between a catalytically incompetent, open conformation and a catalytically competent, closed conformation is linked to ALAS catalysis. Reversion to the open conformation, coincident with ALA dissociation, defines the slowest step of the reaction cycle. These findings were further substantiated by introducing seven mutations in the16-amino acid loop that gates the active site, yielding an ALAS variant with a greatly increased rate of catalytic turnover and heightened specificity constants for both substrates. Recently, molecular dynamics (MD) simulation analysis of various dimeric ALAS forms revealed that the seven active site loop mutations caused the proteins to adopt different conformations. In particular, the emergence of a β-strand in the mutated loop, which interacted with two preexisting β-strands to form an anti-parallel three-stranded β-sheet, conferred the murine heptavariant with a more stable open conformation and prompted faster product release than wild-type mALAS2. Moreover, the dynamics of the mALAS2 active site loop anti-correlated with that of the 35 amino acid C-terminal sequence. This led us to propose that this C-terminal extension, which is absent in prokaryotic ALASs, finely tunes mammalian ALAS activity. Based on the above results, we extend our previous proposal to include that discovery of a ligand inducing the mammalian C-terminal extension to fold offers a good prospect for the development of a new drug for X-linked protoporphyria and/or other porphyrias associated with enhanced ALAS activity and/or porphyrin accumulation.
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Affiliation(s)
- Bosko M Stojanovski
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA.
| | - Gregory A Hunter
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
| | - Insung Na
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA.
| | - Vladimir N Uversky
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA; USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA; Institute for Biological Instrumentation of the Russian Academy of Sciences, Pushchino, Moscow region 142290, Russia
| | - Rays H Y Jiang
- Department of Global Health, College of Public Health, University of South Florida, Tampa, FL 33612, USA
| | - Gloria C Ferreira
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA; Department of Global Health, College of Public Health, University of South Florida, Tampa, FL 33612, USA; Department of Chemistry, College of Arts and Sciences, University of South Florida, Tampa, FL 33612, USA.
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13
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Kernbach ME, Newhouse DJ, Miller JM, Hall RJ, Gibbons J, Oberstaller J, Selechnik D, Jiang RHY, Unnasch TR, Balakrishnan CN, Martin LB. Light pollution increases West Nile virus competence of a ubiquitous passerine reservoir species. Proc Biol Sci 2019; 286:20191051. [PMID: 31337318 DOI: 10.1098/rspb.2019.1051] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Among the many anthropogenic changes that impact humans and wildlife, one of the most pervasive but least understood is light pollution. Although detrimental physiological and behavioural effects resulting from exposure to light at night are widely appreciated, the impacts of light pollution on infectious disease risk have not been studied. Here, we demonstrate that artificial light at night (ALAN) extends the infectious-to-vector period of the house sparrow (Passer domesticus), an urban-dwelling avian reservoir host of West Nile virus (WNV). Sparrows exposed to ALAN maintained transmissible viral titres for 2 days longer than controls but did not experience greater WNV-induced mortality during this window. Transcriptionally, ALAN altered the expression of gene regulatory networks including key hubs (OASL, PLBD1 and TRAP1) and effector genes known to affect WNV dissemination (SOCS). Despite mounting anti-viral immune responses earlier, transcriptomic signatures indicated that ALAN-exposed individuals probably experienced pathogen-induced damage and immunopathology, potentially due to evasion of immune effectors. A simple mathematical modelling exercise indicated that ALAN-induced increases of host infectious-to-vector period could increase WNV outbreak potential by approximately 41%. ALAN probably affects other host and vector traits relevant to transmission, and additional research is needed to advise the management of zoonotic diseases in light-polluted areas.
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Affiliation(s)
- Meredith E Kernbach
- Center for Global Health Infectious Disease Research, University of South Florida, Tampa, FL 33620, USA
| | - Daniel J Newhouse
- Department of Biology, East Carolina University, Greenville, NC 27858, USA
| | - Jeanette M Miller
- Center for Global Health Infectious Disease Research, University of South Florida, Tampa, FL 33620, USA
| | - Richard J Hall
- Center for the Ecology of Infectious Diseases, Odum School of Ecology and Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA 30602, USA
| | - Justin Gibbons
- Center for Global Health Infectious Disease Research, University of South Florida, Tampa, FL 33620, USA.,Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33620, USA
| | - Jenna Oberstaller
- Center for Global Health Infectious Disease Research, University of South Florida, Tampa, FL 33620, USA
| | - Daniel Selechnik
- School of Life and Environmental Sciences (SOLES), University of Sydney, Sydney 2006, Australia
| | - Rays H Y Jiang
- Center for Global Health Infectious Disease Research, University of South Florida, Tampa, FL 33620, USA
| | - Thomas R Unnasch
- Center for Global Health Infectious Disease Research, University of South Florida, Tampa, FL 33620, USA
| | | | - Lynn B Martin
- Center for Global Health Infectious Disease Research, University of South Florida, Tampa, FL 33620, USA
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14
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Ferreira GC, Oberstaller J, Fonseca R, Keller TE, Adapa SR, Gibbons J, Wang C, Liu X, Li C, Pham M, Dayhoff Ii GW, Duong LM, Reyes LT, Laratelli LE, Franz D, Fatumo S, Bari AG, Freischel A, Fiedler L, Dokur O, Sharma K, Cragun D, Busby B, Jiang RHY. Iron Hack - A symposium/hackathon focused on porphyrias, Friedreich's ataxia, and other rare iron-related diseases. F1000Res 2019; 8:1135. [PMID: 31824661 PMCID: PMC6894363 DOI: 10.12688/f1000research.19140.1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/05/2019] [Indexed: 01/14/2023] Open
Abstract
Background: Basic and clinical scientific research at the University of South Florida (USF) have intersected to support a multi-faceted approach around a common focus on rare iron-related diseases. We proposed a modified version of the National Center for Biotechnology Information’s (NCBI) Hackathon-model to take full advantage of local expertise in building “Iron Hack”, a rare disease-focused hackathon. As the collaborative, problem-solving nature of hackathons tends to attract participants of highly-diverse backgrounds, organizers facilitated a symposium on rare iron-related diseases, specifically porphyrias and Friedreich’s ataxia, pitched at general audiences. Methods: The hackathon was structured to begin each day with presentations by expert clinicians, genetic counselors, researchers focused on molecular and cellular biology, public health/global health, genetics/genomics, computational biology, bioinformatics, biomolecular science, bioengineering, and computer science, as well as guest speakers from the American Porphyria Foundation (APF) and Friedreich’s Ataxia Research Alliance (FARA) to inform participants as to the human impact of these diseases. Results: As a result of this hackathon, we developed resources that are relevant not only to these specific disease-models, but also to other rare diseases and general bioinformatics problems. Within two and a half days, “Iron Hack” participants successfully built collaborative projects to visualize data, build databases, improve rare disease diagnosis, and study rare-disease inheritance. Conclusions: The purpose of this manuscript is to demonstrate the utility of a hackathon model to generate prototypes of generalizable tools for a given disease and train clinicians and data scientists to interact more effectively.
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Affiliation(s)
- Gloria C Ferreira
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, MDC 7, Tampa, FL, 33612, USA
| | - Jenna Oberstaller
- Global and Planetary Health, College of Public Health, University of South Florida, USF Genomics Program, 3720 Spectrum Blvd, Tampa, FL, 33612, USA
| | - Renée Fonseca
- Morsani College of Medicine, University of South Florida, 12901 Bruce B Downs Blvd, Tampa, FL, 33612, USA
| | - Thomas E Keller
- University of South Florida, USF Genomics Program, 3720 Spectrum Blvd, Tampa, FL, 33612, USA
| | - Swamy Rakesh Adapa
- Global and Planetary Health, College of Public Health, University of South Florida, USF Genomics Program, 3720 Spectrum Blvd, Tampa, FL, 33612, USA
| | - Justin Gibbons
- Morsani College of Medicine, University of South Florida, 12901 Bruce B Downs Blvd, Tampa, FL, 33612, USA
| | - Chengqi Wang
- Global and Planetary Health, College of Public Health, University of South Florida, USF Genomics Program, 3720 Spectrum Blvd, Tampa, FL, 33612, USA
| | - Xiaoming Liu
- Global and Planetary Health, College of Public Health, University of South Florida, USF Genomics Program, 3720 Spectrum Blvd, Tampa, FL, 33612, USA
| | - Chang Li
- Global and Planetary Health, College of Public Health, University of South Florida, USF Genomics Program, 3720 Spectrum Blvd, Tampa, FL, 33612, USA
| | - Minh Pham
- Center for Urban Transportation Research, University of South Florida, 4202 E. Fowler Avenue, CUT100, Tampa, FL, 33620, USA
| | - Guy W Dayhoff Ii
- Department of Chemistry, University of South Florida, 4202 E. Fowler Avenue, CHE 205, Tampa, FL, 33620-5250, USA
| | - Linh M Duong
- College of Public Health, University of South Florida, 13201 Bruce B. Downs Blvd., MDC 56, Tampa, FL, 33612, USA.,Moffitt Cancer Center, Tampa, FL, 33612, USA
| | - Luis Tañón Reyes
- Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida, 4202 East Fowler Ave, ISA 2015 Tampa, FL, 33620, USA
| | - Luciano Enrique Laratelli
- Department of Chemistry, University of South Florida, 4202 E. Fowler Avenue, CHE 205, Tampa, FL, 33620-5250, USA
| | - Douglas Franz
- Department of Chemistry, University of South Florida, 4202 E. Fowler Avenue, CHE 205, Tampa, FL, 33620-5250, USA
| | - Segun Fatumo
- MRC/UVRI and LSHTM (Uganda Research Unit), Entebbe, Uganda
| | - Atm Golam Bari
- Department of Computer Science and Engineering, University of South Florida, Tampa, FL, USA
| | | | - Lindsey Fiedler
- College of Public Health, University of South Florida, 13201 Bruce B. Downs Blvd., MDC 56, Tampa, FL, 33612, USA
| | - Omkar Dokur
- Department of Computer Science and Engineering, University of South Florida, Tampa, FL, USA
| | | | - Deborah Cragun
- Global and Planetary Health, College of Public Health, University of South Florida, USF Genomics Program, 3720 Spectrum Blvd, Tampa, FL, 33612, USA
| | - Ben Busby
- National Library of Medicine, 8600 Rockville Pike, Bethesda, MD, 20894-6075, USA
| | - Rays H Y Jiang
- Global and Planetary Health, College of Public Health, University of South Florida, USF Genomics Program, 3720 Spectrum Blvd, Tampa, FL, 33612, USA
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15
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Bouchard C, Boudko DY, Jiang RHY. A SLC6 transporter cloned from the lion's mane jellyfish (Cnidaria, Scyphozoa) is expressed in neurons. PLoS One 2019; 14:e0218806. [PMID: 31233570 PMCID: PMC6590891 DOI: 10.1371/journal.pone.0218806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 06/10/2019] [Indexed: 11/18/2022] Open
Abstract
In the course of recent comparative genomic studies conducted on nervous systems across the phylogeny, current thinking is leaning in favor of more heterogeneity among nervous systems than what was initially expected. The isolation and characterization of molecular components that constitute the cnidarian neuron is not only of interest to the physiologist but also, on a larger scale, to those who study the evolution of nervous systems. Understanding the function of those ancient neurons involves the identification of neurotransmitters and their precursors, the description of nutrients used by neurons for metabolic purposes and the identification of integral membrane proteins that bind to those compounds. Using a molecular cloning strategy targeting membrane proteins that are known to be present in all forms of life, we isolated a member of the solute carrier family 6 from the scyphozoan jellyfish Cyanea capillata. The phylogenetic analysis suggested that the new transporter sequence belongs to an ancestral group of the nutrient amino acid transporter subfamily and is part of a cluster of cnidarian sequences which may translocate the same substrate. We found that the jellyfish transporter is expressed in neurons of the motor nerve net of the animal. To this end, we established an in situ hybridization protocol for the tissues of C. capillata and developed a specific antibody to the jellyfish transporter. Finally, we showed that the gene that codes for the jellyfish transporter also expresses a long non-coding RNA. We hope that this research will contribute to studies that seek to understand what constitutes a neuron in species that belong to an ancient phylum.
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Affiliation(s)
- Christelle Bouchard
- College of Science and Mathematics, University of South Florida, Sarasota, Florida, United States of America
- * E-mail:
| | - Dmitri Y. Boudko
- Department of Physiology and Biophysics, Rosalind Franklin University of Medicine and Science, Chicago Medical School, North Chicago, Illinois, United States of America
| | - Rays H. Y. Jiang
- Global and Planetary Health, College of Public Health, University of South Florida USF Genomics Program, Tampa, Florida, United States of America
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16
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Adapa SR, Taylor RA, Wang C, Thomson-Luque R, Johnson LR, Jiang RHY. Plasmodium vivax readiness to transmit: implication for malaria eradication. BMC Syst Biol 2019; 13:5. [PMID: 30634978 PMCID: PMC6330404 DOI: 10.1186/s12918-018-0669-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Accepted: 12/04/2018] [Indexed: 12/15/2022]
Abstract
Background The lack of a continuous long-term in vitro culture system for Plasmodium vivax severely limits our knowledge of pathophysiology of the most widespread malaria parasite. To gain direct understanding of P. vivax human infections, we used Next Generation Sequencing data mining to unravel parasite in vivo expression profiles for P. vivax, and P. falciparum as comparison. Results We performed cloud and local computing to extract parasite transcriptomes from publicly available raw data of human blood samples. We developed a Poisson Modelling (PM) method to confidently identify parasite derived transcripts in mixed RNAseq signals of infected host tissues. We successfully retrieved and reconstructed parasite transcriptomes from infected patient blood as early as the first blood stage cycle; and the same methodology did not recover any significant signal from controls. Surprisingly, these first generation blood parasites already show strong signature of transmission, which indicates the commitment from asexual-to-sexual stages. Further, we place the results within the context of P. vivax’s complex life cycle, by developing mathematical models for P. vivax and P. falciparum and using sensitivity analysis assess the relative epidemiological impact of possible early stage transmission. Conclusion The study uncovers the earliest onset of P. vivax blood pathogenesis and highlights the challenges of P. vivax eradication programs. Electronic supplementary material The online version of this article (10.1186/s12918-018-0669-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Swamy Rakesh Adapa
- Department of Global Health (GH) & Center for Drug Discovery and Innovation (CDDI), College of Public Health, University of South Florida, Tampa, FL, 33612, USA
| | - Rachel A Taylor
- Department of Integrative Biology, University of South Florida, Tampa, FL, USA
| | - Chengqi Wang
- Department of Global Health (GH) & Center for Drug Discovery and Innovation (CDDI), College of Public Health, University of South Florida, Tampa, FL, 33612, USA
| | - Richard Thomson-Luque
- Department of Global Health (GH) & Center for Drug Discovery and Innovation (CDDI), College of Public Health, University of South Florida, Tampa, FL, 33612, USA
| | - Leah R Johnson
- Department of Integrative Biology, University of South Florida, Tampa, FL, USA
| | - Rays H Y Jiang
- Department of Global Health (GH) & Center for Drug Discovery and Innovation (CDDI), College of Public Health, University of South Florida, Tampa, FL, 33612, USA.
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17
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Gibbons J, Button-Simons KA, Adapa SR, Li S, Pietsch M, Zhang M, Liao X, Adams JH, Ferdig MT, Jiang RHY. Altered expression of K13 disrupts DNA replication and repair in Plasmodium falciparum. BMC Genomics 2018; 19:849. [PMID: 30486796 PMCID: PMC6263542 DOI: 10.1186/s12864-018-5207-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Accepted: 10/30/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Plasmodium falciparum exhibits resistance to the artemisinin component of the frontline antimalarial treatment Artemisinin-based Combination Therapy in South East Asia. Millions of lives will be at risk if artemisinin resistance (ART-R) spreads to Africa. Single non-synonymous mutations in the propeller region of PF3D7_1343700,"K13" are implicated in resistance. In this work, we use transcriptional profiling to characterize a laboratory-generated k13 insertional mutant previously demonstrated to have increased sensitivity to artemisinins to explore the functional role of k13. RESULTS A set of RNA-seq and microarray experiments confirmed that the expression profile of k13 is specifically altered during the early ring and early trophozoite stages of the mutant intraerythrocytic development cycle. The down-regulation of k13 transcripts in this mutant during the early ring stage is associated with a transcriptome advance towards a more trophozoite-like state. To discover the specific downstream effect of k13 dysregulation, we developed a new computational method to search for differential gene expression while accounting for the temporal sequence of transcription. We found that the strongest biological signature of the transcriptome shift is an up-regulation of DNA replication and repair genes during the early ring developmental stage and a down-regulation of DNA replication and repair genes during the early trophozoite stage; by contrast, the expressions of housekeeping genes are unchanged. This effect, due to k13 dysregulation, is antagonistic, such that k13 levels are negatively correlated with DNA replication and repair gene expression. CONCLUSION Our results support a role for k13 as a stress response regulator consistent with the hypothesis that artemisinins mode of action is oxidative stress and k13 as a functional homolog of Keap1 which in humans regulates DNA replication and repair genes in response to oxidative stress.
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Affiliation(s)
- Justin Gibbons
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, USA.,Center for Global Health and Infectious Diseases Research, College of Public Health, University of South Florida, Tampa, USA
| | - Katrina A Button-Simons
- Eck Institute for Global Health, Department of Biological Sciences, University of Notre Dame, Notre Dame, USA
| | - Swamy R Adapa
- Center for Global Health and Infectious Diseases Research, College of Public Health, University of South Florida, Tampa, USA
| | - Suzanne Li
- Center for Global Health and Infectious Diseases Research, College of Public Health, University of South Florida, Tampa, USA
| | - Maxwell Pietsch
- Department of Computer Science & Engineering, University of South Florida, Tampa, USA
| | - Min Zhang
- Center for Global Health and Infectious Diseases Research, College of Public Health, University of South Florida, Tampa, USA
| | - Xiangyun Liao
- Center for Global Health and Infectious Diseases Research, College of Public Health, University of South Florida, Tampa, USA
| | - John H Adams
- Center for Global Health and Infectious Diseases Research, College of Public Health, University of South Florida, Tampa, USA
| | - Michael T Ferdig
- Eck Institute for Global Health, Department of Biological Sciences, University of Notre Dame, Notre Dame, USA
| | - Rays H Y Jiang
- Center for Global Health and Infectious Diseases Research, College of Public Health, University of South Florida, Tampa, USA.
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18
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Roth A, Adapa SR, Zhang M, Liao X, Saxena V, Goffe R, Li S, Ubalee R, Saggu GS, Pala ZR, Garg S, Davidson S, Jiang RHY, Adams JH. Unraveling the Plasmodium vivax sporozoite transcriptional journey from mosquito vector to human host. Sci Rep 2018; 8:12183. [PMID: 30111801 PMCID: PMC6093925 DOI: 10.1038/s41598-018-30713-1] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Accepted: 08/03/2018] [Indexed: 02/07/2023] Open
Abstract
Malaria parasites transmitted by mosquito bite are remarkably efficient in establishing human infections. The infection process requires roughly 30 minutes and is highly complex as quiescent sporozoites injected with mosquito saliva must be rapidly activated in the skin, migrate through the body, and infect the liver. This process is poorly understood for Plasmodium vivax due to low infectivity in the in vitro models. To study this skin-to-liver-stage of malaria, we used quantitative bioassays coupled with transcriptomics to evaluate parasite changes linked with mammalian microenvironmental factors. Our in vitro phenotyping and RNA-seq analyses revealed key microenvironmental relationships with distinct biological functions. Most notable, preservation of sporozoite quiescence by exposure to insect-like factors coupled with strategic activation limits untimely activation of invasion-associated genes to dramatically increase hepatocyte invasion rates. We also report the first transcriptomic analysis of the P. vivax sporozoite interaction in salivary glands identifying 118 infection-related differentially-regulated Anopheles dirus genes. These results provide important new insights in malaria parasite biology and identify priority targets for antimalarial therapeutic interventions to block P. vivax infection.
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Affiliation(s)
- Alison Roth
- Center for Global Health and Infectious Diseases Research, College of Public Health, University of South Florida, Tampa, Florida, USA
| | - Swamy R Adapa
- Center for Global Health and Infectious Diseases Research, College of Public Health, University of South Florida, Tampa, Florida, USA
| | - Min Zhang
- Center for Global Health and Infectious Diseases Research, College of Public Health, University of South Florida, Tampa, Florida, USA
| | - Xiangyun Liao
- Center for Global Health and Infectious Diseases Research, College of Public Health, University of South Florida, Tampa, Florida, USA
| | - Vishal Saxena
- Molecular Parasitology and System Biology Lab, Department of Biological Sciences, Birla Institute of Technology and Science, Pilani, Rajasthan, India
| | - Raaven Goffe
- Center for Global Health and Infectious Diseases Research, College of Public Health, University of South Florida, Tampa, Florida, USA
| | - Suzanne Li
- Center for Global Health and Infectious Diseases Research, College of Public Health, University of South Florida, Tampa, Florida, USA
| | - Ratawan Ubalee
- Department of Entomology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Gagandeep S Saggu
- Laboratory of Malaria and Vector Research, National Institute of Allergic and Infectious Diseases, National Institute of Health, Rockville, Maryland, USA
| | - Zarna R Pala
- Molecular Parasitology and System Biology Lab, Department of Biological Sciences, Birla Institute of Technology and Science, Pilani, Rajasthan, India
| | - Shilpi Garg
- Molecular Parasitology and System Biology Lab, Department of Biological Sciences, Birla Institute of Technology and Science, Pilani, Rajasthan, India
| | - Silas Davidson
- Department of Entomology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Rays H Y Jiang
- Center for Global Health and Infectious Diseases Research, College of Public Health, University of South Florida, Tampa, Florida, USA.
| | - John H Adams
- Center for Global Health and Infectious Diseases Research, College of Public Health, University of South Florida, Tampa, Florida, USA.
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19
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Zhang M, Wang C, Otto TD, Oberstaller J, Liao X, Adapa SR, Udenze K, Bronner IF, Casandra D, Mayho M, Brown J, Li S, Swanson J, Rayner JC, Jiang RHY, Adams JH. Uncovering the essential genes of the human malaria parasite Plasmodium falciparum by saturation mutagenesis. Science 2018; 360:360/6388/eaap7847. [PMID: 29724925 DOI: 10.1126/science.aap7847] [Citation(s) in RCA: 502] [Impact Index Per Article: 83.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Accepted: 03/02/2018] [Indexed: 12/22/2022]
Abstract
Severe malaria is caused by the apicomplexan parasite Plasmodium falciparum. Despite decades of research, the distinct biology of these parasites has made it challenging to establish high-throughput genetic approaches to identify and prioritize therapeutic targets. Using transposon mutagenesis of P. falciparum in an approach that exploited its AT-rich genome, we generated more than 38,000 mutants, saturating the genome and defining mutability and fitness costs for over 87% of genes. Of 5399 genes, our study defined 2680 genes as essential for optimal growth of asexual blood stages in vitro. These essential genes are associated with drug resistance, represent leading vaccine candidates, and include approximately 1000 Plasmodium-conserved genes of unknown function. We validated this approach by testing proteasome pathways for individual mutants associated with artemisinin sensitivity.
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Affiliation(s)
- Min Zhang
- Center for Global Health and Infectious Diseases, Department of Global Health, University of South Florida, 3720 Spectrum Boulevard, Suite 404, Tampa, FL 33612, USA
| | - Chengqi Wang
- Center for Global Health and Infectious Diseases, Department of Global Health, University of South Florida, 3720 Spectrum Boulevard, Suite 404, Tampa, FL 33612, USA
| | - Thomas D Otto
- Malaria Programme, Wellcome Trust Sanger Institute, Genome Campus, Hinxton Cambridgeshire CB10 1SA, UK
| | - Jenna Oberstaller
- Center for Global Health and Infectious Diseases, Department of Global Health, University of South Florida, 3720 Spectrum Boulevard, Suite 404, Tampa, FL 33612, USA
| | - Xiangyun Liao
- Center for Global Health and Infectious Diseases, Department of Global Health, University of South Florida, 3720 Spectrum Boulevard, Suite 404, Tampa, FL 33612, USA
| | - Swamy R Adapa
- Center for Global Health and Infectious Diseases, Department of Global Health, University of South Florida, 3720 Spectrum Boulevard, Suite 404, Tampa, FL 33612, USA
| | - Kenneth Udenze
- Center for Global Health and Infectious Diseases, Department of Global Health, University of South Florida, 3720 Spectrum Boulevard, Suite 404, Tampa, FL 33612, USA
| | - Iraad F Bronner
- Malaria Programme, Wellcome Trust Sanger Institute, Genome Campus, Hinxton Cambridgeshire CB10 1SA, UK
| | - Deborah Casandra
- Center for Global Health and Infectious Diseases, Department of Global Health, University of South Florida, 3720 Spectrum Boulevard, Suite 404, Tampa, FL 33612, USA
| | - Matthew Mayho
- Malaria Programme, Wellcome Trust Sanger Institute, Genome Campus, Hinxton Cambridgeshire CB10 1SA, UK
| | - Jacqueline Brown
- Malaria Programme, Wellcome Trust Sanger Institute, Genome Campus, Hinxton Cambridgeshire CB10 1SA, UK
| | - Suzanne Li
- Center for Global Health and Infectious Diseases, Department of Global Health, University of South Florida, 3720 Spectrum Boulevard, Suite 404, Tampa, FL 33612, USA
| | - Justin Swanson
- Center for Global Health and Infectious Diseases, Department of Global Health, University of South Florida, 3720 Spectrum Boulevard, Suite 404, Tampa, FL 33612, USA
| | - Julian C Rayner
- Malaria Programme, Wellcome Trust Sanger Institute, Genome Campus, Hinxton Cambridgeshire CB10 1SA, UK.
| | - Rays H Y Jiang
- Center for Global Health and Infectious Diseases, Department of Global Health, University of South Florida, 3720 Spectrum Boulevard, Suite 404, Tampa, FL 33612, USA.
| | - John H Adams
- Center for Global Health and Infectious Diseases, Department of Global Health, University of South Florida, 3720 Spectrum Boulevard, Suite 404, Tampa, FL 33612, USA.
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20
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Thomson-Luque R, Wang C, Ntumngia FB, Xu S, Szekeres K, Conway A, Adapa SR, Barnes SJ, Adams JH, Jiang RHY. In-depth phenotypic characterization of reticulocyte maturation using mass cytometry. Blood Cells Mol Dis 2018; 72:22-33. [PMID: 30007855 PMCID: PMC6097872 DOI: 10.1016/j.bcmd.2018.06.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Revised: 06/24/2018] [Accepted: 06/24/2018] [Indexed: 12/17/2022]
Abstract
Progress towards an in-depth understanding of the final steps of the erythroid lineage development is paramount for many hematological diseases. We have characterized the final stages of reticulocyte maturation from bone marrow to peripheral blood using for the first time single-cell Mass Cytometry (CyTOF). We were able to measure the expression of 31 surface markers within a single red blood cell (RBC). We demonstrate the validity of CyTOF for RBC phenotyping by confirming the progressive reduction of transferrin receptor 1 (CD71) during reticulocyte maturation to mature RBC. We highlight the high-dimensional nature of mass cytometry data by correlating the expression of multiple proteins on individual RBCs. We further describe a more drastic reduction pattern for a component of the alpha4/beta1 integrin CD49d at the very early steps of reticulocyte maturation in bone marrow and directly linked with the mitochondria remnants clearance pattern. The enhanced and accurate RBC phenotyping potential of CyTOF described herein could be beneficial to decipher RBC preferences, as well as still not well understood receptor-ligand interaction of some hemotropic parasites such as the malaria causing agent Plasmodium vivax.
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Affiliation(s)
- Richard Thomson-Luque
- Center for Global Health and Infectious Diseases Research, College of Public Health, University of South Florida, Tampa, USA
| | - Chengqi Wang
- Center for Global Health and Infectious Diseases Research, College of Public Health, University of South Florida, Tampa, USA
| | - Francis B Ntumngia
- Center for Global Health and Infectious Diseases Research, College of Public Health, University of South Florida, Tampa, USA
| | - Shulin Xu
- Center for Global Health and Infectious Diseases Research, College of Public Health, University of South Florida, Tampa, USA
| | - Karoly Szekeres
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, USA
| | - Amy Conway
- Center for Global Health and Infectious Diseases Research, College of Public Health, University of South Florida, Tampa, USA
| | - Swamy Rakesh Adapa
- Center for Global Health and Infectious Diseases Research, College of Public Health, University of South Florida, Tampa, USA
| | - Samantha J Barnes
- Center for Global Health and Infectious Diseases Research, College of Public Health, University of South Florida, Tampa, USA
| | - John H Adams
- Center for Global Health and Infectious Diseases Research, College of Public Health, University of South Florida, Tampa, USA.
| | - Rays H Y Jiang
- Center for Global Health and Infectious Diseases Research, College of Public Health, University of South Florida, Tampa, USA.
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21
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Roth A, Maher SP, Conway AJ, Ubalee R, Chaumeau V, Andolina C, Kaba SA, Vantaux A, Bakowski MA, Thomson-Luque R, Adapa SR, Singh N, Barnes SJ, Cooper CA, Rouillier M, McNamara CW, Mikolajczak SA, Sather N, Witkowski B, Campo B, Kappe SHI, Lanar DE, Nosten F, Davidson S, Jiang RHY, Kyle DE, Adams JH. A comprehensive model for assessment of liver stage therapies targeting Plasmodium vivax and Plasmodium falciparum. Nat Commun 2018; 9:1837. [PMID: 29743474 PMCID: PMC5943321 DOI: 10.1038/s41467-018-04221-9] [Citation(s) in RCA: 101] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Accepted: 04/10/2018] [Indexed: 12/26/2022] Open
Abstract
Malaria liver stages represent an ideal therapeutic target with a bottleneck in parasite load and reduced clinical symptoms; however, current in vitro pre-erythrocytic (PE) models for Plasmodium vivax and P. falciparum lack the efficiency necessary for rapid identification and effective evaluation of new vaccines and drugs, especially targeting late liver-stage development and hypnozoites. Herein we report the development of a 384-well plate culture system using commercially available materials, including cryopreserved primary human hepatocytes. Hepatocyte physiology is maintained for at least 30 days and supports development of P. vivax hypnozoites and complete maturation of P. vivax and P. falciparum schizonts. Our multimodal analysis in antimalarial therapeutic research identifies important PE inhibition mechanisms: immune antibodies against sporozoite surface proteins functionally inhibit liver stage development and ion homeostasis is essential for schizont and hypnozoite viability. This model can be implemented in laboratories in disease-endemic areas to accelerate vaccine and drug discovery research.
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Affiliation(s)
- Alison Roth
- Department of Global Health, College of Public Health, Center for Global Health and Infectious Diseases Research, University of South Florida, 3720 Spectrum Blvd 404, Tampa, FL, 33612, USA
| | - Steven P Maher
- Department of Global Health, College of Public Health, Center for Global Health and Infectious Diseases Research, University of South Florida, 3720 Spectrum Blvd 404, Tampa, FL, 33612, USA
- Center for Tropical and Emerging Global Diseases, University of Georgia, 500 DW Brooks Dr. Suite 370, Athens, GA, 30602, USA
| | - Amy J Conway
- Department of Global Health, College of Public Health, Center for Global Health and Infectious Diseases Research, University of South Florida, 3720 Spectrum Blvd 404, Tampa, FL, 33612, USA
| | - Ratawan Ubalee
- Department of Entomology, Armed Forces Research Institute of Medical Sciences (AFRIMS), 315/6 Rajvithi Rd, Bangkok, 10400, Thailand
| | - Victor Chaumeau
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Shoklo Malaria Research Unit, Mahidol Oxford Research Unit, Faculty of Tropical Medicine, Mahidol University, 68/30 Bantung Rd, Mae Sot, Tak, 63110, Thailand
| | - Chiara Andolina
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Shoklo Malaria Research Unit, Mahidol Oxford Research Unit, Faculty of Tropical Medicine, Mahidol University, 68/30 Bantung Rd, Mae Sot, Tak, 63110, Thailand
| | - Stephen A Kaba
- Malaria Vaccine Branch, Walter Reed Army Institute of Research, 503 Robert Grant Ave, Silver Spring, MD, 20910, USA
| | - Amélie Vantaux
- Malaria Molecular Epidemiology Unit, Institut Pasteur du Cambodge, 5 Boulevard Monivong-PO Box 983, Phnom Penh, 12 201, Cambodia
| | - Malina A Bakowski
- California Institute for Biomedical Research (Calibr), 11119N. Torrey Pines Rd, Suite 100, La Jolla, CA, 92037, USA
| | - Richard Thomson-Luque
- Department of Global Health, College of Public Health, Center for Global Health and Infectious Diseases Research, University of South Florida, 3720 Spectrum Blvd 404, Tampa, FL, 33612, USA
| | - Swamy Rakesh Adapa
- Department of Global Health, College of Public Health, Center for Global Health and Infectious Diseases Research, University of South Florida, 3720 Spectrum Blvd 404, Tampa, FL, 33612, USA
| | - Naresh Singh
- Department of Global Health, College of Public Health, Center for Global Health and Infectious Diseases Research, University of South Florida, 3720 Spectrum Blvd 404, Tampa, FL, 33612, USA
| | - Samantha J Barnes
- Department of Global Health, College of Public Health, Center for Global Health and Infectious Diseases Research, University of South Florida, 3720 Spectrum Blvd 404, Tampa, FL, 33612, USA
| | - Caitlin A Cooper
- Center for Tropical and Emerging Global Diseases, University of Georgia, 500 DW Brooks Dr. Suite 370, Athens, GA, 30602, USA
| | - Mélanie Rouillier
- Medicines for Malaria Venture, Pré-Bois Rd 20, Meyrin, 1215, Switzerland
| | - Case W McNamara
- California Institute for Biomedical Research (Calibr), 11119N. Torrey Pines Rd, Suite 100, La Jolla, CA, 92037, USA
| | - Sebastian A Mikolajczak
- Center for Infectious Disease Research, 307 Westlake Ave N Suite 500, Seattle, WA, 98109, USA
| | - Noah Sather
- Center for Infectious Disease Research, 307 Westlake Ave N Suite 500, Seattle, WA, 98109, USA
| | - Benoît Witkowski
- California Institute for Biomedical Research (Calibr), 11119N. Torrey Pines Rd, Suite 100, La Jolla, CA, 92037, USA
| | - Brice Campo
- Medicines for Malaria Venture, Pré-Bois Rd 20, Meyrin, 1215, Switzerland
| | - Stefan H I Kappe
- Center for Infectious Disease Research, 307 Westlake Ave N Suite 500, Seattle, WA, 98109, USA
| | - David E Lanar
- Malaria Vaccine Branch, Walter Reed Army Institute of Research, 503 Robert Grant Ave, Silver Spring, MD, 20910, USA
| | - François Nosten
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Shoklo Malaria Research Unit, Mahidol Oxford Research Unit, Faculty of Tropical Medicine, Mahidol University, 68/30 Bantung Rd, Mae Sot, Tak, 63110, Thailand
| | - Silas Davidson
- Department of Entomology, Armed Forces Research Institute of Medical Sciences (AFRIMS), 315/6 Rajvithi Rd, Bangkok, 10400, Thailand
| | - Rays H Y Jiang
- Department of Global Health, College of Public Health, Center for Global Health and Infectious Diseases Research, University of South Florida, 3720 Spectrum Blvd 404, Tampa, FL, 33612, USA
| | - Dennis E Kyle
- Department of Global Health, College of Public Health, Center for Global Health and Infectious Diseases Research, University of South Florida, 3720 Spectrum Blvd 404, Tampa, FL, 33612, USA
- Center for Tropical and Emerging Global Diseases, University of Georgia, 500 DW Brooks Dr. Suite 370, Athens, GA, 30602, USA
| | - John H Adams
- Department of Global Health, College of Public Health, Center for Global Health and Infectious Diseases Research, University of South Florida, 3720 Spectrum Blvd 404, Tampa, FL, 33612, USA.
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22
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Babatunde KA, Mbagwu S, Hernández-Castañeda MA, Adapa SR, Walch M, Filgueira L, Falquet L, Jiang RHY, Ghiran I, Mantel PY. Malaria infected red blood cells release small regulatory RNAs through extracellular vesicles. Sci Rep 2018; 8:884. [PMID: 29343745 PMCID: PMC5772623 DOI: 10.1038/s41598-018-19149-9] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Accepted: 12/04/2017] [Indexed: 12/11/2022] Open
Abstract
The parasite Plasmodium falciparum causes the most severe form of malaria. Cell communication between parasites is an important mechanism to control population density and differentiation. The infected red blood cells (iRBCs) release small extracellular vesicles (EVs) that transfer cargoes between cells. The EVs synchronize the differentiation of the asexual parasites into gametocytes to initiate the transmission to the mosquito. Beside their role in parasite communication, EVs regulate vascular function. So far, the exact cargoes responsible for cellular communication remain unknown. We isolated EVs from cultured iRBCs to determine their small RNA content. We identified several types of human and plasmodial regulatory RNAs. While the miRNAs and tRNA-derived fragments were the most abundant human RNAs, we also found Y-RNAs, vault RNAs, snoRNAs and piRNAs. Interestingly, we found about 120 plasmodial RNAs, including mRNAs coding for exported proteins and proteins involved in drug resistance, as well as non-coding RNAs, such as rRNAs, small nuclear (snRNAs) and tRNAs. These data show, that iRBC-EVs carry small regulatory RNAs. A role in cellular communication is possible since the RNAs were transferred to endothelial cells. Furthermore, the presence of Plasmodium RNAs, in EVs suggests that they may be used as biomarker to track and detect disease.
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Affiliation(s)
| | - Smart Mbagwu
- Department of Medicine, University of Fribourg, 1700, Fribourg, Switzerland
| | | | - Swamy R Adapa
- Department of Global Health (GH) & Center for Drug Discovery and Innovation (CDDI), College of Public Health, University of South Florida, Tampa, FL, 33612, USA
| | - Michael Walch
- Department of Medicine, University of Fribourg, 1700, Fribourg, Switzerland
| | - Luis Filgueira
- Department of Medicine, University of Fribourg, 1700, Fribourg, Switzerland
| | - Laurent Falquet
- Department of Medicine, University of Fribourg, 1700, Fribourg, Switzerland
| | - Rays H Y Jiang
- Department of Global Health (GH) & Center for Drug Discovery and Innovation (CDDI), College of Public Health, University of South Florida, Tampa, FL, 33612, USA
| | - Ionita Ghiran
- Division of Allergy and Infection, Beth Israel Deaconess Medical Center, Boston, MA, 02115, USA
| | - Pierre-Yves Mantel
- Department of Medicine, University of Fribourg, 1700, Fribourg, Switzerland.
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23
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Brancucci NMB, Gerdt JP, Wang C, De Niz M, Philip N, Adapa SR, Zhang M, Hitz E, Niederwieser I, Boltryk SD, Laffitte MC, Clark MA, Grüring C, Ravel D, Blancke Soares A, Demas A, Bopp S, Rubio-Ruiz B, Conejo-Garcia A, Wirth DF, Gendaszewska-Darmach E, Duraisingh MT, Adams JH, Voss TS, Waters AP, Jiang RHY, Clardy J, Marti M. Lysophosphatidylcholine Regulates Sexual Stage Differentiation in the Human Malaria Parasite Plasmodium falciparum. Cell 2017; 171:1532-1544.e15. [PMID: 29129376 PMCID: PMC5733390 DOI: 10.1016/j.cell.2017.10.020] [Citation(s) in RCA: 185] [Impact Index Per Article: 26.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Revised: 07/17/2017] [Accepted: 10/12/2017] [Indexed: 01/11/2023]
Abstract
Transmission represents a population bottleneck in the Plasmodium life cycle and a key intervention target of ongoing efforts to eradicate malaria. Sexual differentiation is essential for this process, as only sexual parasites, called gametocytes, are infective to the mosquito vector. Gametocyte production rates vary depending on environmental conditions, but external stimuli remain obscure. Here, we show that the host-derived lipid lysophosphatidylcholine (LysoPC) controls P. falciparum cell fate by repressing parasite sexual differentiation. We demonstrate that exogenous LysoPC drives biosynthesis of the essential membrane component phosphatidylcholine. LysoPC restriction induces a compensatory response, linking parasite metabolism to the activation of sexual-stage-specific transcription and gametocyte formation. Our results reveal that malaria parasites can sense and process host-derived physiological signals to regulate differentiation. These data close a critical knowledge gap in parasite biology and introduce a major component of the sexual differentiation pathway in Plasmodium that may provide new approaches for blocking malaria transmission.
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Affiliation(s)
- Nicolas M B Brancucci
- Wellcome Centre for Molecular Parasitology, Institute of Infection, Immunity & Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK; Harvard T.H. Chan School of Public Health, Department of Immunology and Infectious Diseases, Boston, MA 02155, USA
| | - Joseph P Gerdt
- Harvard Medical School, Department of Biological Chemistry and Molecular Pharmacology, Boston, MA 02155, USA
| | - ChengQi Wang
- Center for Global Health & Infectious Diseases Research, Department of Global Health, College of Public Health, University of South Florida, Tampa, FL 33620, USA
| | - Mariana De Niz
- Wellcome Centre for Molecular Parasitology, Institute of Infection, Immunity & Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK; Harvard T.H. Chan School of Public Health, Department of Immunology and Infectious Diseases, Boston, MA 02155, USA
| | - Nisha Philip
- Wellcome Centre for Molecular Parasitology, Institute of Infection, Immunity & Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK; Centre for Immunity, Infection and Evolution, Institute for Immunology and Infection Research, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Swamy R Adapa
- Center for Global Health & Infectious Diseases Research, Department of Global Health, College of Public Health, University of South Florida, Tampa, FL 33620, USA
| | - Min Zhang
- Center for Global Health & Infectious Diseases Research, Department of Global Health, College of Public Health, University of South Florida, Tampa, FL 33620, USA
| | - Eva Hitz
- Swiss Tropical and Public Health Institute, 4051 Basel, Switzerland; University of Basel, 4001 Basel, Switzerland
| | - Igor Niederwieser
- Swiss Tropical and Public Health Institute, 4051 Basel, Switzerland; University of Basel, 4001 Basel, Switzerland
| | - Sylwia D Boltryk
- Swiss Tropical and Public Health Institute, 4051 Basel, Switzerland; University of Basel, 4001 Basel, Switzerland
| | - Marie-Claude Laffitte
- Wellcome Centre for Molecular Parasitology, Institute of Infection, Immunity & Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
| | - Martha A Clark
- Harvard T.H. Chan School of Public Health, Department of Immunology and Infectious Diseases, Boston, MA 02155, USA
| | - Christof Grüring
- Harvard T.H. Chan School of Public Health, Department of Immunology and Infectious Diseases, Boston, MA 02155, USA
| | - Deepali Ravel
- Harvard T.H. Chan School of Public Health, Department of Immunology and Infectious Diseases, Boston, MA 02155, USA
| | - Alexandra Blancke Soares
- Wellcome Centre for Molecular Parasitology, Institute of Infection, Immunity & Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
| | - Allison Demas
- Harvard T.H. Chan School of Public Health, Department of Immunology and Infectious Diseases, Boston, MA 02155, USA
| | - Selina Bopp
- Harvard T.H. Chan School of Public Health, Department of Immunology and Infectious Diseases, Boston, MA 02155, USA
| | - Belén Rubio-Ruiz
- Department of Pharmaceutical and Organic Chemistry, Faculty of Pharmacy, University of Granada, 18010 Granada, Spain
| | - Ana Conejo-Garcia
- Department of Pharmaceutical and Organic Chemistry, Faculty of Pharmacy, University of Granada, 18010 Granada, Spain
| | - Dyann F Wirth
- Harvard T.H. Chan School of Public Health, Department of Immunology and Infectious Diseases, Boston, MA 02155, USA
| | - Edyta Gendaszewska-Darmach
- Institute of Technical Biochemistry, Faculty of Biotechnology and Food Sciences, Lodz University of Technology, 90-924 Lodz, Poland
| | - Manoj T Duraisingh
- Harvard T.H. Chan School of Public Health, Department of Immunology and Infectious Diseases, Boston, MA 02155, USA
| | - John H Adams
- Center for Global Health & Infectious Diseases Research, Department of Global Health, College of Public Health, University of South Florida, Tampa, FL 33620, USA
| | - Till S Voss
- Swiss Tropical and Public Health Institute, 4051 Basel, Switzerland; University of Basel, 4001 Basel, Switzerland
| | - Andrew P Waters
- Wellcome Centre for Molecular Parasitology, Institute of Infection, Immunity & Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
| | - Rays H Y Jiang
- Center for Global Health & Infectious Diseases Research, Department of Global Health, College of Public Health, University of South Florida, Tampa, FL 33620, USA
| | - Jon Clardy
- Harvard Medical School, Department of Biological Chemistry and Molecular Pharmacology, Boston, MA 02155, USA.
| | - Matthias Marti
- Wellcome Centre for Molecular Parasitology, Institute of Infection, Immunity & Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK; Harvard T.H. Chan School of Public Health, Department of Immunology and Infectious Diseases, Boston, MA 02155, USA.
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24
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Ganter M, Goldberg JM, Dvorin JD, Paulo JA, King JG, Tripathi AK, Paul AS, Yang J, Coppens I, Jiang RHY, Elsworth B, Baker DA, Dinglasan RR, Gygi SP, Duraisingh MT. Erratum: Plasmodium falciparum CRK4 directs continuous rounds of DNA replication during schizogony. Nat Microbiol 2017; 2:17038. [PMID: 28263306 PMCID: PMC10777684 DOI: 10.1038/nmicrobiol.2017.38] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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25
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Ganter M, Goldberg JM, Dvorin JD, Paulo JA, King JG, Tripathi AK, Paul AS, Yang J, Coppens I, Jiang RHY, Elsworth B, Baker DA, Dinglasan RR, Gygi SP, Duraisingh MT. Plasmodium falciparum CRK4 directs continuous rounds of DNA replication during schizogony. Nat Microbiol 2017; 2:17017. [PMID: 28211852 PMCID: PMC5328244 DOI: 10.1038/nmicrobiol.2017.17] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2016] [Accepted: 01/13/2017] [Indexed: 02/08/2023]
Abstract
Plasmodium parasites, the causative agents of malaria, have evolved a unique cell division cycle in the clinically relevant asexual blood-stage of infection1. DNA replication commences approximately halfway through the intracellular development following invasion and parasite growth. The schizont stage is associated with multiple rounds of DNA replication and nuclear division without cytokinesis resulting in a multinucleated cell. Nuclei divide asynchronously through schizogony, with only the final round of DNA replication and segregation being synchronous and coordinated with daughter cell assembly2,3. However, the control mechanisms for this divergent mode of replication are unknown. Here we show that the Plasmodium-specific kinase PfCRK4 is a key cell cycle regulator that orchestrates the multiple rounds of DNA replication throughout schizogony in P. falciparum. PfCRK4 depletion led to a complete block in nuclear division and profoundly inhibited DNA replication. Quantitative phosphoproteomic profiling identified a set of PfCRK4-regulated phosphoproteins with greatest functional similarity to CDK2 substrates, particularly proteins involved in origin of replication firing. PfCRK4 was required for the initial and subsequent rounds of DNA replication during schizogony, and in addition was essential for development in the mosquito vector. Our results identified an essential S phase promoting factor of the unconventional P. falciparum cell cycle. PfCRK4 is required for both a prolonged period of the intraerythrocytic blood-stage of malaria infection, as well as for transmission, revealing a broad window for PfCRK4-targeted chemotherapeutics.
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Affiliation(s)
- Markus Ganter
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, 651 Huntington Avenue, FXB, Room 202, Boston, Massachusetts 02115, USA
| | - Jonathan M Goldberg
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, 651 Huntington Avenue, FXB, Room 202, Boston, Massachusetts 02115, USA
| | - Jeffrey D Dvorin
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, 651 Huntington Avenue, FXB, Room 202, Boston, Massachusetts 02115, USA.,Division of Infectious Diseases, Boston Children's Hospital, Boston, Massachusetts 02115, USA
| | - Joao A Paulo
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Jonas G King
- W. Harry Feinstone Department of Molecular Microbiology &Immunology, The Johns Hopkins Malaria Research Institute, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland 21205, USA
| | - Abhai K Tripathi
- W. Harry Feinstone Department of Molecular Microbiology &Immunology, The Johns Hopkins Malaria Research Institute, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland 21205, USA
| | - Aditya S Paul
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, 651 Huntington Avenue, FXB, Room 202, Boston, Massachusetts 02115, USA
| | - Jing Yang
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, 651 Huntington Avenue, FXB, Room 202, Boston, Massachusetts 02115, USA
| | - Isabelle Coppens
- W. Harry Feinstone Department of Molecular Microbiology &Immunology, The Johns Hopkins Malaria Research Institute, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland 21205, USA
| | - Rays H Y Jiang
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, 651 Huntington Avenue, FXB, Room 202, Boston, Massachusetts 02115, USA
| | - Brendan Elsworth
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, 651 Huntington Avenue, FXB, Room 202, Boston, Massachusetts 02115, USA
| | - David A Baker
- Faculty of Infectious and Tropical Diseases, London School of Hygiene &Tropical Medicine, London WC1E 7HT, UK
| | - Rhoel R Dinglasan
- W. Harry Feinstone Department of Molecular Microbiology &Immunology, The Johns Hopkins Malaria Research Institute, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland 21205, USA
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Manoj T Duraisingh
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, 651 Huntington Avenue, FXB, Room 202, Boston, Massachusetts 02115, USA
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26
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Wang C, Adapa SR, Gibbons J, Sutton S, Jiang RHY. Punctuated chromatin states regulate Plasmodium falciparum antigenic variation at the intron and 2 kb upstream regions. BMC Genomics 2016; 17:652. [PMID: 27538502 PMCID: PMC4990864 DOI: 10.1186/s12864-016-3005-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 08/10/2016] [Indexed: 11/27/2022] Open
Abstract
Background Understanding the regulation mechanism of var gene expression is crucial for explaining antigenic variation in Plasmodium falciparum. Recent work observed that while all var genes produce transcripts, only a few var genes exhibit high expression levels. However, the global regulation of var expression and the relationship between epigenetic and genetic control remains to be established. Result We have systematically reanalyzed the existing genomic data including chromatin configurations and gene expressions; and for the first time used robust statistical methods to show that the intron and 2 kb upstream regions of each endogenous var gene always maintain high chromatin accessibility, with high potential to bind transcription factors (TFs). The levels of transcripts for different var gene family members are associated with this chromatin accessibility. Any given var gene thus shows punctuated chromatin states throughout the asexual life cycle. This is demonstrated by three independent transcript datasets. Chromatin accessibility in the var intron and 2 kb upstream regions are also positively correlated with their GC content, suggesting the level of var genes silencing might be encoded in their intron sequences. Interestingly, both var intron and 2 kb upstream regions exhibit higher chromatin accessibility when the genes have relatively lower transcription levels, suggesting a punctuated repressive function for these regulatory elements. Conclusion By integrating and analyzing epigenomic, genomic and transcriptomic data, our work reveals a novel distal element in var control. We found dynamic modulations of specific epigenetic marks around the var intron and distal upstream regions are involved in the general var gene expression patterns in malarial antigenic variation. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3005-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Chengqi Wang
- Department of Global Health (GH) & Center for Drug Discovery and Innovation (CDDI), College of Public Health, University of South Florida, Tampa, FL, 33612, USA
| | - Swamy R Adapa
- Department of Global Health (GH) & Center for Drug Discovery and Innovation (CDDI), College of Public Health, University of South Florida, Tampa, FL, 33612, USA
| | - Justin Gibbons
- Department of Global Health (GH) & Center for Drug Discovery and Innovation (CDDI), College of Public Health, University of South Florida, Tampa, FL, 33612, USA.,Department of Molecular Medicine, University of South Florida, Tampa, FL, 33612, USA
| | - Stephen Sutton
- Department of Global Health (GH) & Center for Drug Discovery and Innovation (CDDI), College of Public Health, University of South Florida, Tampa, FL, 33612, USA
| | - Rays H Y Jiang
- Department of Global Health (GH) & Center for Drug Discovery and Innovation (CDDI), College of Public Health, University of South Florida, Tampa, FL, 33612, USA.
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27
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Bronner IF, Otto TD, Zhang M, Udenze K, Wang C, Quail MA, Jiang RHY, Adams JH, Rayner JC. Quantitative insertion-site sequencing (QIseq) for high throughput phenotyping of transposon mutants. Genome Res 2016; 26:980-9. [PMID: 27197223 PMCID: PMC4937560 DOI: 10.1101/gr.200279.115] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Accepted: 05/04/2016] [Indexed: 01/06/2023]
Abstract
Genetic screening using random transposon insertions has been a powerful tool for uncovering biology in prokaryotes, where whole-genome saturating screens have been performed in multiple organisms. In eukaryotes, such screens have proven more problematic, in part because of the lack of a sensitive and robust system for identifying transposon insertion sites. We here describe quantitative insertion-site sequencing, or QIseq, which uses custom library preparation and Illumina sequencing technology and is able to identify insertion sites from both the 5′ and 3′ ends of the transposon, providing an inbuilt level of validation. The approach was developed using piggyBac mutants in the human malaria parasite Plasmodium falciparum but should be applicable to many other eukaryotic genomes. QIseq proved accurate, confirming known sites in >100 mutants, and sensitive, identifying and monitoring sites over a >10,000-fold dynamic range of sequence counts. Applying QIseq to uncloned parasites shortly after transfections revealed multiple insertions in mixed populations and suggests that >4000 independent mutants could be generated from relatively modest scales of transfection, providing a clear pathway to genome-scale screens in P. falciparum. QIseq was also used to monitor the growth of pools of previously cloned mutants and reproducibly differentiated between deleterious and neutral mutations in competitive growth. Among the mutants with fitness defects was a mutant with a piggyBac insertion immediately upstream of the kelch protein K13 gene associated with artemisinin resistance, implying mutants in this gene may have competitive fitness costs. QIseq has the potential to enable the scale-up of piggyBac-mediated genetics across multiple eukaryotic systems.
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Affiliation(s)
- Iraad F Bronner
- Malaria Programme, Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridgeshire CB10 1SA, United Kingdom
| | - Thomas D Otto
- Malaria Programme, Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridgeshire CB10 1SA, United Kingdom
| | - Min Zhang
- Center for Global Health and Infectious Diseases, Department of Global Health, University of South Florida, Tampa, Florida 33612, USA
| | - Kenneth Udenze
- Center for Global Health and Infectious Diseases, Department of Global Health, University of South Florida, Tampa, Florida 33612, USA
| | - Chengqi Wang
- Center for Global Health and Infectious Diseases, Department of Global Health, University of South Florida, Tampa, Florida 33612, USA
| | - Michael A Quail
- Malaria Programme, Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridgeshire CB10 1SA, United Kingdom
| | - Rays H Y Jiang
- Center for Global Health and Infectious Diseases, Department of Global Health, University of South Florida, Tampa, Florida 33612, USA
| | - John H Adams
- Center for Global Health and Infectious Diseases, Department of Global Health, University of South Florida, Tampa, Florida 33612, USA
| | - Julian C Rayner
- Malaria Programme, Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridgeshire CB10 1SA, United Kingdom
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28
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Dankwa S, Lim C, Bei AK, Jiang RHY, Abshire JR, Patel SD, Goldberg JM, Moreno Y, Kono M, Niles JC, Duraisingh MT. Ancient human sialic acid variant restricts an emerging zoonotic malaria parasite. Nat Commun 2016; 7:11187. [PMID: 27041489 PMCID: PMC4822025 DOI: 10.1038/ncomms11187] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Accepted: 02/25/2016] [Indexed: 01/19/2023] Open
Abstract
Plasmodium knowlesi is a zoonotic parasite transmitted from macaques causing malaria in humans in Southeast Asia. Plasmodium parasites bind to red blood cell (RBC) surface receptors, many of which are sialylated. While macaques synthesize the sialic acid variant N-glycolylneuraminic acid (Neu5Gc), humans cannot because of a mutation in the enzyme CMAH that converts N-acetylneuraminic acid (Neu5Ac) to Neu5Gc. Here we reconstitute CMAH in human RBCs for the reintroduction of Neu5Gc, which results in enhancement of P. knowlesi invasion. We show that two P. knowlesi invasion ligands, PkDBPβ and PkDBPγ, bind specifically to Neu5Gc-containing receptors. A human-adapted P. knowlesi line invades human RBCs independently of Neu5Gc, with duplication of the sialic acid-independent invasion ligand, PkDBPα and loss of PkDBPγ. Our results suggest that absence of Neu5Gc on human RBCs limits P. knowlesi invasion, but that parasites may evolve to invade human RBCs through the use of sialic acid-independent pathways.
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Affiliation(s)
- Selasi Dankwa
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts 02115, USA
| | - Caeul Lim
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts 02115, USA
| | - Amy K Bei
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts 02115, USA
| | - Rays H Y Jiang
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts 02115, USA
| | - James R Abshire
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Saurabh D Patel
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts 02115, USA.,Division of Gastroenterology, Hepatology and Nutrition, Boston Children's Hospital, Boston, Massachusetts 02115, USA
| | - Jonathan M Goldberg
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts 02115, USA
| | - Yovany Moreno
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts 02115, USA
| | - Maya Kono
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts 02115, USA
| | - Jacquin C Niles
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Manoj T Duraisingh
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts 02115, USA
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29
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Mhashilkar AS, Adapa SR, Jiang RHY, Williams SA, Zaky W, Slatko BE, Luck AN, Moorhead AR, Unnasch TR. Phenotypic and molecular analysis of the effect of 20-hydroxyecdysone on the human filarial parasite Brugia malayi. Int J Parasitol 2016; 46:333-41. [PMID: 26896576 DOI: 10.1016/j.ijpara.2016.01.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Revised: 01/20/2016] [Accepted: 01/22/2016] [Indexed: 11/18/2022]
Abstract
A homologue of the ecdysone receptor has been identified and shown to be responsive to 20-hydroxyecdysone in Brugia malayi. However, the role of this master regulator of insect development has not been delineated in filarial nematodes. Gravid adult female B. malayi cultured in the presence of 20-hydroxyecdysone produced significantly more microfilariae and abortive immature progeny than control worms, implicating the ecdysone receptor in regulation of embryogenesis and microfilarial development. Transcriptome analyses identified 30 genes whose expression was significantly up-regulated in 20-hydroxyecdysone-treated parasites compared with untreated controls. Of these, 18% were identified to be regulating transcription. A comparative proteomic analysis revealed 932 proteins to be present in greater amounts in extracts of 20-hydroxyecdysone-treated adult females than in extracts prepared from worms cultured in the absence of the hormone. Of the proteins exhibiting a greater than two-fold difference in the 20-hydroxyecdysone-treated versus untreated parasite extracts, 16% were involved in transcriptional regulation. RNA interference (RNAi) phenotype analysis of Caenorhabditis elegans orthologs revealed that phenotypes involved in developmental processes associated with embryogenesis were significantly over-represented in the transcripts and proteins that were up-regulated by exposure to 20-hydroxyecdysone. Taken together, the transcriptomic, proteomic and phenotypic data suggest that the filarial ecdysone receptor may play a role analogous to that in insects, where it serves as a regulator of egg development.
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Affiliation(s)
- Amruta S Mhashilkar
- Department of Global Health, College of Public Health, University of South Florida, Tampa, FL 33612, USA
| | - Swamy R Adapa
- Department of Global Health, College of Public Health, University of South Florida, Tampa, FL 33612, USA
| | - Rays H Y Jiang
- Department of Global Health, College of Public Health, University of South Florida, Tampa, FL 33612, USA
| | - Steven A Williams
- Department of Biological Sciences, 100 Green Street, Ford Hall, Smith College, Northampton, MA 01063, USA
| | - Weam Zaky
- Department of Biological Sciences, 100 Green Street, Ford Hall, Smith College, Northampton, MA 01063, USA
| | - Barton E Slatko
- Genome Biology Division, Molecular Parasitology Group, New England Biolabs, 240 County Road, Ipswich, MA 01938, USA
| | - Ashley N Luck
- Genome Biology Division, Molecular Parasitology Group, New England Biolabs, 240 County Road, Ipswich, MA 01938, USA
| | - Andrew R Moorhead
- Department of Infectious Diseases, University of Georgia, College of Veterinary Medicine, 501 D. W. Brooks Drive, Athens, GA 30602, USA
| | - Thomas R Unnasch
- Department of Global Health, College of Public Health, University of South Florida, Tampa, FL 33612, USA.
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30
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Pellé KG, Jiang RHY, Mantel PY, Xiao YP, Hjelmqvist D, Gallego-Lopez GM, O T Lau A, Kang BH, Allred DR, Marti M. Shared elements of host-targeting pathways among apicomplexan parasites of differing lifestyles. Cell Microbiol 2015; 17:1618-39. [PMID: 25996544 DOI: 10.1111/cmi.12460] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2013] [Revised: 04/27/2015] [Accepted: 05/14/2015] [Indexed: 11/30/2022]
Abstract
Apicomplexans are a diverse group of obligate parasites occupying different intracellular niches that require modification to meet the needs of the parasite. To efficiently manipulate their environment, apicomplexans translocate numerous parasite proteins into the host cell. Whereas some parasites remain contained within a parasitophorous vacuole membrane (PVM) throughout their developmental cycle, others do not, a difference that affects the machinery needed for protein export. A signal-mediated pathway for protein export into the host cell has been characterized in Plasmodium parasites, which maintain the PVM. Here, we functionally demonstrate an analogous host-targeting pathway involving organellar staging prior to secretion in the related bovine parasite, Babesia bovis, a parasite that destroys the PVM shortly after invasion. Taking into account recent identification of a similar signal-mediated pathway in the coccidian parasite Toxoplasma gondii, we suggest a model in which this conserved pathway has evolved in multiple steps from signal-mediated trafficking to specific secretory organelles for controlled secretion to a complex protein translocation process across the PVM.
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Affiliation(s)
- Karell G Pellé
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, MA, USA
| | - Rays H Y Jiang
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, MA, USA.,The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Pierre-Yves Mantel
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, MA, USA
| | - Yu-Ping Xiao
- Department of Infectious Diseases and Pathology, University of Florida, Gainesville, FL, USA
| | - Daisy Hjelmqvist
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, MA, USA
| | - Gina M Gallego-Lopez
- Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, WA, USA
| | - Audrey O T Lau
- Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, WA, USA
| | - Byung-Ho Kang
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, USA
| | - David R Allred
- Department of Infectious Diseases and Pathology, University of Florida, Gainesville, FL, USA.,Genetics Institute, University of Florida, Gainesville, FL, USA
| | - Matthias Marti
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, MA, USA
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31
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Paul AS, Saha S, Engelberg K, Jiang RHY, Coleman BI, Kosber AL, Chen CT, Ganter M, Espy N, Gilberger TW, Gubbels MJ, Duraisingh MT. Parasite Calcineurin Regulates Host Cell Recognition and Attachment by Apicomplexans. Cell Host Microbe 2015; 18:49-60. [PMID: 26118996 DOI: 10.1016/j.chom.2015.06.003] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Revised: 04/30/2015] [Accepted: 05/28/2015] [Indexed: 12/12/2022]
Abstract
Apicomplexans invade a variety of metazoan host cells through mechanisms involving host cell receptor engagement and secretion of parasite factors to facilitate cellular attachment. We find that the parasite homolog of calcineurin, a calcium-regulated phosphatase complex central to signal transduction in eukaryotes, also contributes to host cell invasion by the malaria parasite Plasmodium falciparum and related Toxoplasma gondii. Using reverse-genetic and chemical-genetic approaches, we determine that calcineurin critically regulates and stabilizes attachment of extracellular P. falciparum to host erythrocytes before intracellular entry and has similar functions in host cell engagement by T. gondii. Calcineurin-mediated Plasmodium invasion is strongly associated with host receptors required for host cell recognition, and calcineurin function distinguishes this form of receptor-mediated attachment from a second mode of host-parasite adhesion independent of host receptors. This specific role of calcineurin in coordinating physical interactions with host cells highlights an ancestral mechanism for parasitism used by apicomplexans.
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Affiliation(s)
- Aditya S Paul
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Sudeshna Saha
- Department of Biology, Boston College, Chestnut Hill, MA 02467, USA
| | | | - Rays H Y Jiang
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | | | - Aziz L Kosber
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Chun-Ti Chen
- Department of Biology, Boston College, Chestnut Hill, MA 02467, USA
| | - Markus Ganter
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Nicole Espy
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Tim W Gilberger
- Bernhard Nocht Institute for Tropical Medicine, 20359 Hamburg, Germany; Centre for Structural Systems Biology, 22607 Hamburg, Germany
| | - Marc-Jan Gubbels
- Department of Biology, Boston College, Chestnut Hill, MA 02467, USA
| | - Manoj T Duraisingh
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA.
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Egan ES, Jiang RHY, Moechtar MA, Barteneva NS, Weekes MP, Nobre LV, Gygi SP, Paulo JA, Frantzreb C, Tani Y, Takahashi J, Watanabe S, Goldberg J, Paul AS, Brugnara C, Root DE, Wiegand RC, Doench JG, Duraisingh MT. Malaria. A forward genetic screen identifies erythrocyte CD55 as essential for Plasmodium falciparum invasion. Science 2015; 348:711-4. [PMID: 25954012 DOI: 10.1126/science.aaa3526] [Citation(s) in RCA: 87] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Efforts to identify host determinants for malaria have been hindered by the absence of a nucleus in erythrocytes, which precludes genetic manipulation in the cell in which the parasite replicates. We used cultured red blood cells derived from hematopoietic stem cells to carry out a forward genetic screen for Plasmodium falciparum host determinants. We found that CD55 is an essential host factor for P. falciparum invasion. CD55-null erythrocytes were refractory to invasion by all isolates of P. falciparum because parasites failed to attach properly to the erythrocyte surface. Thus, CD55 is an attractive target for the development of malaria therapeutics. Hematopoietic stem cell-based forward genetic screens may be valuable for the identification of additional host determinants of malaria pathogenesis.
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Affiliation(s)
- Elizabeth S Egan
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA. Division of Infectious Diseases, Boston Children's Hospital, Boston, MA, USA
| | - Rays H Y Jiang
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA. Department of Global Health and Center for Drug Discovery and Innovation, University of South Florida, Tampa, FL, USA
| | - Mischka A Moechtar
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Natasha S Barteneva
- Department of Pediatrics, Harvard Medical School and Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
| | - Michael P Weekes
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | - Luis V Nobre
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Joao A Paulo
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Charles Frantzreb
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Yoshihiko Tani
- Japanese Red Cross Kinki Block Blood Center, Osaka, Japan
| | | | - Seishi Watanabe
- Japanese Red Cross Kyushu Block Blood Center, Fukuoka, Japan
| | - Jonathan Goldberg
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Aditya S Paul
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Carlo Brugnara
- Department of Laboratory Medicine, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
| | - David E Root
- The Broad Institute of Harvard and Massachussetts Insititute of Technology, Cambridge, MA, USAA
| | - Roger C Wiegand
- The Broad Institute of Harvard and Massachussetts Insititute of Technology, Cambridge, MA, USAA
| | - John G Doench
- The Broad Institute of Harvard and Massachussetts Insititute of Technology, Cambridge, MA, USAA
| | - Manoj T Duraisingh
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA. The Broad Institute of Harvard and Massachussetts Insititute of Technology, Cambridge, MA, USAA.
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Coleman BI, Skillman KM, Jiang RHY, Childs LM, Altenhofen LM, Ganter M, Leung Y, Goldowitz I, Kafsack BFC, Marti M, Llinás M, Buckee CO, Duraisingh MT. A Plasmodium falciparum histone deacetylase regulates antigenic variation and gametocyte conversion. Cell Host Microbe 2015; 16:177-186. [PMID: 25121747 DOI: 10.1016/j.chom.2014.06.014] [Citation(s) in RCA: 147] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2014] [Revised: 05/06/2014] [Accepted: 06/06/2014] [Indexed: 01/20/2023]
Abstract
The asexual forms of the malaria parasite Plasmodium falciparum are adapted for chronic persistence in human red blood cells, continuously evading host immunity using epigenetically regulated antigenic variation of virulence-associated genes. Parasite survival on a population level also requires differentiation into sexual forms, an obligatory step for further human transmission. We reveal that the essential nuclear gene, P. falciparum histone deacetylase 2 (PfHda2), is a global silencer of virulence gene expression and controls the frequency of switching from the asexual cycle to sexual development. PfHda2 depletion leads to dysregulated expression of both virulence-associated var genes and PfAP2-g, a transcription factor controlling sexual conversion, and is accompanied by increases in gametocytogenesis. Mathematical modeling further indicates that PfHda2 has likely evolved to optimize the parasite's infectious period by achieving low frequencies of virulence gene expression switching and sexual conversion. This common regulation of cellular transcriptional programs mechanistically links parasite transmissibility and virulence.
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Affiliation(s)
- Bradley I Coleman
- Department of Immunology & Infectious Diseases Harvard School of Public Health, Boston, MA 02115 USA
| | - Kristen M Skillman
- Department of Immunology & Infectious Diseases Harvard School of Public Health, Boston, MA 02115 USA
| | - Rays H Y Jiang
- Department of Immunology & Infectious Diseases Harvard School of Public Health, Boston, MA 02115 USA
| | - Lauren M Childs
- Department of Epidemiology and Center for Communicable Disease Dynamics, Harvard School of Public Health, Boston MA 02115 USA
| | - Lindsey M Altenhofen
- Department of Molecular Biology and Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton NJ 08544 USA
| | - Markus Ganter
- Department of Immunology & Infectious Diseases Harvard School of Public Health, Boston, MA 02115 USA
| | - Yvette Leung
- Department of Immunology & Infectious Diseases Harvard School of Public Health, Boston, MA 02115 USA
| | - Ilana Goldowitz
- Department of Immunology & Infectious Diseases Harvard School of Public Health, Boston, MA 02115 USA
| | - Björn F C Kafsack
- Department of Molecular Biology and Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton NJ 08544 USA
| | - Matthias Marti
- Department of Immunology & Infectious Diseases Harvard School of Public Health, Boston, MA 02115 USA
| | - Manuel Llinás
- Department of Molecular Biology and Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton NJ 08544 USA
| | - Caroline O Buckee
- Department of Epidemiology and Center for Communicable Disease Dynamics, Harvard School of Public Health, Boston MA 02115 USA
| | - Manoj T Duraisingh
- Department of Immunology & Infectious Diseases Harvard School of Public Health, Boston, MA 02115 USA
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Merrick CJ, Jiang RHY, Skillman KM, Samarakoon U, Moore RM, Dzikowski R, Ferdig MT, Duraisingh MT. Functional analysis of sirtuin genes in multiple Plasmodium falciparum strains. PLoS One 2015; 10:e0118865. [PMID: 25780929 PMCID: PMC4364008 DOI: 10.1371/journal.pone.0118865] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Accepted: 01/07/2015] [Indexed: 12/22/2022] Open
Abstract
Plasmodium falciparum, the causative agent of severe human malaria, employs antigenic variation to avoid host immunity. Antigenic variation is achieved by transcriptional switching amongst polymorphic var genes, enforced by epigenetic modification of chromatin. The histone-modifying 'sirtuin' enzymes PfSir2a and PfSir2b have been implicated in this process. Disparate patterns of var expression have been reported in patient isolates as well as in cultured strains. We examined var expression in three commonly used laboratory strains (3D7, NF54 and FCR-3) in parallel. NF54 parasites express significantly lower levels of var genes compared to 3D7, despite the fact that 3D7 was originally a clone of the NF54 strain. To investigate whether this was linked to the expression of sirtuins, genetic disruption of both sirtuins was attempted in all three strains. No dramatic changes in var gene expression occurred in NF54 or FCR-3 following PfSir2b disruption, contrasting with previous observations in 3D7. In 3D7, complementation of the PfSir2a genetic disruption resulted in a significant decrease in previously-elevated var gene expression levels, but with the continued expression of multiple var genes. Finally, rearranged chromosomes were observed in the 3D7 PfSir2a knockout line. Our results focus on the potential for parasite genetic background to contribute to sirtuin function in regulating virulence gene expression and suggest a potential role for sirtuins in maintaining genome integrity.
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Affiliation(s)
- Catherine J. Merrick
- Department of Immunology & Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts, United States of America
| | - Rays H. Y. Jiang
- Department of Immunology & Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts, United States of America
| | - Kristen M. Skillman
- Department of Immunology & Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts, United States of America
| | - Upeka Samarakoon
- Department of Biological Sciences, Eck Institute for Global Health, University of Notre Dame, Notre Dame, Indiana, United States of America
| | - Rachel M. Moore
- Department of Immunology & Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts, United States of America
| | - Ron Dzikowski
- Department of Microbiology & Molecular Genetics, The Kuvin Center for the Study of Infectious and Tropical Diseases, IMRIC, The Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Michael T. Ferdig
- Department of Biological Sciences, Eck Institute for Global Health, University of Notre Dame, Notre Dame, Indiana, United States of America
| | - Manoj T. Duraisingh
- Department of Immunology & Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts, United States of America
- * E-mail:
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35
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Jiang RHY, de Bruijn I, Haas BJ, Belmonte R, Löbach L, Christie J, van den Ackerveken G, Bottin A, Bulone V, Díaz-Moreno SM, Dumas B, Fan L, Gaulin E, Govers F, Grenville-Briggs LJ, Horner NR, Levin JZ, Mammella M, Meijer HJG, Morris P, Nusbaum C, Oome S, Phillips AJ, van Rooyen D, Rzeszutek E, Saraiva M, Secombes CJ, Seidl MF, Snel B, Stassen JHM, Sykes S, Tripathy S, van den Berg H, Vega-Arreguin JC, Wawra S, Young SK, Zeng Q, Dieguez-Uribeondo J, Russ C, Tyler BM, van West P. Distinctive expansion of potential virulence genes in the genome of the oomycete fish pathogen Saprolegnia parasitica. PLoS Genet 2013; 9:e1003272. [PMID: 23785293 PMCID: PMC3681718 DOI: 10.1371/journal.pgen.1003272] [Citation(s) in RCA: 129] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2012] [Accepted: 12/10/2012] [Indexed: 01/31/2023] Open
Abstract
Oomycetes in the class Saprolegniomycetidae of the Eukaryotic kingdom Stramenopila have evolved as severe pathogens of amphibians, crustaceans, fish and insects, resulting in major losses in aquaculture and damage to aquatic ecosystems. We have sequenced the 63 Mb genome of the fresh water fish pathogen, Saprolegnia parasitica. Approximately 1/3 of the assembled genome exhibits loss of heterozygosity, indicating an efficient mechanism for revealing new variation. Comparison of S. parasitica with plant pathogenic oomycetes suggests that during evolution the host cellular environment has driven distinct patterns of gene expansion and loss in the genomes of plant and animal pathogens. S. parasitica possesses one of the largest repertoires of proteases (270) among eukaryotes that are deployed in waves at different points during infection as determined from RNA-Seq data. In contrast, despite being capable of living saprotrophically, parasitism has led to loss of inorganic nitrogen and sulfur assimilation pathways, strikingly similar to losses in obligate plant pathogenic oomycetes and fungi. The large gene families that are hallmarks of plant pathogenic oomycetes such as Phytophthora appear to be lacking in S. parasitica, including those encoding RXLR effectors, Crinkler's, and Necrosis Inducing-Like Proteins (NLP). S. parasitica also has a very large kinome of 543 kinases, 10% of which is induced upon infection. Moreover, S. parasitica encodes several genes typical of animals or animal-pathogens and lacking from other oomycetes, including disintegrins and galactose-binding lectins, whose expression and evolutionary origins implicate horizontal gene transfer in the evolution of animal pathogenesis in S. parasitica. Fish are an increasingly important source of animal protein globally, with aquaculture production rising dramatically over the past decade. Saprolegnia is a fungal-like oomycete and one of the most destructive fish pathogens, causing millions of dollars in losses to the aquaculture industry annually. Saprolegnia has also been linked to a worldwide decline in wild fish and amphibian populations. Here we describe the genome sequence of the first animal pathogenic oomycete and compare the genome content with the available plant pathogenic oomycetes. We found that Saprolegnia lacks the large effector families that are hallmarks of plant pathogenic oomycetes, showing evolutionary adaptation to the host. Moreover, Saprolegnia harbors pathogenesis-related genes that were derived by lateral gene transfer from the host and other animal pathogens. The retrotransposon LINE family also appears to be acquired from animal lineages. By transcriptome analysis we show a high rate of allelic variation, which reveals rapidly evolving genes and potentially adaptive evolutionary mechanisms coupled to selective pressures exerted by the animal host. The genome and transcriptome data, as well as subsequent biochemical analyses, provided us with insight in the disease process of Saprolegnia at a molecular and cellular level, providing us with targets for sustainable control of Saprolegnia.
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Affiliation(s)
- Rays H Y Jiang
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
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Jiang RHY, Stahelin RV, Bhattacharjee S, Haldar K. Eukaryotic virulence determinants utilize phosphoinositides at the ER and host cell surface. Trends Microbiol 2013; 21:145-56. [PMID: 23375057 DOI: 10.1016/j.tim.2012.12.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2012] [Revised: 12/12/2012] [Accepted: 12/18/2012] [Indexed: 01/03/2023]
Abstract
Similar to bacteria, eukaryotic pathogens may utilize common strategies of pathogenic secretion, because effector proteins from the oomycete Phytophthora infestans and virulence determinants from the human malaria parasite Plasmodium falciparum share a functionally equivalent host-cell-targeting motif (RxLR-dEER in P. infestans and RxLxE/D/Q in P. falciparum). Here we summarize recent studies that reveal that the malarial motif may function differently than previously envisioned. Binding of the lipid phosphatidylinositol 3-phosphate [PI(3)P] is a critical step in accessing the host for both pathogens, but occurs in different locations. Nanomolar affinity for PI(3)P by these short amino acid motifs suggests that a newly identified mechanism of phosphoinositide binding that unexpectedly occurs in secretory locations has been exploited for virulence by diverse eukaryotic pathogens.
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Affiliation(s)
- Rays H Y Jiang
- Department of Infectious Diseases and Immunology, Harvard School of Public Health, 665 Huntington Avenue, Boston, MA 02115, USA
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37
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Neafsey DE, Galinsky K, Jiang RHY, Young L, Sykes SM, Saif S, Gujja S, Goldberg JM, Young S, Zeng Q, Chapman SB, Dash AP, Anvikar AR, Sutton PL, Birren BW, Escalante AA, Barnwell JW, Carlton JM. The malaria parasite Plasmodium vivax exhibits greater genetic diversity than Plasmodium falciparum. Nat Genet 2012; 44:1046-50. [PMID: 22863733 PMCID: PMC3432710 DOI: 10.1038/ng.2373] [Citation(s) in RCA: 210] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2012] [Accepted: 07/09/2012] [Indexed: 11/09/2022]
Abstract
We sequenced and annotated the genomes of four P. vivax strains collected from disparate geographic locations, tripling the number of genome sequences available for this understudied parasite and providing the first genome-wide perspective of global variability in this species. We observe approximately twice as much SNP diversity among these isolates as we do among a comparable collection of isolates of P. falciparum, a malaria-causing parasite that results in higher mortality. This indicates a distinct history of global colonization and/or a more stable demographic history for P. vivax relative to P. falciparum, which is thought to have undergone a recent population bottleneck. The SNP diversity, as well as additional microsatellite and gene family variability, suggests a capacity for greater functional variation in the global population of P. vivax. These findings warrant a deeper survey of variation in P. vivax to equip disease interventions targeting the distinctive biology of this neglected but major pathogen.
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38
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Jiang RHY, Marti M. A PIP Gets the plasmodium protein export pathway going. Cell Host Microbe 2012; 11:99-100. [PMID: 22341457 DOI: 10.1016/j.chom.2012.01.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Survival of blood stage malaria parasites requires extensive host cell remodeling, which is facilitated by secretion of parasite proteins via a dedicated protein export pathway. In a recent Cell paper, Bhattacharjee et al., (2012) describe PI(3)P binding as one of the first steps in targeting parasite proteins to the host cell.
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Affiliation(s)
- Rays H Y Jiang
- The Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA
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Abstract
Next-Generation Sequencing (NGS) methods have revolutionized various aspects of genomics including transcriptome analysis. Digital expression analysis is all set to replace analog expression analysis that uses microarray chips through their cost-effectiveness, reproducibility, accuracy, and speed. The last 2 years have seen a surge in the development of statistical methods and software tools for analysis and visualization of NGS data. Large amounts of NGS data are available for pathogenic fungi and oomycetes. As the analysis results start pouring in, it brings about a paradigm shift in the understanding of host pathogen interactions with discovery of new transcripts, splice variants, mutations, regulatory elements, and epigenetic controls. Here we describe the core technology of the new sequencing platforms, the methodology of data analysis, and different aspects of applications.
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Affiliation(s)
- Sucheta Tripathy
- Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA.
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Abstract
Many destructive diseases of plants and animals are caused by oomycetes, a group of eukaryotic pathogens important to agricultural, ornamental, and natural ecosystems. Understanding the mechanisms underlying oomycete virulence and the genomic processes by which those mechanisms rapidly evolve is essential to developing effective long-term control measures for oomycete diseases. Several common mechanisms underlying oomycete virulence, including protein toxins and cell-entering effectors, have emerged from comparing oomycetes with different genome characteristics, parasitic lifestyles, and host ranges. Oomycete genomes display a strongly bipartite organization in which conserved housekeeping genes are concentrated in syntenic gene-rich blocks, whereas virulence genes are dispersed into highly dynamic, repeat-rich regions. There is also evidence that key virulence genes have been acquired by horizontal transfer from other eukaryotic and prokaryotic species.
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Affiliation(s)
- Rays H Y Jiang
- The Broad Institute of the Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02142, USA.
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Links MG, Holub E, Jiang RHY, Sharpe AG, Hegedus D, Beynon E, Sillito D, Clarke WE, Uzuhashi S, Borhan MH. De novo sequence assembly of Albugo candida reveals a small genome relative to other biotrophic oomycetes. BMC Genomics 2011; 12:503. [PMID: 21995639 PMCID: PMC3206522 DOI: 10.1186/1471-2164-12-503] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2011] [Accepted: 10/13/2011] [Indexed: 11/28/2022] Open
Abstract
Background Albugo candida is a biotrophic oomycete that parasitizes various species of Brassicaceae, causing a disease (white blister rust) with remarkable convergence in behaviour to unrelated rusts of basidiomycete fungi. Results A recent genome analysis of the oomycete Hyaloperonospora arabidopsidis suggests that a reduction in the number of genes encoding secreted pathogenicity proteins, enzymes for assimilation of inorganic nitrogen and sulphur represent a genomic signature for the evolution of obligate biotrophy. Here, we report a draft reference genome of a major crop pathogen Albugo candida (another obligate biotrophic oomycete) with an estimated genome of 45.3 Mb. This is very similar to the genome size of a necrotrophic oomycete Pythium ultimum (43 Mb) but less than half that of H. arabidopsidis (99 Mb). Sequencing of A. candida transcripts from infected host tissue and zoosporangia combined with genome-wide annotation revealed 15,824 predicted genes. Most of the predicted genes lack significant similarity with sequences from other oomycetes. Most intriguingly, A. candida appears to have a much smaller repertoire of pathogenicity-related proteins than H. arabidopsidis including genes that encode RXLR effector proteins, CRINKLER-like genes, and elicitins. Necrosis and Ethylene inducing Peptides were not detected in the genome of A. candida. Putative orthologs of tat-C, a component of the twin arginine translocase system, were identified from multiple oomycete genera along with proteins containing putative tat-secretion signal peptides. Conclusion Albugo candida has a comparatively small genome amongst oomycetes, retains motility of sporangial inoculum, and harbours a much smaller repertoire of candidate effectors than was recently reported for H. arabidopsidis. This minimal gene repertoire could indicate a lack of expansion, rather than a reduction, in the number of genes that signify the evolution of biotrophy in oomycetes.
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Affiliation(s)
- Matthew G Links
- Agriculture and Agri-Food Canada, Saskatoon, SK, S7N 0X2 Canada
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42
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Raffaele S, Farrer RA, Cano LM, Studholme DJ, MacLean D, Thines M, Jiang RHY, Zody MC, Kunjeti SG, Donofrio NM, Meyers BC, Nusbaum C, Kamoun S. Genome evolution following host jumps in the Irish potato famine pathogen lineage. Science 2010; 330:1540-3. [PMID: 21148391 DOI: 10.1126/science.1193070] [Citation(s) in RCA: 271] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Many plant pathogens, including those in the lineage of the Irish potato famine organism Phytophthora infestans, evolve by host jumps followed by specialization. However, how host jumps affect genome evolution remains largely unknown. To determine the patterns of sequence variation in the P. infestans lineage, we resequenced six genomes of four sister species. This revealed uneven evolutionary rates across genomes with genes in repeat-rich regions showing higher rates of structural polymorphisms and positive selection. These loci are enriched in genes induced in planta, implicating host adaptation in genome evolution. Unexpectedly, genes involved in epigenetic processes formed another class of rapidly evolving residents of the gene-sparse regions. These results demonstrate that dynamic repeat-rich genome compartments underpin accelerated gene evolution following host jumps in this pathogen lineage.
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Affiliation(s)
- Sylvain Raffaele
- The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH, UK
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43
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Baxter L, Tripathy S, Ishaque N, Boot N, Cabral A, Kemen E, Thines M, Ah-Fong A, Anderson R, Badejoko W, Bittner-Eddy P, Boore JL, Chibucos MC, Coates M, Dehal P, Delehaunty K, Dong S, Downton P, Dumas B, Fabro G, Fronick C, Fuerstenberg SI, Fulton L, Gaulin E, Govers F, Hughes L, Humphray S, Jiang RHY, Judelson H, Kamoun S, Kyung K, Meijer H, Minx P, Morris P, Nelson J, Phuntumart V, Qutob D, Rehmany A, Rougon-Cardoso A, Ryden P, Torto-Alalibo T, Studholme D, Wang Y, Win J, Wood J, Clifton SW, Rogers J, Van den Ackerveken G, Jones JDG, McDowell JM, Beynon J, Tyler BM. Signatures of adaptation to obligate biotrophy in the Hyaloperonospora arabidopsidis genome. Science 2010; 330:1549-1551. [PMID: 21148394 PMCID: PMC3971456 DOI: 10.1126/science.1195203] [Citation(s) in RCA: 321] [Impact Index Per Article: 22.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Many oomycete and fungal plant pathogens are obligate biotrophs, which extract nutrients only from living plant tissue and cannot grow apart from their hosts. Although these pathogens cause substantial crop losses, little is known about the molecular basis or evolution of obligate biotrophy. Here, we report the genome sequence of the oomycete Hyaloperonospora arabidopsidis (Hpa), an obligate biotroph and natural pathogen of Arabidopsis thaliana. In comparison with genomes of related, hemibiotrophic Phytophthora species, the Hpa genome exhibits dramatic reductions in genes encoding (i) RXLR effectors and other secreted pathogenicity proteins, (ii) enzymes for assimilation of inorganic nitrogen and sulfur, and (iii) proteins associated with zoospore formation and motility. These attributes comprise a genomic signature of evolution toward obligate biotrophy.
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Affiliation(s)
- Laura Baxter
- School of Life Sciences, Warwick University, Wellesbourne, CV35 9EF, UK
| | - Sucheta Tripathy
- Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA, 24061, USA
| | - Naveed Ishaque
- Sainsbury Laboratory, University of East Anglia, John Innes Centre, Norwich NR4 7UH, UK
| | - Nico Boot
- Centre for Biosystems Genomics, P.O. Box 98,6700 AB Wageningen, The Netherlands
| | - Adriana Cabral
- Centre for Biosystems Genomics, P.O. Box 98,6700 AB Wageningen, The Netherlands
| | - Eric Kemen
- Sainsbury Laboratory, University of East Anglia, John Innes Centre, Norwich NR4 7UH, UK
| | - Marco Thines
- Sainsbury Laboratory, University of East Anglia, John Innes Centre, Norwich NR4 7UH, UK
- Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, D-60325 Frankfurt (Main), Germany
- Johann Wolfgang Goethe University, Department of Biological Sciences, Institute of Ecology, Evolution and Diversity, Siesmayerstr. 70, D-60323 Frankfurt (Main), Germany
| | - Audrey Ah-Fong
- Department of Plant Pathology and Microbiology, University of California, Riverside, CA 92521, USA
| | - Ryan Anderson
- Department of Plant Pathology, Physiology and Weed Science, Virginia Tech, Blacksburg, VA 24061, USA
| | - Wole Badejoko
- School of Life Sciences, Warwick University, Wellesbourne, CV35 9EF, UK
| | | | - Jeffrey L Boore
- Department of Integrative Biology, University of California, Berkeley, USA
| | - Marcus C Chibucos
- Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA, 24061, USA
| | - Mary Coates
- School of Life Sciences, Warwick University, Wellesbourne, CV35 9EF, UK
| | - Paramvir Dehal
- Lawrence Berkeley National Laboratories, Berkeley, CA, 94720, USA
| | - Kim Delehaunty
- Genome Sequencing Centre, Washington University School of Medicine, St Louis, MO63110, USA
| | - Suomeng Dong
- Agriculture and Agri-Food Canada, London, Ontario, N5V 4T3, Canada
- Department of Plant Pathology, Nanjing Agricultural University, China
| | - Polly Downton
- School of Life Sciences, Warwick University, Wellesbourne, CV35 9EF, UK
| | - Bernard Dumas
- Université de Toulouse, UPS, Surfaces Cellulaires et Signalisation chez les Végétaux, 24 chemin de Borde Rouge, BP42617, Auzeville, F-31326, Castanet-Tolosan, France
- CNRS, Surfaces Cellulaires et Signalisation chez les Végétaux, 24 chemin de Borde Rouge, BP42617, Auzeville, F-31326, Castanet-Tolosan, France
| | - Georgina Fabro
- Sainsbury Laboratory, University of East Anglia, John Innes Centre, Norwich NR4 7UH, UK
| | - Catrina Fronick
- Genome Sequencing Centre, Washington University School of Medicine, St Louis, MO63110, USA
| | | | - Lucinda Fulton
- Genome Sequencing Centre, Washington University School of Medicine, St Louis, MO63110, USA
| | - Elodie Gaulin
- Université de Toulouse, UPS, Surfaces Cellulaires et Signalisation chez les Végétaux, 24 chemin de Borde Rouge, BP42617, Auzeville, F-31326, Castanet-Tolosan, France
- CNRS, Surfaces Cellulaires et Signalisation chez les Végétaux, 24 chemin de Borde Rouge, BP42617, Auzeville, F-31326, Castanet-Tolosan, France
| | - Francine Govers
- Laboratory of Phytopathology, Wageningen University, and Centre for BioSystems Genomics, NL-1-6708 PB Wageningen, The Netherlands
| | - Linda Hughes
- School of Life Sciences, Warwick University, Wellesbourne, CV35 9EF, UK
| | - Sean Humphray
- Sanger, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Rays H Y Jiang
- Laboratory of Phytopathology, Wageningen University, and Centre for BioSystems Genomics, NL-1-6708 PB Wageningen, The Netherlands
- The Broad Institute of MIT and Harvard, Cambridge, MA 02141-2023, USA
| | - Howard Judelson
- Department of Plant Pathology and Microbiology, University of California, Riverside, CA 92521, USA
| | - Sophien Kamoun
- Sainsbury Laboratory, University of East Anglia, John Innes Centre, Norwich NR4 7UH, UK
| | - Kim Kyung
- Genome Sequencing Centre, Washington University School of Medicine, St Louis, MO63110, USA
| | - Harold Meijer
- Laboratory of Phytopathology, Wageningen University, and Centre for BioSystems Genomics, NL-1-6708 PB Wageningen, The Netherlands
| | - Patrick Minx
- Genome Sequencing Centre, Washington University School of Medicine, St Louis, MO63110, USA
| | - Paul Morris
- Department of Biological Sciences, Bowling Green State University, Bowling Green, Ohio 43403-0212, USA
| | - Joanne Nelson
- Genome Sequencing Centre, Washington University School of Medicine, St Louis, MO63110, USA
| | - Vipa Phuntumart
- Department of Biological Sciences, Bowling Green State University, Bowling Green, Ohio 43403-0212, USA
| | - Dinah Qutob
- Agriculture and Agri-Food Canada, London, Ontario, N5V 4T3, Canada
| | - Anne Rehmany
- School of Life Sciences, Warwick University, Wellesbourne, CV35 9EF, UK
| | | | - Peter Ryden
- School of Life Sciences, Warwick University, Wellesbourne, CV35 9EF, UK
| | - Trudy Torto-Alalibo
- Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA, 24061, USA
| | - David Studholme
- Sainsbury Laboratory, University of East Anglia, John Innes Centre, Norwich NR4 7UH, UK
| | - Yuanchao Wang
- Department of Plant Pathology, Nanjing Agricultural University, China
| | - Joe Win
- Sainsbury Laboratory, University of East Anglia, John Innes Centre, Norwich NR4 7UH, UK
| | - Jo Wood
- Sanger, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Sandra W Clifton
- Genome Sequencing Centre, Washington University School of Medicine, St Louis, MO63110, USA
| | - Jane Rogers
- Sanger, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Guido Van den Ackerveken
- Johann Wolfgang Goethe University, Department of Biological Sciences, Institute of Ecology, Evolution and Diversity, Siesmayerstr. 70, D-60323 Frankfurt (Main), Germany
| | - Jonathan D G Jones
- Sainsbury Laboratory, University of East Anglia, John Innes Centre, Norwich NR4 7UH, UK
| | - John M McDowell
- Department of Plant Pathology, Physiology and Weed Science, Virginia Tech, Blacksburg, VA 24061, USA
| | - Jim Beynon
- School of Life Sciences, Warwick University, Wellesbourne, CV35 9EF, UK
| | - Brett M Tyler
- Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA, 24061, USA
- Department of Plant Pathology, Physiology and Weed Science, Virginia Tech, Blacksburg, VA 24061, USA
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VAN Poppel PMJA, Jiang RHY, Sliwka J, Govers F. Recognition of Phytophthora infestans Avr4 by potato R4 is triggered by C-terminal domains comprising W motifs. Mol Plant Pathol 2009; 10:611-20. [PMID: 19694952 PMCID: PMC6640270 DOI: 10.1111/j.1364-3703.2009.00556.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
SUMMARY Oomycete RXLR-dEER effector proteins are rapidly evolving proteins with the selective pressure targeted predominantly at their C-terminal ends. The majority of RXLR-dEER proteins have recognizable motifs of 21-30 amino acids in the C-terminal domain that are named after conserved amino acid residues at fixed positions within the respective motifs. In this article, it is reported that the Phytophthora infestans RXLR-dEER protein Avr4 contains three W motifs and one Y motif in its C-terminal domain. Agroinfection assays using constructs encoding modified forms of PiAvr4 have shown that the region containing the W2 motif, in combination with either the W1 or W3 motif, triggers a necrotic response in potato plants carrying the resistance gene R4. By mining the superfamily of avirulence homologues (Avh) deduced from three sequenced Phytophthora genomes, several Avh proteins were identified as homologues of PiAvr4: six in P. infestans, one in P. ramorum and seven in P. sojae. One very close homologue of PiAvr4 was cloned from the sibling species, P. mirabilis. This species is not pathogenic on potato but, similar to PiAvr4, PmirAvh4 triggered a necrotic response on potato clones carrying R4, but not on clones lacking R4. Genes encoding RXLR-dEER effectors are often located in regions showing genome rearrangements. Alignment of the genomic region harbouring PiAvr4 with syntenic regions in P. sojae and P. ramorum revealed that PiAvr4 is located on a 100-kb indel block and is surrounded by transposable elements.
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Affiliation(s)
- Pieter M J A VAN Poppel
- Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
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45
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Dou D, Kale SD, Wang X, Jiang RHY, Bruce NA, Arredondo FD, Zhang X, Tyler BM. RXLR-mediated entry of Phytophthora sojae effector Avr1b into soybean cells does not require pathogen-encoded machinery. Plant Cell 2008; 20:1930-47. [PMID: 18621946 PMCID: PMC2518231 DOI: 10.1105/tpc.107.056093] [Citation(s) in RCA: 271] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2007] [Revised: 06/06/2008] [Accepted: 06/27/2008] [Indexed: 05/18/2023]
Abstract
Effector proteins secreted by oomycete and fungal pathogens have been inferred to enter host cells, where they interact with host resistance gene products. Using the effector protein Avr1b of Phytophthora sojae, an oomycete pathogen of soybean (Glycine max), we show that a pair of sequence motifs, RXLR and dEER, plus surrounding sequences, are both necessary and sufficient to deliver the protein into plant cells. Particle bombardment experiments demonstrate that these motifs function in the absence of the pathogen, indicating that no additional pathogen-encoded machinery is required for effector protein entry into host cells. Furthermore, fusion of the Avr1b RXLR-dEER domain to green fluorescent protein (GFP) allows GFP to enter soybean root cells autonomously. The conclusion that RXLR and dEER serve to transduce oomycete effectors into host cells indicates that the >370 RXLR-dEER-containing proteins encoded in the genome sequence of P. sojae are candidate effectors. We further show that the RXLR and dEER motifs can be replaced by the closely related erythrocyte targeting signals found in effector proteins of Plasmodium, the protozoan that causes malaria in humans. Mutational analysis of the RXLR motif shows that the required residues are very similar in the motifs of Plasmodium and Phytophthora. Thus, the machinery of the hosts (soybean and human) targeted by the effectors may be very ancient.
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Affiliation(s)
- Daolong Dou
- Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, USA
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46
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Dou D, Kale SD, Wang X, Chen Y, Wang Q, Wang X, Jiang RHY, Arredondo FD, Anderson RG, Thakur PB, McDowell JM, Wang Y, Tyler BM. Conserved C-terminal motifs required for avirulence and suppression of cell death by Phytophthora sojae effector Avr1b. Plant Cell 2008; 20:1118-33. [PMID: 18390593 PMCID: PMC2390733 DOI: 10.1105/tpc.107.057067] [Citation(s) in RCA: 221] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2007] [Revised: 02/26/2008] [Accepted: 03/17/2008] [Indexed: 05/17/2023]
Abstract
The sequenced genomes of oomycete plant pathogens contain large superfamilies of effector proteins containing the protein translocation motif RXLR-dEER. However, the contributions of these effectors to pathogenicity remain poorly understood. Here, we show that the Phytophthora sojae effector protein Avr1b can contribute positively to virulence and can suppress programmed cell death (PCD) triggered by the mouse BAX protein in yeast, soybean (Glycine max), and Nicotiana benthamiana cells. We identify three conserved motifs (K, W, and Y) in the C terminus of the Avr1b protein and show that mutations in the conserved residues of the W and Y motifs reduce or abolish the ability of Avr1b to suppress PCD and also abolish the avirulence interaction of Avr1b with the Rps1b resistance gene in soybean. W and Y motifs are present in at least half of the identified oomycete RXLR-dEER effector candidates, and we show that three of these candidates also suppress PCD in soybean. Together, these results indicate that the W and Y motifs are critical for the interaction of Avr1b with host plant target proteins and support the hypothesis that these motifs are critical for the functions of the very large number of predicted oomycete effectors that contain them.
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Affiliation(s)
- Daolong Dou
- Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, USA
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47
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Zhang X, Scheuring C, Tripathy S, Xu Z, Wu C, Ko A, Tian SK, Arredondo F, Lee MK, Santos FA, Jiang RHY, Zhang HB, Tyler BM. An integrated BAC and genome sequence physical map of Phytophthora sojae. Mol Plant Microbe Interact 2006; 19:1302-10. [PMID: 17153914 DOI: 10.1094/mpmi-19-1302] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Phytophthora spp. are serious pathogens that threaten numerous cultivated crops, trees, and natural vegetation worldwide. The soybean pathogen P. sojae has been developed as a model oomycete. Here, we report a bacterial artificial chromosome (BAC)-based, integrated physical map of the P. sojae genome. We constructed two BAC libraries, digested 8,681 BACs with seven restriction enzymes, end labeled the digested fragments with four dyes, and analyzed them with capillary electrophoresis. Fifteen data sets were constructed from the fingerprints, using individual dyes and all possible combinations, and were evaluated for contig assembly. In all, 257 contigs were assembled from the XhoI data set, collectively spanning approximately 132 Mb in physical length. The BAC contigs were integrated with the draft genome sequence of P. sojae by end sequencing a total of 1,440 BACs that formed a minimal tiling path. This enabled the 257 contigs of the BAC map to be merged with 207 sequence scaffolds to form an integrated map consisting of 79 superscaffolds. The map represents the first genome-wide physical map of a Phytophthora sp. and provides a valuable resource for genomics and molecular biology research in P. sojae and other Phytophthora spp. In one illustration of this value, we have placed the 350 members of a superfamily of putative pathogenicity effector genes onto the map, revealing extensive clustering of these genes.
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Affiliation(s)
- Xuemin Zhang
- Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061-0477, USA
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Jiang RHY, Tyler BM, Govers F. Comparative analysis of Phytophthora genes encoding secreted proteins reveals conserved synteny and lineage-specific gene duplications and deletions. Mol Plant Microbe Interact 2006; 19:1311-21. [PMID: 17153915 DOI: 10.1094/mpmi-19-1311] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Comparative analysis of two Phytophthora genomes revealed overall colinearity in four genomic regions consisting of a 1.5-Mb sequence of Phytophthora sojae and a 0.9-Mb sequence of P. ramorum. In these regions with conserved synteny, the gene order is largely similar; however, genome rearrangements also have occurred. Deletions and duplications often were found in association with genes encoding secreted proteins, including effectors that are important for interaction with host plants. Among secreted protein genes, different evolutionary patterns were found. Elicitin genes that code for a complex family of highly conserved Phytophthora-specific elicitors show conservation in gene number and order, and often are clustered. In contrast, the race-specific elicitor gene Avrlb-1 appeared to be missing from the region with conserved synteny, as were its five homologs that are scattered over the four genomic regions. Some gene families encoding secreted proteins were found to be expanded in one species compared with the other. This could be the result of either repeated gene duplications in one species or specific deletions in the other. These different evolutionary patterns may shed light on the functions of these secreted proteins in the biology and pathology of the two Phytophthora spp.
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Affiliation(s)
- Rays H Y Jiang
- Laboratory of Phytopathology, Plant Sciences Group, Wageningen University, Binnenhaven 5, NL-6709 PD Wageningen, The Netherlands
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49
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Tyler BM, Tripathy S, Zhang X, Dehal P, Jiang RHY, Aerts A, Arredondo FD, Baxter L, Bensasson D, Beynon JL, Chapman J, Damasceno CMB, Dorrance AE, Dou D, Dickerman AW, Dubchak IL, Garbelotto M, Gijzen M, Gordon SG, Govers F, Grunwald NJ, Huang W, Ivors KL, Jones RW, Kamoun S, Krampis K, Lamour KH, Lee MK, McDonald WH, Medina M, Meijer HJG, Nordberg EK, Maclean DJ, Ospina-Giraldo MD, Morris PF, Phuntumart V, Putnam NH, Rash S, Rose JKC, Sakihama Y, Salamov AA, Savidor A, Scheuring CF, Smith BM, Sobral BWS, Terry A, Torto-Alalibo TA, Win J, Xu Z, Zhang H, Grigoriev IV, Rokhsar DS, Boore JL. Phytophthora genome sequences uncover evolutionary origins and mechanisms of pathogenesis. Science 2006; 313:1261-6. [PMID: 16946064 DOI: 10.1126/science.1128796] [Citation(s) in RCA: 719] [Impact Index Per Article: 39.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Draft genome sequences have been determined for the soybean pathogen Phytophthora sojae and the sudden oak death pathogen Phytophthora ramorum. Oömycetes such as these Phytophthora species share the kingdom Stramenopila with photosynthetic algae such as diatoms, and the presence of many Phytophthora genes of probable phototroph origin supports a photosynthetic ancestry for the stramenopiles. Comparison of the two species' genomes reveals a rapid expansion and diversification of many protein families associated with plant infection such as hydrolases, ABC transporters, protein toxins, proteinase inhibitors, and, in particular, a superfamily of 700 proteins with similarity to known oömycete avirulence genes.
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Affiliation(s)
- Brett M Tyler
- Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA.
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Abstract
Phytophthora is a genus entirely comprised of destructive plant pathogens. It belongs to the Stramenopila, a unique branch of eukaryotes, phylogenetically distinct from plants, animals, or fungi. Phytophthora genes show a strong preference for usage of codons ending with G or C (high GC3). The presence of high GC3 in genes can be utilized to differentiate coding regions from noncoding regions in the genome. We found that both selective pressure and mutation bias drive codon bias in Phytophthora. Indicative for selection pressure is the higher GC3 value of highly expressed genes in different Phytophthora species. Lineage specific GC increase of noncoding regions is reminiscent of whole-genome mutation bias, whereas the elevated Phytophthora GC3 is primarily a result of translation efficiency-driven selection. Heterogeneous retrotransposons exist in Phytophthora genomes and many of them vary in their GC content. Interestingly, the most widespread groups of retroelements in Phytophthora show high GC3 and a codon bias that is similar to host genes. Apparently, selection pressure has been exerted on the retroelement's codon usage, and such mimicry of host codon bias might be beneficial for the propagation of retrotransposons.
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Affiliation(s)
- Rays H Y Jiang
- Laboratory of Phytopathology, Plant Sciences Group, and Graduate School of Experimental Plant Sciences, Wageningen University, Binnenhaven 5, NL-6709 PD, Wageningen, The Netherlands
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