1
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Chahine Z, Abel S, Hollin T, Chung JH, Barnes GL, Daub ME, Renard I, Choi JY, Pratap V, Pal A, Alba-Argomaniz M, Banks CAS, Kirkwood J, Saraf A, Camino I, Castaneda P, Cuevas MC, De Mercado-Arnanz J, Fernandez-Alvaro E, Garcia-Perez A, Ibarz N, Viera-Morilla S, Prudhomme J, Joyner CJ, Bei AK, Florens L, Ben Mamoun C, Vanderwal CD, Le Roch KG. A Potent Kalihinol Analogue Disrupts Apicoplast Function and Vesicular Trafficking in P. falciparum Malaria. bioRxiv 2023:2023.11.21.568162. [PMID: 38045341 PMCID: PMC10690269 DOI: 10.1101/2023.11.21.568162] [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] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
Here we report the discovery of MED6-189, a new analogue of the kalihinol family of isocyanoterpene (ICT) natural products. MED6-189 is effective against drug-sensitive and -resistant P. falciparum strains blocking both intraerythrocytic asexual replication and sexual differentiation. This compound was also effective against P. knowlesi and P. cynomolgi. In vivo efficacy studies using a humanized mouse model of malaria confirms strong efficacy of the compound in animals with no apparent hemolytic activity or apparent toxicity. Complementary chemical biology, molecular biology, genomics and cell biological analyses revealed that MED6-189 primarily targets the parasite apicoplast and acts by inhibiting lipid biogenesis and cellular trafficking. Genetic analyses in P. falciparum revealed that a mutation in PfSec13, which encodes a component of the parasite secretory machinery, reduced susceptibility to the drug. The high potency of MED6-189 in vitro and in vivo, its broad range of efficacy, excellent therapeutic profile, and unique mode of action make it an excellent addition to the antimalarial drug pipeline.
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Affiliation(s)
- Z Chahine
- Department of Molecular, Cell and Systems Biology, University of California Riverside, CA, USA
| | - S Abel
- Department of Molecular, Cell and Systems Biology, University of California Riverside, CA, USA
| | - T Hollin
- Department of Molecular, Cell and Systems Biology, University of California Riverside, CA, USA
| | - JH Chung
- Department of Chemistry, University of California, Irvine, California, 92617, USA
| | - GL Barnes
- Department of Chemistry, University of California, Irvine, California, 92617, USA
| | - ME Daub
- Department of Chemistry, University of California, Irvine, California, 92617, USA
| | - I Renard
- Department of Internal Medicine, Section of Infectious Diseases, Yale School of Medicine, New Haven, Connecticut, USA
| | - JY Choi
- Department of Internal Medicine, Section of Infectious Diseases, Yale School of Medicine, New Haven, Connecticut, USA
| | - V Pratap
- Department of Internal Medicine, Section of Infectious Diseases, Yale School of Medicine, New Haven, Connecticut, USA
| | - A Pal
- Department of Internal Medicine, Section of Infectious Diseases, Yale School of Medicine, New Haven, Connecticut, USA
| | - M Alba-Argomaniz
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA, United States
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA, United States
- Center for Vaccines and Immunology, University of Georgia, Athens, GA, United States
| | - CAS Banks
- Stowers Institute for Medical Research, 1000 E. 50th Street, Kansas City, MO 64110, USA
| | - J Kirkwood
- Metabolomics Core Facility, University of California, Riverside, CA 92521, USA
| | - A Saraf
- Stowers Institute for Medical Research, 1000 E. 50th Street, Kansas City, MO 64110, USA
| | - I Camino
- GSK, C/ Severo Ochoa, 2 PTM, 28760 Tres Cantos (Madrid), Spain
| | - P Castaneda
- GSK, C/ Severo Ochoa, 2 PTM, 28760 Tres Cantos (Madrid), Spain
| | - MC Cuevas
- GSK, C/ Severo Ochoa, 2 PTM, 28760 Tres Cantos (Madrid), Spain
| | | | | | - A Garcia-Perez
- GSK, C/ Severo Ochoa, 2 PTM, 28760 Tres Cantos (Madrid), Spain
| | - N Ibarz
- GSK, C/ Severo Ochoa, 2 PTM, 28760 Tres Cantos (Madrid), Spain
| | - S Viera-Morilla
- GSK, C/ Severo Ochoa, 2 PTM, 28760 Tres Cantos (Madrid), Spain
| | - J Prudhomme
- Department of Molecular, Cell and Systems Biology, University of California Riverside, CA, USA
| | - CJ Joyner
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA, United States
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA, United States
- Center for Vaccines and Immunology, University of Georgia, Athens, GA, United States
| | - AK Bei
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
| | - L Florens
- Stowers Institute for Medical Research, 1000 E. 50th Street, Kansas City, MO 64110, USA
| | - C Ben Mamoun
- Department of Internal Medicine, Section of Infectious Diseases, Yale School of Medicine, New Haven, Connecticut, USA
| | - CD Vanderwal
- Department of Chemistry, University of California, Irvine, California, 92617, USA
| | - KG Le Roch
- Department of Molecular, Cell and Systems Biology, University of California Riverside, CA, USA
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2
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Hollin T, Chahine Z, Le Roch KG. Epigenetic Regulation and Chromatin Remodeling in Malaria Parasites. Annu Rev Microbiol 2023; 77:255-276. [PMID: 37268002 PMCID: PMC10961138 DOI: 10.1146/annurev-micro-032521-041554] [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] [Indexed: 06/04/2023]
Abstract
Plasmodium falciparum, the human malaria parasite, infects two hosts and various cell types, inducing distinct morphological and physiological changes in the parasite in response to different environmental conditions. These variations required the parasite to adapt and develop elaborate molecular mechanisms to ensure its spread and transmission. Recent findings have significantly improved our understanding of the regulation of gene expression in P. falciparum. Here, we provide an up-to-date overview of technologies used to highlight the transcriptomic adjustments occurring in the parasite throughout its life cycle. We also emphasize the complementary and complex epigenetic mechanisms regulating gene expression in malaria parasites. This review concludes with an outlook on the chromatin architecture, the remodeling systems, and how this 3D genome organization is critical in various biological processes.
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Affiliation(s)
- Thomas Hollin
- Department of Molecular, Cell and Systems Biology, University of California, Riverside, California, USA;
| | - Zeinab Chahine
- Department of Molecular, Cell and Systems Biology, University of California, Riverside, California, USA;
| | - Karine G Le Roch
- Department of Molecular, Cell and Systems Biology, University of California, Riverside, California, USA;
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3
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Chahine Z, Gupta M, Lenz T, Hollin T, Abel S, Banks CAS, Saraf A, Prudhomme J, Florens L, Le Roch KG. PfMORC protein regulates chromatin accessibility and transcriptional repression in the human malaria parasite, P. falciparum. bioRxiv 2023:2023.09.11.557253. [PMID: 37745554 PMCID: PMC10515874 DOI: 10.1101/2023.09.11.557253] [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] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
The environmental challenges the human malaria parasite, Plasmodium falciparum, faces during its progression into its various lifecycle stages warrant the use of effective and highly regulated access to chromatin for transcriptional regulation. Microrchidia (MORC) proteins have been implicated in DNA compaction and gene silencing across plant and animal kingdoms. Accumulating evidence has shed light into the role MORC protein plays as a transcriptional switch in apicomplexan parasites. In this study, using CRISPR/Cas9 genome editing tool along with complementary molecular and genomics approaches, we demonstrate that PfMORC not only modulates chromatin structure and heterochromatin formation throughout the parasite erythrocytic cycle, but is also essential to the parasite survival. Chromatin immunoprecipitation followed by deep sequencing (ChIP-seq) experiments suggest that PfMORC binds to not only sub-telomeric regions and genes involved in antigenic variation but is also most likely a key modulator of stage transition. Protein knockdown experiments followed by chromatin conformation capture (Hi-C) studies indicate that downregulation of PfMORC induces the collapse of the parasite heterochromatin structure leading to its death. All together these findings confirm that PfMORC plays a crucial role in chromatin structure and gene regulation, validating this factor as a strong candidate for novel antimalarial strategies.
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Affiliation(s)
- Z Chahine
- Department of Molecular, Cell and Systems Biology, University of California Riverside, CA, USA
| | - M Gupta
- Department of Molecular, Cell and Systems Biology, University of California Riverside, CA, USA
| | - T Lenz
- Department of Molecular, Cell and Systems Biology, University of California Riverside, CA, USA
| | - T Hollin
- Department of Molecular, Cell and Systems Biology, University of California Riverside, CA, USA
| | - S Abel
- Department of Molecular, Cell and Systems Biology, University of California Riverside, CA, USA
| | - CAS Banks
- Stowers Institute for Medical Research, 1000 E. 50th Street, Kansas City, MO 64110, USA
| | - A Saraf
- Stowers Institute for Medical Research, 1000 E. 50th Street, Kansas City, MO 64110, USA
| | - J Prudhomme
- Department of Molecular, Cell and Systems Biology, University of California Riverside, CA, USA
| | - L Florens
- Stowers Institute for Medical Research, 1000 E. 50th Street, Kansas City, MO 64110, USA
| | - KG Le Roch
- Department of Molecular, Cell and Systems Biology, University of California Riverside, CA, USA
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4
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Batugedara G, Lu XM, Hristov B, Abel S, Chahine Z, Hollin T, Williams D, Wang T, Cort A, Lenz T, Thompson TA, Prudhomme J, Tripathi AK, Xu G, Cudini J, Dogga S, Lawniczak M, Noble WS, Sinnis P, Le Roch KG. Novel insights into the role of long non-coding RNA in the human malaria parasite, Plasmodium falciparum. Nat Commun 2023; 14:5086. [PMID: 37607941 PMCID: PMC10444892 DOI: 10.1038/s41467-023-40883-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [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: 08/19/2022] [Accepted: 08/10/2023] [Indexed: 08/24/2023] Open
Abstract
The complex life cycle of Plasmodium falciparum requires coordinated gene expression regulation to allow host cell invasion, transmission, and immune evasion. Increasing evidence now suggests a major role for epigenetic mechanisms in gene expression in the parasite. In eukaryotes, many lncRNAs have been identified to be pivotal regulators of genome structure and gene expression. To investigate the regulatory roles of lncRNAs in P. falciparum we explore the intergenic lncRNA distribution in nuclear and cytoplasmic subcellular locations. Using nascent RNA expression profiles, we identify a total of 1768 lncRNAs, of which 718 (~41%) are novels in P. falciparum. The subcellular localization and stage-specific expression of several putative lncRNAs are validated using RNA-FISH. Additionally, the genome-wide occupancy of several candidate nuclear lncRNAs is explored using ChIRP. The results reveal that lncRNA occupancy sites are focal and sequence-specific with a particular enrichment for several parasite-specific gene families, including those involved in pathogenesis and sexual differentiation. Genomic and phenotypic analysis of one specific lncRNA demonstrate its importance in sexual differentiation and reproduction. Our findings bring a new level of insight into the role of lncRNAs in pathogenicity, gene regulation and sexual differentiation, opening new avenues for targeted therapeutic strategies against the deadly malaria parasite.
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Affiliation(s)
- Gayani Batugedara
- Department of Molecular Cell and Systems Biology, University of California Riverside, Riverside, CA, 92521, USA
| | - Xueqing M Lu
- Department of Molecular Cell and Systems Biology, University of California Riverside, Riverside, CA, 92521, USA
| | - Borislav Hristov
- Department of Genome Sciences, University of Washington, Seattle, WA, 98195-5065, USA
| | - Steven Abel
- Department of Molecular Cell and Systems Biology, University of California Riverside, Riverside, CA, 92521, USA
| | - Zeinab Chahine
- Department of Molecular Cell and Systems Biology, University of California Riverside, Riverside, CA, 92521, USA
| | - Thomas Hollin
- Department of Molecular Cell and Systems Biology, University of California Riverside, Riverside, CA, 92521, USA
| | - Desiree Williams
- Department of Molecular Cell and Systems Biology, University of California Riverside, Riverside, CA, 92521, USA
| | - Tina Wang
- Department of Molecular Cell and Systems Biology, University of California Riverside, Riverside, CA, 92521, USA
| | - Anthony Cort
- Department of Molecular Cell and Systems Biology, University of California Riverside, Riverside, CA, 92521, USA
| | - Todd Lenz
- Department of Molecular Cell and Systems Biology, University of California Riverside, Riverside, CA, 92521, USA
| | - Trevor A Thompson
- Department of Molecular Cell and Systems Biology, University of California Riverside, Riverside, CA, 92521, USA
| | - Jacques Prudhomme
- Department of Molecular Cell and Systems Biology, University of California Riverside, Riverside, CA, 92521, USA
| | - Abhai K Tripathi
- Department of Molecular Microbiology and Immunology and the Johns Hopkins Malaria Research Institute, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205, USA
| | - Guoyue Xu
- Department of Molecular Microbiology and Immunology and the Johns Hopkins Malaria Research Institute, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205, USA
| | | | - Sunil Dogga
- Wellcome Sanger Institute, Hinxton, CB10 1SA, UK
| | | | | | - Photini Sinnis
- Department of Molecular Microbiology and Immunology and the Johns Hopkins Malaria Research Institute, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205, USA
| | - Karine G Le Roch
- Department of Molecular Cell and Systems Biology, University of California Riverside, Riverside, CA, 92521, USA.
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5
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Thompson TA, Chahine Z, Le Roch KG. The role of long noncoding RNAs in malaria parasites. Trends Parasitol 2023; 39:517-531. [PMID: 37121862 DOI: 10.1016/j.pt.2023.03.016] [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: 02/01/2023] [Revised: 03/16/2023] [Accepted: 03/18/2023] [Indexed: 05/02/2023]
Abstract
The human malaria parasites, including Plasmodium falciparum, persist as a major cause of global morbidity and mortality. The recent stalling of progress toward malaria elimination substantiates a need for novel interventions. Controlled gene expression is central to the parasite's numerous life cycle transformations and adaptation. With few specific transcription factors (TFs) identified, crucial roles for chromatin states and epigenetics in parasite transcription have become evident. Although many chromatin-modifying enzymes are known, less is known about which factors mediate their impacts on transcriptional variation. Like those of higher eukaryotes, long noncoding RNAs (lncRNAs) have recently been shown to have integral roles in parasite gene regulation. This review aims to summarize recent developments and key findings on the role of lncRNAs in P. falciparum.
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Affiliation(s)
- Trevor A Thompson
- Department of Molecular, Cell and Systems Biology, University of California Riverside, CA, USA
| | - Zeinab Chahine
- Department of Molecular, Cell and Systems Biology, University of California Riverside, CA, USA
| | - Karine G Le Roch
- Department of Molecular, Cell and Systems Biology, University of California Riverside, CA, USA.
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6
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Romano PS, Akematsu T, Besteiro S, Bindschedler A, Carruthers VB, Chahine Z, Coppens I, Descoteaux A, Alberto Duque TL, He CY, Heussler V, Le Roch KG, Li FJ, de Menezes JPB, Menna-Barreto RFS, Mottram JC, Schmuckli-Maurer J, Turk B, Tavares Veras PS, Salassa BN, Vanrell MC. Autophagy in protists and their hosts: When, how and why? Autophagy Rep 2023; 2:2149211. [PMID: 37064813 PMCID: PMC10104450 DOI: 10.1080/27694127.2022.2149211] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Accepted: 11/15/2022] [Indexed: 03/12/2023]
Abstract
Pathogenic protists are a group of organisms responsible for causing a variety of human diseases including malaria, sleeping sickness, Chagas disease, leishmaniasis, and toxoplasmosis, among others. These diseases, which affect more than one billion people globally, mainly the poorest populations, are characterized by severe chronic stages and the lack of effective antiparasitic treatment. Parasitic protists display complex life-cycles and go through different cellular transformations in order to adapt to the different hosts they live in. Autophagy, a highly conserved cellular degradation process, has emerged as a key mechanism required for these differentiation processes, as well as other functions that are crucial to parasite fitness. In contrast to yeasts and mammals, protist autophagy is characterized by a modest number of conserved autophagy-related proteins (ATGs) that, even though, can drive the autophagosome formation and degradation. In addition, during their intracellular cycle, the interaction of these pathogens with the host autophagy system plays a crucial role resulting in a beneficial or harmful effect that is important for the outcome of the infection. In this review, we summarize the current state of knowledge on autophagy and other related mechanisms in pathogenic protists and their hosts. We sought to emphasize when, how, and why this process takes place, and the effects it may have on the parasitic cycle. A better understanding of the significance of autophagy for the protist life-cycle will potentially be helpful to design novel anti-parasitic strategies.
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Affiliation(s)
- Patricia Silvia Romano
- Laboratorio de Biología de Trypanosoma cruzi y de la célula hospedadora. Instituto de Histología y Embriología de Mendoza. Universidad Nacional de Cuyo. (IHEM-CONICET-UNCUYO). Facultad de Ciencias Médicas. Universidad Nacional de Cuyo. Av. Libertador 80 (5500), Mendoza, Argentina
| | - Takahiko Akematsu
- Department of Biosciences, College of Humanities and Sciences, Nihon University, Tokyo, Japan
| | | | | | - Vern B Carruthers
- Department of Microbiology and Immunology, University of Michigan School of Medicine, Ann Arbor, MI, USA
| | - Zeinab Chahine
- Department of Molecular, Cell and Systems Biology, University of California Riverside, CA, USA
| | - Isabelle Coppens
- Department of Molecular Microbiology and Immunology. Department of Molecular Microbiology and Immunology. Johns Hopkins Malaria Research Institute. Johns Hopkins University Bloomberg School of Public Health. Baltimore 21205, MD, USA
| | - Albert Descoteaux
- Centre Armand-Frappier Santé Biotechnologie, Institut national de la recherche scientifique, Laval, QC
| | - Thabata Lopes Alberto Duque
- Autophagy Inflammation and Metabolism Center, University of New Mexico Health Sciences Center, Albuquerque, NM, USA; Department of Molecular Genetics and Microbiology, University of New Mexico Health Sciences Center, Albuquerque, NM, USA
| | - Cynthia Y He
- Department of Biological Sciences, National University of Singapore, Singapore
| | - Volker Heussler
- Institute of Cell Biology.University of Bern. Baltzerstr. 4 3012 Bern
| | - Karine G Le Roch
- Department of Molecular, Cell and Systems Biology, University of California Riverside, CA, USA
| | - Feng-Jun Li
- Department of Biological Sciences, National University of Singapore, Singapore
| | | | | | - Jeremy C Mottram
- York Biomedical Research Institute, Department of Biology, University of York, York, UK
| | | | - Boris Turk
- Department of Biochemistry and Molecular and Structural Biology, Jožef Stefan Institute, SI-1000 Ljubljana, Slovenia
| | - Patricia Sampaio Tavares Veras
- Laboratory of Host-Parasite Interaction and Epidemiology, Gonçalo Moniz Institute, Fiocruz-Bahia
- National Institute of Science and Technology of Tropical Diseases - National Council for Scientific Research and Development (CNPq)
| | - Betiana Nebai Salassa
- Laboratorio de Biología de Trypanosoma cruzi y de la célula hospedadora. Instituto de Histología y Embriología de Mendoza. Universidad Nacional de Cuyo. (IHEM-CONICET-UNCUYO). Facultad de Ciencias Médicas. Universidad Nacional de Cuyo. Av. Libertador 80 (5500), Mendoza, Argentina
| | - María Cristina Vanrell
- Laboratorio de Biología de Trypanosoma cruzi y de la célula hospedadora. Instituto de Histología y Embriología de Mendoza. Universidad Nacional de Cuyo. (IHEM-CONICET-UNCUYO). Facultad de Ciencias Médicas. Universidad Nacional de Cuyo. Av. Libertador 80 (5500), Mendoza, Argentina
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7
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Dwulet N, Chahine Z, Le Roch KG, Vanderwal CD. An Enantiospecific Synthesis of Isoneoamphilectane Confirms Its Strained Tricyclic Structure. J Am Chem Soc 2023; 145:3716-3726. [PMID: 36730688 PMCID: PMC9936588 DOI: 10.1021/jacs.2c13137] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
We describe a total synthesis of the rare isocyanoterpene natural product isoneoamphilectane and two of its unnatural diastereomers. The significantly strained ring system of the reported natural product─along with a hypothesis about a biosynthetic relationship to related family members─inspired us to consider a potential misassignment in the structure's relative configuration. As a result, we initially targeted two less strained, more accessible, stereoisomers of the reported natural product. When these compounds failed to exhibit spectroscopic data that matched those of isoneoamphilectane, we embarked on a synthesis of the originally proposed strained structure via an approach that hinged on a challenging cis-to-trans decalone epimerization. Ultimately, we implemented a novel cyclic sulfite pinacol-type rearrangement to generate the strained ring system. Additional features of this work include the application of a stereocontrolled Mukaiyama-Michael addition of an acyclic silylketene acetal, an unusual intramolecular alkoxide-mediated regioselective elimination, and an HAT-mediated alkene hydroazidation to forge the C-N bond of the tertiary isonitrile. Throughout this work, our synthetic planning was heavily guided by computational analyses to inform on key issues of stereochemical control.
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Affiliation(s)
- Natalie
C. Dwulet
- Department
of Chemistry, University of California, Irvine, California 92697-2025, United
States
| | - Zeinab Chahine
- Institute
for Integrative Genome Biology, Center for Infectious Disease and
Vector Research, 900 University Avenue, Department of Molecular, Cell,
and Systems Biology, University of California, Riverside, California 92521, United States
| | - Karine G. Le Roch
- Institute
for Integrative Genome Biology, Center for Infectious Disease and
Vector Research, 900 University Avenue, Department of Molecular, Cell,
and Systems Biology, University of California, Riverside, California 92521, United States
| | - Christopher D. Vanderwal
- Department
of Chemistry, University of California, Irvine, California 92697-2025, United
States,Department
of Pharmaceutical Sciences, 101 Theory, University of California, Irvine, California 92697, United States,
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8
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Zeeshan M, Rashpa R, Ferguson DJP, Abel S, Chahine Z, Brady D, Vaughan S, Moores CA, Le Roch KG, Brochet M, Holder AA, Tewari R. Genome-wide functional analysis reveals key roles for kinesins in the mammalian and mosquito stages of the malaria parasite life cycle. PLoS Biol 2022; 20:e3001704. [PMID: 35900985 PMCID: PMC9333250 DOI: 10.1371/journal.pbio.3001704] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [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: 03/15/2022] [Accepted: 06/10/2022] [Indexed: 11/18/2022] Open
Abstract
Kinesins are microtubule (MT)-based motors important in cell division, motility, polarity, and intracellular transport in many eukaryotes. However, they are poorly studied in the divergent eukaryotic pathogens Plasmodium spp., the causative agents of malaria, which manifest atypical aspects of cell division and plasticity of morphology throughout the life cycle in both mammalian and mosquito hosts. Here, we describe a genome-wide screen of Plasmodium kinesins, revealing diverse subcellular locations and functions in spindle assembly, axoneme formation, and cell morphology. Surprisingly, only kinesin-13 is essential for growth in the mammalian host while the other 8 kinesins are required during the proliferative and invasive stages of parasite transmission through the mosquito vector. In-depth analyses of kinesin-13 and kinesin-20 revealed functions in MT dynamics during apical cell polarity formation, spindle assembly, and axoneme biogenesis. These findings help us to understand the importance of MT motors and may be exploited to discover new therapeutic interventions against malaria. A comprehensive study reveals that kinesins in the malaria parasite Plasmodium have diverse cellular roles and locations, including functions in spindle assembly during proliferation, axoneme formation in flagellum biogenesis, and determining the apical morphology of the cell.
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Affiliation(s)
- Mohammad Zeeshan
- University of Nottingham, School of Life Sciences, Nottingham, United Kingdom
- * E-mail: (MZ); (RT)
| | - Ravish Rashpa
- University of Geneva, Faculty of Medicine, Geneva, Switzerland
| | - David J. P. Ferguson
- Oxford Brookes University, Department of Biological and Medical Sciences, Oxford, United Kingdom
- University of Oxford, John Radcliffe Hospital, Nuffield Department of Clinical Laboratory Science, Oxford, United Kingdom
| | - Steven Abel
- Department of Molecular, Cell and Systems Biology, University of California Riverside, Riverside, California, United States of America
| | - Zeinab Chahine
- Department of Molecular, Cell and Systems Biology, University of California Riverside, Riverside, California, United States of America
| | - Declan Brady
- University of Nottingham, School of Life Sciences, Nottingham, United Kingdom
| | - Sue Vaughan
- Oxford Brookes University, Department of Biological and Medical Sciences, Oxford, United Kingdom
| | - Carolyn A. Moores
- Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck College, London, United Kingdom
| | - Karine G. Le Roch
- Department of Molecular, Cell and Systems Biology, University of California Riverside, Riverside, California, United States of America
| | - Mathieu Brochet
- University of Geneva, Faculty of Medicine, Geneva, Switzerland
| | - Anthony A. Holder
- The Francis Crick Institute, Malaria Parasitology Laboratory, London, United Kingdom
| | - Rita Tewari
- University of Nottingham, School of Life Sciences, Nottingham, United Kingdom
- * E-mail: (MZ); (RT)
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9
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Abstract
The human malaria parasite, Plasmodium falciparum, is a unicellular protozoan responsible for over half a million deaths annually. With a complex life cycle alternating between human and invertebrate hosts, this apicomplexan is notoriously adept at evading host immune responses and developing resistance to all clinically administered treatments. Advances in omics-based technologies, increased sensitivity of sequencing platforms and enhanced CRISPR based gene editing tools, have given researchers access to more in-depth and untapped information about this enigmatic micro-organism, a feat thought to be infeasible in the past decade. Here we discuss some of the most important scientific achievements made over the past few years with a focus on novel technologies and platforms that set the stage for subsequent discoveries. We also describe some of the systems-based methods applied to uncover gaps of knowledge left through single-omics applications with the hope that we will soon be able to overcome the spread of this life-threatening disease.
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10
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Clifton BD, Jimenez J, Kimura A, Chahine Z, Librado P, Sánchez-Gracia A, Abbassi M, Carranza F, Chan C, Marchetti M, Zhang W, Shi M, Vu C, Yeh S, Fanti L, Xia XQ, Rozas J, Ranz JM. Understanding the Early Evolutionary Stages of a Tandem Drosophilamelanogaster-Specific Gene Family: A Structural and Functional Population Study. Mol Biol Evol 2021; 37:2584-2600. [PMID: 32359138 PMCID: PMC7475035 DOI: 10.1093/molbev/msaa109] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [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] [Indexed: 12/22/2022] Open
Abstract
Gene families underlie genetic innovation and phenotypic diversification. However, our understanding of the early genomic and functional evolution of tandemly arranged gene families remains incomplete as paralog sequence similarity hinders their accurate characterization. The Drosophila melanogaster-specific gene family Sdic is tandemly repeated and impacts sperm competition. We scrutinized Sdic in 20 geographically diverse populations using reference-quality genome assemblies, read-depth methodologies, and qPCR, finding that ∼90% of the individuals harbor 3-7 copies as well as evidence of population differentiation. In strains with reliable gene annotations, copy number variation (CNV) and differential transposable element insertions distinguish one structurally distinct version of the Sdic region per strain. All 31 annotated copies featured protein-coding potential and, based on the protein variant encoded, were categorized into 13 paratypes differing in their 3' ends, with 3-5 paratypes coexisting in any strain examined. Despite widespread gene conversion, the only copy present in all strains has functionally diverged at both coding and regulatory levels under positive selection. Contrary to artificial tandem duplications of the Sdic region that resulted in increased male expression, CNV in cosmopolitan strains did not correlate with expression levels, likely as a result of differential genome modifier composition. Duplicating the region did not enhance sperm competitiveness, suggesting a fitness cost at high expression levels or a plateau effect. Beyond facilitating a minimally optimal expression level, Sdic CNV acts as a catalyst of protein and regulatory diversity, showcasing a possible evolutionary path recently formed tandem multigene families can follow toward long-term consolidation in eukaryotic genomes.
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Affiliation(s)
- Bryan D Clifton
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA
| | - Jamie Jimenez
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA
| | - Ashlyn Kimura
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA
| | - Zeinab Chahine
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA
| | - Pablo Librado
- Laboratoire AMIS CNRS UMR 5288, Faculté de Médicine de Purpan, Université Paul Sabatier, Toulouse, France
| | - Alejandro Sánchez-Gracia
- Departament de Genètica, Microbiologia i Estadistica, Universitat de Barcelona, Barcelona, Spain.,Institut de Recerca de la Biodiversitat, Universitat de Barcelona, Barcelona, Spain
| | - Mashya Abbassi
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA
| | - Francisco Carranza
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA
| | - Carolus Chan
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA
| | - Marcella Marchetti
- Istituto Pasteur Italia, Fondazione Cenci-Bolognetti, Rome, Italy.,Department of Biology and Biotechnology "C. Darwin", Sapienza University of Rome, Rome, Italy
| | - Wanting Zhang
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei Province, China
| | - Mijuan Shi
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei Province, China
| | - Christine Vu
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA
| | - Shudan Yeh
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA.,Department of Life Sciences, National Central University, Taoyuan City, Zhongli District, Taiwan
| | - Laura Fanti
- Istituto Pasteur Italia, Fondazione Cenci-Bolognetti, Rome, Italy.,Department of Biology and Biotechnology "C. Darwin", Sapienza University of Rome, Rome, Italy
| | - Xiao-Qin Xia
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei Province, China
| | - Julio Rozas
- Departament de Genètica, Microbiologia i Estadistica, Universitat de Barcelona, Barcelona, Spain.,Institut de Recerca de la Biodiversitat, Universitat de Barcelona, Barcelona, Spain
| | - José M Ranz
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA
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Karns AS, Ellis BD, Roosen PC, Chahine Z, Le Roch KG, Vanderwal CD. Concise Synthesis of the Antiplasmodial Isocyanoterpene 7,20‐Diisocyanoadociane. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201906834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Alexander S. Karns
- 1102 Natural Sciences II Department of Chemistry University of California Irvine CA 92697-2025 USA
| | - Bryan D. Ellis
- 1102 Natural Sciences II Department of Chemistry University of California Irvine CA 92697-2025 USA
| | - Philipp C. Roosen
- 1102 Natural Sciences II Department of Chemistry University of California Irvine CA 92697-2025 USA
| | - Zeinab Chahine
- Institute for Integrative Genome Biology Center for Infectious Disease and Vector Research Department of Molecular, Cell, and Systems Biology University of California, Riverside 900 University Avenue Riverside CA 92521 USA
| | - Karine G. Le Roch
- Institute for Integrative Genome Biology Center for Infectious Disease and Vector Research Department of Molecular, Cell, and Systems Biology University of California, Riverside 900 University Avenue Riverside CA 92521 USA
| | - Christopher D. Vanderwal
- 1102 Natural Sciences II Department of Chemistry University of California Irvine CA 92697-2025 USA
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Karns AS, Ellis BD, Roosen PC, Chahine Z, Le Roch KG, Vanderwal CD. Concise Synthesis of the Antiplasmodial Isocyanoterpene 7,20-Diisocyanoadociane. Angew Chem Int Ed Engl 2019; 58:13749-13752. [PMID: 31270921 DOI: 10.1002/anie.201906834] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [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: 06/01/2019] [Indexed: 01/08/2023]
Abstract
The flagship member of the antiplasmodial isocyanoterpenes, 7,20-diisocyanoadociane (DICA), was synthesized from dehydrocryptone in 10 steps, and in 13 steps from commercially available material. Our previous formal synthesis was reengineered, leveraging only productive transformations to deliver DICA in fewer than half the number of steps of our original effort. Important contributions, in addition to the particularly concise strategy, include a solution to the problem of axial nucleophilic methylation of a late-stage cyclohexanone, and the first selective synthesis and antiplasmodial evaluation of the DICA stereoisomer with both isonitriles equatorial.
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Affiliation(s)
- Alexander S Karns
- 1102 Natural Sciences II, Department of Chemistry, University of California, Irvine, CA, 92697-2025, USA
| | - Bryan D Ellis
- 1102 Natural Sciences II, Department of Chemistry, University of California, Irvine, CA, 92697-2025, USA
| | - Philipp C Roosen
- 1102 Natural Sciences II, Department of Chemistry, University of California, Irvine, CA, 92697-2025, USA
| | - Zeinab Chahine
- Institute for Integrative Genome Biology, Center for Infectious Disease and Vector Research, Department of Molecular, Cell, and Systems Biology, University of California, Riverside, 900 University Avenue, Riverside, CA, 92521, USA
| | - Karine G Le Roch
- Institute for Integrative Genome Biology, Center for Infectious Disease and Vector Research, Department of Molecular, Cell, and Systems Biology, University of California, Riverside, 900 University Avenue, Riverside, CA, 92521, USA
| | - Christopher D Vanderwal
- 1102 Natural Sciences II, Department of Chemistry, University of California, Irvine, CA, 92697-2025, USA
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Chahine Z, Sanders D. The road ahead: comprehensive and innovative approaches for improving safety and preventing child maltreatment fatalities. Child Welfare 2013; 92:237-253. [PMID: 24199332] [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] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
This article presents a high-level overview of the complex issues, opportunities, and challenges involved in improving child safety and preventing child maltreatment fatalities. It emphasizes that improving measurement and classification is critical to understanding and preventing child maltreatment fatalities. It also stresses the need to reframe child maltreatment interventions from a public health perspective. The article draws on the lessons learned from state-of-the-art safety engineering innovations, research, and other expert recommendations presented in this special issue that can inform future policy and practice direction in this important area.
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Chahine Z, Pecora P, Sanders D. Preventing severe maltreatment-related injuries and fatalities: applying a public health framework and innovative approaches to child protection. Child Welfare 2013; 92:13-18. [PMID: 24199320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
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Pecora PJ, Chahine Z, Graham JC. Safety and risk assessment frameworks: overview and implications for child maltreatment fatalities. Child Welfare 2013; 92:143-160. [PMID: 24199327] [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] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
This article highlights current models used in child protection to assess safety and risk, and discusses implications for child maltreatment fatalities. The authors advance that current risk and safety practice approaches were not designed to accurately estimate the likelihood of low base-rate phenomena and have not been empirically tested in their ability to predict or prevent severe or fatal child maltreatment. They advance that, regardless of the ultimate effectiveness of safety and risk tools, competent assessment and decision-making in child protection depend on sound professional judgment and a comprehensive systemic approach that transcends the use of specific tools.
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Chahine Z, van Straaten J. Serving immigrant families and children in New York City's child welfare system. Child Welfare 2005; 84:713-23. [PMID: 16435658] [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] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
This article describes the efforts and special initiatives of New York City's Administration for Children's Services to improve services to immigrant and English language learner populations. Children's Services convened an immigration issues advisory subcommittee, created special tools for child welfare staff, collaborated with legal agencies to assist foster children with immigration status adjustments, improved agency data collection, and launched an agency-wide training initiative on immigration issues. The challenges encountered by Children's Services offer important insight for child welfare agencies in other jurisdictions designing strategies to strengthen their services for immigrant communities.
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Affiliation(s)
- Zeinab Chahine
- Child Welfare Program, New York City Administration for Children's Services, New York City, NY, USA
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Chahine Z, van Straaten J, Williams-Isom A. The New York City neighborhood-based services strategy. Child Welfare 2005; 84:141-152. [PMID: 15828405] [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] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The New York City Administration for Children's Services (ACS) instituted a neighborhood-based services system through the realignment of all foster care, preventive, and protective services along community district lines. ACS, with its community partners, also formed neighborhood-based networks to improve service coordination and collaboration among key community stakeholders and to shape a multisystem strategy tailored to each district informed by child welfare data. Based on analysis of neighborhood-specific census tract child welfare data, ACS initiated the Community Partnership to Strengthen Families project to address the disproportionate number of foster care placements originating from a small group of high-need communities, including Manhattan's Central Harlem. This article describes examples of specific strategies based on the Central Harlem experience.
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Affiliation(s)
- Zeinab Chahine
- Office of External Affairs, New York City Administration for Children's Services, New York, NY, USA
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