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Mitesser V, Simantov K, Dzikowski R. Time to switch gears: how long noncoding RNAs function as epigenetic regulators in Apicomplexan parasites. Curr Opin Microbiol 2024; 79:102484. [PMID: 38688159 DOI: 10.1016/j.mib.2024.102484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Revised: 04/08/2024] [Accepted: 04/16/2024] [Indexed: 05/02/2024]
Abstract
Long noncoding RNAs (lncRNA) are emerging as important regulators of gene expression in eukaryotes. In recent years, a large repertoire of lncRNA were discovered in Apicomplexan parasites and were implicated in several mechanisms of gene expression, including marking genes for activation, contributing to the formation of subnuclear compartments and organization, regulating the deposition of epigenetic modifications, influencing chromatin and chromosomal structure and manipulating host gene expression. Here, we aim to update recent knowledge on the role of lncRNAs as regulators in Apicomplexan parasites and highlight the possible molecular mechanisms by which they function. We hope that some of the hypotheses raised here will contribute to further investigation and lead to new mechanistic insight and better understanding of the role of lncRNA in parasite's biology.
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Affiliation(s)
- Vera Mitesser
- Department of Microbiology & Molecular Genetics, The Kuvin Center for the Study of Infectious and Tropical Diseases, IMRIC, The Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel
| | - Karina Simantov
- Department of Microbiology & Molecular Genetics, The Kuvin Center for the Study of Infectious and Tropical Diseases, IMRIC, The Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel
| | - Ron Dzikowski
- Department of Microbiology & Molecular Genetics, The Kuvin Center for the Study of Infectious and Tropical Diseases, IMRIC, The Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel.
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2
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Schmidt S, Wichers-Misterek JS, Behrens HM, Birnbaum J, Henshall IG, Dröge J, Jonscher E, Flemming S, Castro-Peña C, Mesén-Ramírez P, Spielmann T. The Kelch13 compartment contains highly divergent vesicle trafficking proteins in malaria parasites. PLoS Pathog 2023; 19:e1011814. [PMID: 38039338 PMCID: PMC10718435 DOI: 10.1371/journal.ppat.1011814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 12/13/2023] [Accepted: 11/09/2023] [Indexed: 12/03/2023] Open
Abstract
Single amino acid changes in the parasite protein Kelch13 (K13) result in reduced susceptibility of P. falciparum parasites to artemisinin and its derivatives (ART). Recent work indicated that K13 and other proteins co-localising with K13 (K13 compartment proteins) are involved in the endocytic uptake of host cell cytosol (HCCU) and that a reduction in HCCU results in reduced susceptibility to ART. HCCU is critical for parasite survival but is poorly understood, with the K13 compartment proteins among the few proteins so far functionally linked to this process. Here we further defined the composition of the K13 compartment by analysing more hits from a previous BioID, showing that MyoF and MCA2 as well as Kelch13 interaction candidate (KIC) 11 and 12 are found at this site. Functional analyses, tests for ART susceptibility as well as comparisons of structural similarities using AlphaFold2 predictions of these and previously identified proteins showed that vesicle trafficking and endocytosis domains were frequent in proteins involved in resistance or endocytosis (or both), comprising one group of K13 compartment proteins. While this strengthened the link of the K13 compartment to endocytosis, many proteins of this group showed unusual domain combinations and large parasite-specific regions, indicating a high level of taxon-specific adaptation of this process. Another group of K13 compartment proteins did not influence endocytosis or ART susceptibility and lacked detectable vesicle trafficking domains. We here identified the first protein of this group that is important for asexual blood stage development and showed that it likely is involved in invasion. Overall, this work identified novel proteins functioning in endocytosis and at the K13 compartment. Together with comparisons of structural predictions it provides a repertoire of functional domains at the K13 compartment that indicate a high level of adaption of endocytosis in malaria parasites.
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Affiliation(s)
- Sabine Schmidt
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | | | | | - Jakob Birnbaum
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | | | - Jana Dröge
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Ernst Jonscher
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Sven Flemming
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | | | | | - Tobias Spielmann
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
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3
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Lin J, Zeng S, Chen Q, Liu G, Pan S, Liu X. Identification of disease-related genes in Plasmodium berghei by network module analysis. BMC Microbiol 2023; 23:264. [PMID: 37735351 PMCID: PMC10512555 DOI: 10.1186/s12866-023-03019-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 09/12/2023] [Indexed: 09/23/2023] Open
Abstract
BACKGROUND Plasmodium berghei has been used as a preferred model for studying human malaria, but only a limited number of disease-associated genes of P. berghei have been reported to date. Identification of new disease-related genes as many as possible will provide a landscape for better understanding the pathogenesis of P. berghei. METHODS Network module analysis method was developed and applied to identify disease-related genes in P. berghei genome. Sequence feature identification, gene ontology annotation, and T-cell epitope analysis were performed on these genes to illustrate their functions in the pathogenesis of P. berghei. RESULTS 33,314 genes were classified into 4,693 clusters. 4,127 genes shared by six malaria parasites were identified and are involved in many aspects of biological processes. Most of the known essential genes belong to shared genes. A total of 63 clusters consisting of 405 P. berghei genes were enriched in rodent malaria parasites. These genes participate in various stages of parasites such as liver stage development and immune evasion. Combination of these genes might be responsible for P. berghei infecting mice. Comparing with P. chabaudi, none of the clusters were specific to P. berghei. P. berghei lacks some proteins belonging to P. chabaudi and possesses some specific T-cell epitopes binding by class-I MHC, which might together contribute to the occurrence of experimental cerebral malaria (ECM). CONCLUSIONS We successfully identified disease-associated P. berghei genes by network module analysis. These results will deepen understanding of the pathogenesis of P. berghei and provide candidate parasite genes for further ECM investigation.
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Affiliation(s)
- Junhao Lin
- Department of Neurology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Shan Zeng
- Department of Neurology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Qiong Chen
- Department of Neurology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Guanghui Liu
- Department of Neurology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Suyue Pan
- Department of Neurology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China.
| | - Xuewu Liu
- Department of Neurology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China.
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Bowman EK, Nguyen Hoang PT, Gordillo Sierra AR, Vieira Nogueira KM, Alper HS. Temporal sorting of microdroplets can identify productivity differences of itaconic acid from libraries of Yarrowia lipolytica. LAB ON A CHIP 2023; 23:2249-2256. [PMID: 37013836 DOI: 10.1039/d3lc00020f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Microdroplet screening of microorganisms can improve the rate of strain selection and characterization within the canonical design-build-test paradigm. However, a full analysis of the microdroplet environment and how well these conditions translate to culturing conditions and techniques is lacking in the field. Quantification of three different biosensor/analyte combinations at 12 hour timepoints reveals the potential for extended dose-response ranges as compared to traditional in vitro conditions. Using these dynamics, we present an application and analysis of microfluidic droplet screening utilizing whole-cell biosensors, ultimately identifying an altered productivity profile of itaconic acid in a Yarrowia lipolytica-based piggyBac transposon library. Specifically, we demonstrate that the timepoint for microdroplet selection can influence the outcome of the selection and thus shift the identified strain productivity and final titer. In this case, strains selected at earlier timepoints showed increased early productivity in flask scale, with the converse true as well. Differences in response indicate microdroplet assays require tailored development to more accurately sort for phenotypes that are scalable to larger incubation volumes. Likewise, these results further highlight that screening conditions are critical parameters for success in high-throughput applications.
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Affiliation(s)
- Emily K Bowman
- Interdisciplinary Life Sciences Graduate Program, The University of Texas at Austin, Austin, TX 78712, USA.
| | | | - Angela R Gordillo Sierra
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX 78712, USA
| | - Karoline M Vieira Nogueira
- Molecular Biotechnology Laboratory, Department of Biochemistry and Immunology, Ribeirao Preto Medical School (FMRP), University of Sao Paulo, Ribeirao Preto, SP, Brazil
| | - Hal S Alper
- Interdisciplinary Life Sciences Graduate Program, The University of Texas at Austin, Austin, TX 78712, USA.
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX 78712, USA
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5
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Li T, Wei J, Pan G. Advances in the Genetic Manipulation of Nosema bombycis. EXPERIENTIA SUPPLEMENTUM (2012) 2022; 114:137-152. [PMID: 35544002 DOI: 10.1007/978-3-030-93306-7_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The microsporidium Nosema bombycis can infect and transmit both vertically and horizontally in multiple lepidopteran insects including silkworms and crop pests. While there have been several studies on the N. bombycis spore, there have been only limited studies on the N. bombycis sporoplasm. This chapter reviews what is known about this life cycle stage as well as published studies on purification of the N. bombycis sporoplasm and its survival in an in vitro cell culture system. Genetic transformation techniques have revolutionized the study of many pathogenic organisms. While progress has been made on the development of such systems for microsporidia, this critical problem has not been solved for these pathogens. This chapter provides a summary of the latest research progress on genetic manipulation of N. bombycis.
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Affiliation(s)
- Tian Li
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China
- Chongqing Key Laboratory of Microsporidia Infection and Control, Southwest University, Chongqing, China
| | - Junhong Wei
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China
- Chongqing Key Laboratory of Microsporidia Infection and Control, Southwest University, Chongqing, China
| | - Guoqing Pan
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China.
- Chongqing Key Laboratory of Microsporidia Infection and Control, Southwest University, Chongqing, China.
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6
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Feng XB, Zheng ZW, Zhang X, Gu J, Feng QL, Huang LH. Discovering genes responsible for silk synthesis in Bombyx mori by piggyBac-based random insertional mutagenesis. INSECT SCIENCE 2019; 26:821-830. [PMID: 29645353 DOI: 10.1111/1744-7917.12595] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Revised: 03/25/2018] [Accepted: 03/25/2018] [Indexed: 06/08/2023]
Abstract
Silkworm mutants are valuable resources for both transgenic breeding and gene discovery. PiggyBac-based random insertional mutagenesis has been widely used in gene functional studies. In order to discover genes involved in silk synthesis, a piggyBac-based random insertional library was constructed using Bombyx mori, and the mutants with abnormal cocoon were particularly screened. By this means, a "thin cocoon" mutant was identified. This mutant revealed thinner cocoon shell and shorter posterior silk gland (PSG) compared with the wild type. The messenger RNA (mRNA) levels of all the three fibroin genes, including Fib-H, Fib-L and P25, were significantly down-regulated in the PSG of mutants. Four piggyBac insertion sites were identified in Aquaporin (AQP), Longitudinals lacking protein-like (Lola), Glutamyl aminopeptidase-like (GluAP) and Loc101744460. The mRNA levels of all the four genes were significantly altered in the silk gland of mutants. In particular, the mRNA amount of AQP, a gene responsible for the regulation of osmotic pressure, decreased dramatically immediately prior to the spinning stage in the anterior silk gland of mutants. The identification of the genes disrupted in the "thin cocoon" mutant in this study provided useful information for understanding silk production and transgenic breeding of silkworms in the future.
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Affiliation(s)
- Xing-Bao Feng
- Guangzhou Key Laboratory of Insect Development Regulation and Applied Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Zi-Wen Zheng
- Guangzhou Key Laboratory of Insect Development Regulation and Applied Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Xian Zhang
- Guangzhou Key Laboratory of Insect Development Regulation and Applied Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Jun Gu
- Guangzhou Key Laboratory of Insect Development Regulation and Applied Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Qi-Li Feng
- Guangzhou Key Laboratory of Insect Development Regulation and Applied Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Li-Hua Huang
- Guangzhou Key Laboratory of Insect Development Regulation and Applied Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, China
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7
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Walker MP, Lindner SE. Ribozyme-mediated, multiplex CRISPR gene editing and CRISPR interference (CRISPRi) in rodent-infectious Plasmodium yoelii. J Biol Chem 2019; 294:9555-9566. [PMID: 31043479 PMCID: PMC6579477 DOI: 10.1074/jbc.ra118.007121] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 04/23/2019] [Indexed: 11/06/2022] Open
Abstract
Malaria remains a major global health issue, affecting millions and killing hundreds of thousands of people annually. Efforts to break the transmission cycle of the causal Plasmodium parasite, and to cure those that are afflicted, rely upon functional characterization of genes essential to the parasite's growth and development. These studies are often based upon manipulations of the parasite genome to disrupt or modify a gene of interest to understand its importance and function. However, these approaches can be limited by the availability of selectable markers and the time required to generate transgenic parasites. Moreover, there also is a risk of disrupting native gene regulatory elements with the introduction of exogenous sequences. To address these limitations, we have developed CRISPR-RGR, a Streptococcus pyogenes (Sp)Cas9-based gene editing system for Plasmodium that utilizes a ribozyme-guide-ribozyme (RGR) single guide RNA (sgRNA) expression strategy with RNA polymerase II promoters. Using rodent-infectious Plasmodium yoelii, we demonstrate that both gene disruptions and coding sequence insertions are efficiently generated, producing marker-free parasites with homology arms as short as 80-100 bp. Additionally, we find that the common practice of using one sgRNA can produce both unintended plasmid integration and desired locus replacement editing events, whereas the use of two sgRNAs results in only locus replacement editing. Lastly, we show that CRISPR-RGR can be used for CRISPR interference (CRISPRi) by binding catalytically dead SpCas9 (dSpCas9) to the region upstream of a gene of interest, resulting in a position-dependent, but strand-independent reduction in gene expression. This robust and flexible system facilitates efficient genetic characterizations of rodent-infectious Plasmodium species.
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Affiliation(s)
- Michael P Walker
- From the Department of Biochemistry and Molecular Biology, Huck Center for Malaria Research, Pennsylvania State University, University Park, Pennsylvania 16802
| | - Scott E Lindner
- From the Department of Biochemistry and Molecular Biology, Huck Center for Malaria Research, Pennsylvania State University, University Park, Pennsylvania 16802
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8
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Kasai Y, Matsuzaki K, Ikeda F, Yoshimitsu Y, Harayama S. Precise excision of a selectable marker gene in transgenic Coccomyxa strains by the piggyBac transposase. ALGAL RES 2017. [DOI: 10.1016/j.algal.2017.09.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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9
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Lok JB, Shao H, Massey HC, Li X. Transgenesis in Strongyloides and related parasitic nematodes: historical perspectives, current functional genomic applications and progress towards gene disruption and editing. Parasitology 2017; 144:327-342. [PMID: 27000743 PMCID: PMC5364836 DOI: 10.1017/s0031182016000391] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Revised: 02/10/2016] [Accepted: 02/10/2016] [Indexed: 12/20/2022]
Abstract
Transgenesis for Strongyloides and Parastrongyloides was accomplished in 2006 and is based on techniques derived for Caenorhabditis elegans over two decades earlier. Adaptation of these techniques has been possible because Strongyloides and related parasite genera carry out at least one generation of free-living development, with adult males and females residing in soil contaminated by feces from an infected host. Transgenesis in this group of parasites is accomplished by microinjecting DNA constructs into the syncytia of the distal gonads of free-living females. In Strongyloides stercoralis, plasmid-encoded transgenes are expressed in promoter-regulated fashion in the F1 generation following gene transfer but are silenced subsequently. Stable inheritance and expression of transgenes in S. stercoralis requires their integration into the genome, and stable lines have been derived from integrants created using the piggyBac transposon system. More direct investigations of gene function involving expression of mutant transgene constructs designed to alter intracellular trafficking and developmental regulation have shed light on the function of the insulin-regulated transcription factor Ss-DAF-16. Transgenesis in Strongyloides and Parastrongyloides opens the possibility of powerful new methods for genome editing and transcriptional manipulation in this group of parasites. Proof of principle for one of these, CRISPR/Cas9, is presented in this review.
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Affiliation(s)
- J B Lok
- Department of Pathobiology,School of Veterinary Medicine,University of Pennsylvania,3800 Spruce Street,Philadelphia,PA 19104,USA
| | - H Shao
- Department of Pathobiology,School of Veterinary Medicine,University of Pennsylvania,3800 Spruce Street,Philadelphia,PA 19104,USA
| | - H C Massey
- Department of Pathobiology,School of Veterinary Medicine,University of Pennsylvania,3800 Spruce Street,Philadelphia,PA 19104,USA
| | - X Li
- Department of Pathobiology,School of Veterinary Medicine,University of Pennsylvania,3800 Spruce Street,Philadelphia,PA 19104,USA
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10
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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] [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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Abstract
The piggyBac transposon was originally isolated from the cabbage looper moth, Trichoplusia ni, in the 1980s. Despite its early discovery and dissimilarity to the other DNA transposon families, the piggyBac transposon was not recognized as a member of a large transposon superfamily for a long time. Initially, the piggyBac transposon was thought to be a rare transposon. This view, however, has now been completely revised as a number of fully sequenced genomes have revealed the presence of piggyBac-like repetitive elements. The isolation of active copies of the piggyBac-like elements from several distinct species further supported this revision. This includes the first isolation of an active mammalian DNA transposon identified in the bat genome. To date, the piggyBac transposon has been deeply characterized and it represents a number of unique characteristics. In general, all members of the piggyBac superfamily use TTAA as their integration target sites. In addition, the piggyBac transposon shows precise excision, i.e., restoring the sequence to its preintegration state, and can transpose in a variety of organisms such as yeasts, malaria parasites, insects, mammals, and even in plants. Biochemical analysis of the chemical steps of transposition revealed that piggyBac does not require DNA synthesis during the actual transposition event. The broad host range has attracted researchers from many different fields, and the piggyBac transposon is currently the most widely used transposon system for genetic manipulations.
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12
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Swann J, Jamshidi N, Lewis NE, Winzeler EA. Systems analysis of host-parasite interactions. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2015; 7:381-400. [PMID: 26306749 PMCID: PMC4679367 DOI: 10.1002/wsbm.1311] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Revised: 06/25/2015] [Accepted: 06/29/2015] [Indexed: 12/16/2022]
Abstract
Parasitic diseases caused by protozoan pathogens lead to hundreds of thousands of deaths per year in addition to substantial suffering and socioeconomic decline for millions of people worldwide. The lack of effective vaccines coupled with the widespread emergence of drug‐resistant parasites necessitates that the research community take an active role in understanding host–parasite infection biology in order to develop improved therapeutics. Recent advances in next‐generation sequencing and the rapid development of publicly accessible genomic databases for many human pathogens have facilitated the application of systems biology to the study of host–parasite interactions. Over the past decade, these technologies have led to the discovery of many important biological processes governing parasitic disease. The integration and interpretation of high‐throughput ‐omic data will undoubtedly generate extraordinary insight into host–parasite interaction networks essential to navigate the intricacies of these complex systems. As systems analysis continues to build the foundation for our understanding of host–parasite biology, this will provide the framework necessary to drive drug discovery research forward and accelerate the development of new antiparasitic therapies. WIREs Syst Biol Med 2015, 7:381–400. doi: 10.1002/wsbm.1311 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Justine Swann
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Neema Jamshidi
- Department of Radiological Sciences, University of California, Los Angeles, Los Angeles, CA, USA.,Institute of Engineering in Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Nathan E Lewis
- Department of Pediatrics and Novo Nordisk Foundation Center for Biosustainability, University of California, San Diego, La Jolla, CA, USA
| | - Elizabeth A Winzeler
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
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de Koning-Ward TF, Gilson PR, Crabb BS. Advances in molecular genetic systems in malaria. Nat Rev Microbiol 2015; 13:373-87. [DOI: 10.1038/nrmicro3450] [Citation(s) in RCA: 91] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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Matz JM, Kooij TWA. Towards genome-wide experimental genetics in the in vivo malaria model parasite Plasmodium berghei. Pathog Glob Health 2015; 109:46-60. [PMID: 25789828 DOI: 10.1179/2047773215y.0000000006] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Plasmodium berghei was identified as a parasite of thicket rats (Grammomys dolichurus) and Anopheles dureni mosquitoes in African highland forests. Successful adaptation to a range of rodent and mosquito species established P. berghei as a malaria model parasite. The introduction of stable transfection technology, permitted classical reverse genetics strategies and thus systematic functional profiling of the gene repertoire. In the past 10 years following the publication of the P. berghei genome sequence, many new tools for experimental genetics approaches have been developed and existing ones have been improved. The infection of mice is the principal limitation towards a genome-wide repository of mutant parasite lines. In the past few years, there have been some promising and most welcome developments that allow rapid selection and isolation of recombinant parasites while simultaneously minimising animal usage. Here, we provide an overview of all the currently available tools and methods.
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15
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Lok J. piggyBac: A vehicle for integrative DNA transformation of parasitic nematodes. Mob Genet Elements 2014; 3:e24417. [PMID: 23914309 PMCID: PMC3681738 DOI: 10.4161/mge.24417] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2013] [Revised: 03/11/2013] [Accepted: 03/22/2013] [Indexed: 12/18/2022] Open
Abstract
In addition to their natural role in eukaryotic genome evolution, transposons can be powerful tools for functional genomics in diverse taxa. The piggyBac transposon has been applied as such in eukaryotic parasites, both protozoa and helminths, and in several important vector mosquitoes. piggyBac is advantageous for functional genomics because of its ability to transduce a wide range of taxa, its capacity to integrate large DNA ‘cargoes’ relative to other mobile genetic elements, its propensity to target transcriptional units and its ability to re-mobilize without leaving a pattern of non-excised sequences or ‘footprint’ in the genome. We recently demonstrated that piggyBac can integrate transgenes into the genome of the parasitic nematode Strongyloides ratti, an important model for parasitic nematode biology and a close relative of the significant human pathogen S. stercoralis. Unlike transgenes encoded in conventional plasmid vectors, which we assume are assembled into multi-copy episomal arrays as they are in Caenorhabditis elegans, transgenes integrated via piggyBac are not only stably inherited in S. ratti, they are also continuously expressed. This has allowed derivation of the first stable transgene expressing lines in any parasitic nematode, a significant advance in the development of functional genomic tools for these important pathogens.
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Affiliation(s)
- James Lok
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA USA
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Stoco PH, Wagner G, Talavera-Lopez C, Gerber A, Zaha A, Thompson CE, Bartholomeu DC, Lückemeyer DD, Bahia D, Loreto E, Prestes EB, Lima FM, Rodrigues-Luiz G, Vallejo GA, Filho JFDS, Schenkman S, Monteiro KM, Tyler KM, de Almeida LGP, Ortiz MF, Chiurillo MA, de Moraes MH, Cunha ODL, Mendonça-Neto R, Silva R, Teixeira SMR, Murta SMF, Sincero TCM, Mendes TADO, Urmenyi TP, Silva VG, DaRocha WD, Andersson B, Romanha ÁJ, Steindel M, de Vasconcelos ATR, Grisard EC. Genome of the avirulent human-infective trypanosome--Trypanosoma rangeli. PLoS Negl Trop Dis 2014; 8:e3176. [PMID: 25233456 PMCID: PMC4169256 DOI: 10.1371/journal.pntd.0003176] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2013] [Accepted: 08/08/2014] [Indexed: 11/25/2022] Open
Abstract
Background Trypanosoma rangeli is a hemoflagellate protozoan parasite infecting humans and other wild and domestic mammals across Central and South America. It does not cause human disease, but it can be mistaken for the etiologic agent of Chagas disease, Trypanosoma cruzi. We have sequenced the T. rangeli genome to provide new tools for elucidating the distinct and intriguing biology of this species and the key pathways related to interaction with its arthropod and mammalian hosts. Methodology/Principal Findings The T. rangeli haploid genome is ∼24 Mb in length, and is the smallest and least repetitive trypanosomatid genome sequenced thus far. This parasite genome has shorter subtelomeric sequences compared to those of T. cruzi and T. brucei; displays intraspecific karyotype variability and lacks minichromosomes. Of the predicted 7,613 protein coding sequences, functional annotations could be determined for 2,415, while 5,043 are hypothetical proteins, some with evidence of protein expression. 7,101 genes (93%) are shared with other trypanosomatids that infect humans. An ortholog of the dcl2 gene involved in the T. brucei RNAi pathway was found in T. rangeli, but the RNAi machinery is non-functional since the other genes in this pathway are pseudogenized. T. rangeli is highly susceptible to oxidative stress, a phenotype that may be explained by a smaller number of anti-oxidant defense enzymes and heat-shock proteins. Conclusions/Significance Phylogenetic comparison of nuclear and mitochondrial genes indicates that T. rangeli and T. cruzi are equidistant from T. brucei. In addition to revealing new aspects of trypanosome co-evolution within the vertebrate and invertebrate hosts, comparative genomic analysis with pathogenic trypanosomatids provides valuable new information that can be further explored with the aim of developing better diagnostic tools and/or therapeutic targets. Comparative genomics is a powerful tool that affords detailed study of the genetic and evolutionary basis for aspects of lifecycles and pathologies caused by phylogenetically related pathogens. The reference genome sequences of three trypanosomatids, T. brucei, T. cruzi and L. major, and subsequent addition of multiple Leishmania and Trypanosoma genomes has provided data upon which large-scale investigations delineating the complex systems biology of these human parasites has been built. Here, we compare the annotated genome sequence of T. rangeli strain SC-58 to available genomic sequence and annotation data from related species. We provide analysis of gene content, genome architecture and key characteristics associated with the biology of this non-pathogenic trypanosome. Moreover, we report striking new genomic features of T. rangeli compared with its closest relative, T. cruzi, such as (1) considerably less amplification on the gene copy number within multigene virulence factor families such as MASPs, trans-sialidases and mucins; (2) a reduced repertoire of genes encoding anti-oxidant defense enzymes; and (3) the presence of vestigial orthologs of the RNAi machinery, which are insufficient to constitute a functional pathway. Overall, the genome of T. rangeli provides for a much better understanding of the identity, evolution, regulation and function of trypanosome virulence determinants for both mammalian host and insect vector.
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Affiliation(s)
- Patrícia Hermes Stoco
- Universidade Federal de Santa Catarina, Florianópolis, Santa Catarina, Brazil
- * E-mail: (PHS); (ECG)
| | - Glauber Wagner
- Universidade Federal de Santa Catarina, Florianópolis, Santa Catarina, Brazil
- Universidade do Oeste de Santa Catarina, Joaçaba, Santa Catarina, Brazil
| | - Carlos Talavera-Lopez
- Department of Cell and Molecular Biology, Science for Life Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Alexandra Gerber
- Laboratório Nacional de Computação Científica, Petrópolis, Rio de Janeiro, Brazil
| | - Arnaldo Zaha
- Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | | | | | | | - Diana Bahia
- Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
- Universidade Federal de São Paulo - Escola Paulista de Medicina, São Paulo, São Paulo, Brazil
| | - Elgion Loreto
- Universidade Federal de Santa Maria, Santa Maria, Rio Grande do Sul, Brazil
| | | | - Fábio Mitsuo Lima
- Universidade Federal de São Paulo - Escola Paulista de Medicina, São Paulo, São Paulo, Brazil
| | | | | | | | - Sérgio Schenkman
- Universidade Federal de São Paulo - Escola Paulista de Medicina, São Paulo, São Paulo, Brazil
| | | | - Kevin Morris Tyler
- Biomedical Research Centre, School of Medicine, Health Policy and Practice, University of East Anglia, Norwich, United Kingdom
| | | | - Mauro Freitas Ortiz
- Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Miguel Angel Chiurillo
- Universidade Federal de São Paulo - Escola Paulista de Medicina, São Paulo, São Paulo, Brazil
- Universidad Centroccidental Lisandro Alvarado, Barquisimeto, Venezuela
| | | | | | | | - Rosane Silva
- Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
| | | | | | | | | | - Turán Peter Urmenyi
- Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
| | | | | | - Björn Andersson
- Department of Cell and Molecular Biology, Science for Life Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Álvaro José Romanha
- Universidade Federal de Santa Catarina, Florianópolis, Santa Catarina, Brazil
| | - Mário Steindel
- Universidade Federal de Santa Catarina, Florianópolis, Santa Catarina, Brazil
| | | | - Edmundo Carlos Grisard
- Universidade Federal de Santa Catarina, Florianópolis, Santa Catarina, Brazil
- * E-mail: (PHS); (ECG)
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Culleton RL, Abkallo HM. Malaria parasite genetics: doing something useful. Parasitol Int 2014; 64:244-53. [PMID: 25073068 DOI: 10.1016/j.parint.2014.07.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Accepted: 07/11/2014] [Indexed: 01/15/2023]
Abstract
Genetics has informed almost every aspect of the study of malaria parasites, and remains a key component of much of the research that aims to reduce the burden of the disease they cause. We describe the history of genetic studies of malaria parasites and give an overview of the utility of the discipline to malariology.
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Affiliation(s)
- Richard L Culleton
- Malaria Unit, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan.
| | - Hussein M Abkallo
- Malaria Unit, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan
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Frevert U, Nacer A, Cabrera M, Movila A, Leberl M. Imaging Plasmodium immunobiology in the liver, brain, and lung. Parasitol Int 2013; 63:171-86. [PMID: 24076429 DOI: 10.1016/j.parint.2013.09.013] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2012] [Revised: 08/28/2013] [Accepted: 09/18/2013] [Indexed: 01/10/2023]
Abstract
Plasmodium falciparum malaria is responsible for the deaths of over half a million African children annually. Until a decade ago, dynamic analysis of the malaria parasite was limited to in vitro systems with the typical limitations associated with 2D monocultures or entirely artificial surfaces. Due to extremely low parasite densities, the liver was considered a black box in terms of Plasmodium sporozoite invasion, liver stage development, and merozoite release into the blood. Further, nothing was known about the behavior of blood stage parasites in organs such as the brain where clinical signs manifest and the ensuing immune response of the host that may ultimately result in a fatal outcome. The advent of fluorescent parasites, advances in imaging technology, and availability of an ever-increasing number of cellular and molecular probes have helped illuminate many steps along the pathogenetic cascade of this deadly tropical parasite.
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Affiliation(s)
- Ute Frevert
- Division of Medical Parasitology, Department of Microbiology, New York University School of Medicine, 341 E 25 Street, New York, NY 10010, USA.
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Cao Y, Rui B, Wellems DL, Li M, Chen B, Zhang D, Pan W. Identification of piggyBac-mediated insertions in Plasmodium berghei by next generation sequencing. Malar J 2013; 12:287. [PMID: 23961915 PMCID: PMC3765144 DOI: 10.1186/1475-2875-12-287] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Accepted: 08/18/2013] [Indexed: 01/24/2023] Open
Abstract
Background The piggyBac transposon system provides a powerful forward genetics tool to study gene function in Plasmodium parasites via random insertion mutagenesis and phenotypic screening. The identification of genotype of piggyBac mutants in the Plasmodium genome is thus an indispensable step in forward genetic analysis. Several PCR-based approaches have been used to identify the piggyBac insertion sites in Plasmodium falciparum and Plasmodium berghei, but all are tedious and inefficient. Next generation sequencing can produce large amounts of sequence data and is particularly suitable for genome-wide association studies. In this study, the Next generation sequencing technology was employed to efficiently identify piggyBac insertion sites in the genome of P. berghei. Methods Plasmodium berghei parasites were co-transfected with piggyBac donor and helper plasmids. Initially, the classical inverse PCR method was used to identify the existence of piggyBac insertions in the P. berghei genome. The whole genome of post-transfection parasites was subsequently sequenced with a PCR-free paired-end module using the Illumina HiSeq sequencing system. The two distinct methods (‘BLAST method’ and ‘SOAP method’) were employed to identify piggyBac insertion sites in the P. berghei genome with Illumina sequencing data. All the identified piggyBac insertions were further tested by half-nested PCR. Results The inverse PCR method resulted in a very low yield of ten individual insertions identified. Conversely, 47 piggyBac insertions were identified from about 1 Gb of Illumina sequencing data via the two distinct analysis methods. The majority of identified piggyBac insertions were confirmed by half-nested PCR. In addition, 1,850 single nucleotide polymorphisms were identified through alignment of the Illumina sequencing data of the P. berghei ANKA strain used in this study with the reference genome sequences. Conclusion This study demonstrates that a high-throughput genome sequencing approach is an efficient tool for the identification of piggyBac-mediated insertions in Plasmodium parasites.
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Affiliation(s)
- Yi Cao
- Department of Tropical Infectious Diseases, Second Military Medical University, Shanghai, China
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Atypical mitogen-activated protein kinase phosphatase implicated in regulating transition from pre-S-Phase asexual intraerythrocytic development of Plasmodium falciparum. EUKARYOTIC CELL 2013; 12:1171-8. [PMID: 23813392 DOI: 10.1128/ec.00028-13] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Intraerythrocytic development of the human malaria parasite Plasmodium falciparum appears as a continuous flow through growth and proliferation. To develop a greater understanding of the critical regulatory events, we utilized piggyBac insertional mutagenesis to randomly disrupt genes. Screening a collection of piggyBac mutants for slow growth, we isolated the attenuated parasite C9, which carried a single insertion disrupting the open reading frame (ORF) of PF3D7_1305500. This gene encodes a protein structurally similar to a mitogen-activated protein kinase (MAPK) phosphatase, except for two notable characteristics that alter the signature motif of the dual-specificity phosphatase domain, suggesting that it may be a low-activity phosphatase or pseudophosphatase. C9 parasites demonstrated a significantly lower growth rate with delayed entry into the S/M phase of the cell cycle, which follows the stage of maximum PF3D7_1305500 expression in intact parasites. Genetic complementation with the full-length PF3D7_1305500 rescued the wild-type phenotype of C9, validating the importance of the putative protein phosphatase PF3D7_1305500 as a regulator of pre-S-phase cell cycle progression in P. falciparum.
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Su H, Liu X, Yan W, Shi T, Zhao X, Blake DP, Tomley FM, Suo X. piggyBac transposon-mediated transgenesis in the apicomplexan parasite Eimeria tenella. PLoS One 2012; 7:e40075. [PMID: 22768223 PMCID: PMC3386905 DOI: 10.1371/journal.pone.0040075] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2011] [Accepted: 06/05/2012] [Indexed: 01/24/2023] Open
Abstract
piggyBac, a type II transposon that is useful for efficient transgenesis and insertional mutagenesis, has been used for effective and stable transfection in a wide variety of organisms. In this study we investigate the potential use of the piggyBac transposon system for forward genetics studies in the apicomplexan parasite Eimeria tenella. Using the restriction enzyme-mediated integration (REMI) method, E. tenella sporozoites were electroporated with a donor plasmid containing the enhanced yellow fluorescent protein (EYFP) gene flanked by piggyBac inverted terminal repeats (ITRs), an Asc I-linearized helper plasmid containing the transposase gene and the restriction enzyme Asc I. Subsequently, electroporated sporozoites were inoculated into chickens via the cloacal route and transfected progeny oocysts expressing EYFP were sorted by flow cytometry. A transgenic E. tenella population was selected by successive in vivo passage. Southern-blotting analysis showed that exogenous DNA containing the EYFP gene was integrated into the parasite genome at a limited number of integration sites and that the inserted part of the donor plasmid was the fragment located between the 5′ and 3′ ITRs as indicated by primer-specific PCR screening. Genome walking revealed that the insertion sites were TTAA-specific, which is consistent with the transposition characteristics of piggyBac.
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Affiliation(s)
- Huali Su
- National Animal Protozoa Laboratory and College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Xianyong Liu
- National Animal Protozoa Laboratory and College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Wenchao Yan
- National Animal Protozoa Laboratory and College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Tuanyuan Shi
- National Animal Protozoa Laboratory and College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Xinxin Zhao
- National Animal Protozoa Laboratory and College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Damer P. Blake
- Institute for Animal Health, Compton, Berkshire, United Kingdom
- Royal Veterinary College, Pathology and Infectious Diseases, North Mymms, Hertfordshire, United Kingdom
| | - Fiona M. Tomley
- Institute for Animal Health, Compton, Berkshire, United Kingdom
- Royal Veterinary College, Pathology and Infectious Diseases, North Mymms, Hertfordshire, United Kingdom
| | - Xun Suo
- National Animal Protozoa Laboratory and College of Veterinary Medicine, China Agricultural University, Beijing, China
- * E-mail:
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Balu B. Moving "Forward" in Plasmodium Genetics through a Transposon-Based Approach. J Trop Med 2012; 2012:829210. [PMID: 22649460 PMCID: PMC3356940 DOI: 10.1155/2012/829210] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2011] [Revised: 02/07/2012] [Accepted: 02/20/2012] [Indexed: 01/07/2023] Open
Abstract
The genome sequence of the human malaria parasite, Plasmodium falciparum, was released almost a decade ago. A majority of the Plasmodium genome, however, remains annotated to code for hypothetical proteins with unknown functions. The introduction of forward genetics has provided novel means to gain a better understanding of gene functions and their associated phenotypes in Plasmodium. Even with certain limitations, the technique has already shown significant promise to increase our understanding of parasite biology needed for rationalized drug and vaccine design. Further improvements to the mutagenesis technique and the design of novel genetic screens should lead us to some exciting discoveries about the critical weaknesses of Plasmodium, and greatly aid in the development of new disease intervention strategies.
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Affiliation(s)
- Bharath Balu
- Tropical Disease Research Program, Center for Infectious Disease and Biodefense Research, SRI International, Harrisonburg, VA 22802, USA
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Abstract
Transgenesis is an essential tool for assessing gene function in any organism, and it is especially crucial for parasitic nematodes given the dwindling armamentarium of effective anthelmintics and the consequent need to validate essential molecular targets for new drugs and vaccines. Two of the major routes of gene delivery evaluated to date in parasitic nematodes, bombardment with DNA-coated microparticles and intragonadal microinjection of DNA constructs, draw upon experience with the free-living nematode Caenorhabditis elegans. Bombardment has been used to transiently transfect Ascaris suum, Brugia malayi and Litomosoides sigmodontis with both RNA and DNA. Microinjection has been used to achieve heritable transgenesis in Strongyloides stercoralis, S. ratti and Parastrongyloides trichosuri and for additional transient expression studies in B. malayi. A third route of gene delivery revisits a classic method involving DNA transfer facilitated by calcium-mediated permeabilization of recipient cells in developing B. malayi larvae and results in transgene inheritance through host and vector passage. Assembly of microinjected transgenes into multi-copy episomal arrays likely results in their transcriptional silencing in some parasitic nematodes. Methods such as transposon-mediated transgenesis that favour low-copy number chromosomal integration may remedy this impediment to establishing stable transgenic lines. In the future, stable transgenesis in parasitic nematodes could enable loss-of-function approaches by insertional mutagenesis, in situ expression of inhibitory double-stranded RNA or boosting RNAi susceptibility through heterologous expression of dsRNA processing and transport proteins.
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Affiliation(s)
- James B Lok
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, 3800 Spruce Street, Philadelphia, PA 19104, USA.
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Abstract
Gene manipulation is an invaluable tool to investigate and understand the biology of an organism. Although this technology has been applied to both the human and rodent malarial parasites (RMP), Plasmodium berghei in particular offers a more robust system due to a higher and more efficient transformation rate. Here, we describe a comprehensive transfection and selection protocol using P. berghei including a variant negative selection protocol administering 5-fluorocytosine to the animals in drinking water. Additionally, we discuss and assess the latest advances in gene manipulation technologies developed in RMP to gain a better understanding of Plasmodium biology.
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Khan SM, Kroeze H, Franke-Fayard B, Janse CJ. Standardization in generating and reporting genetically modified rodent malaria parasites: the RMgmDB database. Methods Mol Biol 2012; 923:139-50. [PMID: 22990775 DOI: 10.1007/978-1-62703-026-7_9] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Genetically modified Plasmodium parasites are central gene function reagents in malaria research. The Rodent Malaria genetically modified DataBase (RMgmDB) ( www.pberghei.eu ) is a manually curated Web - based repository that contains information on genetically modified rodent malaria parasites. It provides easy and rapid access to information on the genotype and phenotype of genetically modified mutant and reporter parasites. Here, we provide guidelines for generating and describing rodent malaria parasite mutants. Standardization in describing mutant genotypes and phenotypes is important not only to enhance publication quality but also to facilitate cross-linking and mining data from multiple sources, and should permit information derived from mutant parasites to be used in integrative system biology approaches. We also provide guidelines on how to submit information to RMgmDB on non-published mutants, mutants that do not exhibit a clear phenotype, as well as negative attempts to disrupt/mutate genes. Such information helps to prevent unnecessary duplication of experiments in different laboratories, and can provide indirect evidence that these genes are essential for blood-stage development.
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Affiliation(s)
- Shahid M Khan
- Center of Infectious Diseases, Leiden University Medical Center, Leiden, The Netherlands
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Limenitakis J, Soldati-Favre D. Functional genetics in Apicomplexa: potentials and limits. FEBS Lett 2011; 585:1579-88. [PMID: 21557944 DOI: 10.1016/j.febslet.2011.05.002] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2011] [Revised: 05/02/2011] [Accepted: 05/03/2011] [Indexed: 01/15/2023]
Abstract
The Apicomplexans are obligate intracellular protozoan parasites and the causative agents of severe diseases in humans and animals. Although complete genome sequences are available since many years and for several parasites, they are replete with putative genes of unassigned function. Forward and reverse genetic approaches are limited only to a few Apicomplexans that can either be propagated in vitro or in a convenient animal model. This review will compare and contrast the most recent strategies developed for the genetic manipulation of Plasmodium falciparum, Plasmodium berghei and Toxoplasma gondii that have taken advantage of the intrinsic features of their respective genomes. Efforts towards the improvement of the transfection efficiencies in malaria parasites, the development of approaches to study essential genes and the elaboration of high-throughput methods for the identification of gene function will be discussed.
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Affiliation(s)
- Julien Limenitakis
- Department of Microbiology and Molecular Medicine, CMU, University of Geneva, Geneva, Switzerland.
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Crabb BS, de Koning-Ward TF, Gilson PR. Toward forward genetic screens in malaria-causing parasites using the piggyBac transposon. BMC Biol 2011; 9:21. [PMID: 21453557 PMCID: PMC3068990 DOI: 10.1186/1741-7007-9-21] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2011] [Accepted: 03/31/2011] [Indexed: 01/04/2023] Open
Abstract
The ability to analyze gene function in malaria-causing Plasmodium parasites has received a boost with a recent paper in BMC Genomics that describes a genome-wide mutagenesis system in the rodent malaria species Plasmodium berghei using the transposon piggyBac. This advance holds promise for identifying and validating new targets for intervention against malaria. But further improvements are still needed for the full power of genome-wide molecular genetic screens to be utilized in this organism. See research article: http://www.biomedcentral.com/1471-2164/12/155
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Affiliation(s)
- Brendan S Crabb
- Macfarlane Burnet Institute for Medical Research and Public Health, Melbourne, Victoria 3004, Australia.
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