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Harl J, Himmel T, Ilgūnas M, Valkiūnas G, Weissenböck H. The 18S rRNA genes of Haemoproteus (Haemosporida, Apicomplexa) parasites from European songbirds with remarks on improved parasite diagnostics. Malar J 2023; 22:232. [PMID: 37563610 PMCID: PMC10416517 DOI: 10.1186/s12936-023-04661-9] [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: 04/19/2023] [Accepted: 07/27/2023] [Indexed: 08/12/2023] Open
Abstract
BACKGROUND The nuclear ribosomal RNA genes of Plasmodium parasites are assumed to evolve according to a birth-and-death model with new variants originating by duplication and others becoming deleted. For some Plasmodium species, it has been shown that distinct variants of the 18S rRNA genes are expressed differentially in vertebrate hosts and mosquito vectors. The central aim was to evaluate whether avian haemosporidian parasites of the genus Haemoproteus also have substantially distinct 18S variants, focusing on lineages belonging to the Haemoproteus majoris and Haemoproteus belopolskyi species groups. METHODS The almost complete 18S rRNA genes of 19 Haemoproteus lineages of the subgenus Parahaemoproteus, which are common in passeriform birds from the Palaearctic, were sequenced. The PCR products of 20 blood and tissue samples containing 19 parasite lineages were subjected to molecular cloning, and ten clones in mean were sequenced each. The sequence features were analysed and phylogenetic trees were calculated, including sequence data published previously from eight additional Parahaemoproteus lineages. The geographic and host distribution of all 27 lineages was visualised as CytB haplotype networks and pie charts. Based on the 18S sequence data, species-specific oligonucleotide probes were designed to target the parasites in host tissue by in situ hybridization assays. RESULTS Most Haemoproteus lineages had two or more variants of the 18S gene like many Plasmodium species, but the maximum distances between variants were generally lower. Moreover, unlike in most mammalian and avian Plasmodium species, the 18S sequences of all but one parasite lineage clustered into reciprocally monophyletic clades. Considerably distinct 18S clusters were only found in Haemoproteus tartakovskyi hSISKIN1 and Haemoproteus sp. hROFI1. The presence of chimeric 18S variants in some Haemoproteus lineages indicates that their ribosomal units rather evolve in a semi-concerted fashion than according to a strict model of birth-and-death evolution. CONCLUSIONS Parasites of the subgenus Parahaemoproteus contain distinct 18S variants, but the intraspecific variability is lower than in most mammalian and avian Plasmodium species. The new 18S data provides a basis for more thorough investigations on the development of Haemoproteus parasites in host tissue using in situ hybridization techniques targeting specific parasite lineages.
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Affiliation(s)
- Josef Harl
- Department of Pathobiology, Institute of Pathology, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Tanja Himmel
- Department of Pathobiology, Institute of Pathology, University of Veterinary Medicine Vienna, Vienna, Austria
| | | | | | - Herbert Weissenböck
- Department of Pathobiology, Institute of Pathology, University of Veterinary Medicine Vienna, Vienna, Austria
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Sharma I, Fang J, Lewallen EA, Deitsch KW, McCutchan TF. Identification of a long noncoding RNA required for temperature induced expression of stage-specific rRNA in malaria parasites. Gene 2023:147516. [PMID: 37286021 DOI: 10.1016/j.gene.2023.147516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 05/17/2023] [Accepted: 05/24/2023] [Indexed: 06/09/2023]
Abstract
Protozoan parasites of the genus Plasmodium cause malaria, a mosquito borne disease responsible for substantial health and economic costs throughout the developing world. During transition from human host to insect vector, the parasites undergo profound changes in morphology, host cell tropism and gene expression. Unique among eukaryotes, Plasmodium differentiation through each stage of development includes differential expression of singular, stage-specific ribosomal RNAs, permitting real-time adaptability to major environmental changes. In the mosquito vector, these Plasmodium parasites respond to changes in temperature by modulating transcriptional activities, allowing real-time responses to environmental cues. Here, we identify a novel form of long noncoding RNA: a temperature-regulated untranslated lncRNA (tru-lncRNA) that influences the Plasmodium parasite's ability to respond to changes in its local environment. Expression of this tru-lncRNA is specifically induced by shifts in temperature from 37°C to ambient temperature that parallels the transition from mammalian host to insect vector. Interestingly, deletion of tru-lncRNA from the genome may prevent processing of S-type rRNA thereby affecting the protein synthesis machinery. Malaria prevention and mitigation strategies aimed at disrupting the Plasmodium life cycle will benefit from the characterization of ancillary biomolecules (including tru-lncRNAs) that are constitutively sensitive to micro- environmental parameters.
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Affiliation(s)
- Indu Sharma
- Department of Biological Sciences, Hampton University, Hampton Virginia, USA.
| | - Jun Fang
- Molecular Biology Section, Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Eric A Lewallen
- Department of Biological Sciences, Hampton University, Hampton Virginia, USA
| | - Kirk W Deitsch
- Weill Cornell Medicine Graduate School of Medical Sciences, New York, NY
| | - Thomas F McCutchan
- Molecular Biology Section, Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
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3
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Piel L, Rajan KS, Bussotti G, Varet H, Legendre R, Proux C, Douché T, Giai-Gianetto Q, Chaze T, Cokelaer T, Vojtkova B, Gordon-Bar N, Doniger T, Cohen-Chalamish S, Rengaraj P, Besse C, Boland A, Sadlova J, Deleuze JF, Matondo M, Unger R, Volf P, Michaeli S, Pescher P, Späth GF. Experimental evolution links post-transcriptional regulation to Leishmania fitness gain. PLoS Pathog 2022; 18:e1010375. [PMID: 35294501 PMCID: PMC8959184 DOI: 10.1371/journal.ppat.1010375] [Citation(s) in RCA: 2] [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: 12/30/2021] [Revised: 03/28/2022] [Accepted: 02/15/2022] [Indexed: 12/30/2022] Open
Abstract
The protozoan parasite Leishmania donovani causes fatal human visceral leishmaniasis in absence of treatment. Genome instability has been recognized as a driver in Leishmania fitness gain in response to environmental change or chemotherapy. How genome instability generates beneficial phenotypes despite potential deleterious gene dosage effects is unknown. Here we address this important open question applying experimental evolution and integrative systems approaches on parasites adapting to in vitro culture. Phenotypic analyses of parasites from early and late stages of culture adaptation revealed an important fitness tradeoff, with selection for accelerated growth in promastigote culture (fitness gain) impairing infectivity (fitness costs). Comparative genomics, transcriptomics and proteomics analyses revealed a complex regulatory network associated with parasite fitness gain, with genome instability causing highly reproducible, gene dosage-independent and -dependent changes. Reduction of flagellar transcripts and increase in coding and non-coding RNAs implicated in ribosomal biogenesis and protein translation were not correlated to dosage changes of the corresponding genes, revealing a gene dosage-independent, post-transcriptional mechanism of regulation. In contrast, abundance of gene products implicated in post-transcriptional regulation itself correlated to corresponding gene dosage changes. Thus, RNA abundance during parasite adaptation is controled by direct and indirect gene dosage changes. We correlated differential expression of small nucleolar RNAs (snoRNAs) with changes in rRNA modification, providing first evidence that Leishmania fitness gain in culture may be controlled by post-transcriptional and epitranscriptomic regulation. Our findings propose a novel model for Leishmania fitness gain in culture, where differential regulation of mRNA stability and the generation of modified ribosomes may potentially filter deleterious from beneficial gene dosage effects and provide proteomic robustness to genetically heterogenous, adapting parasite populations. This model challenges the current, genome-centric approach to Leishmania epidemiology and identifies the Leishmania transcriptome and non-coding small RNome as potential novel sources for the discovery of biomarkers that may be associated with parasite phenotypic adaptation in clinical settings. Genome instability plays a central yet poorly understood role in human disease. Gene amplifications and deletions drive cancer development, microbial infection and therapeutic failure. The molecular mechanisms that harness the deleterious effects of genome instability to generate beneficial phenotypes in pathogenic systems are unknown. Here we study this important open question in the protozoan parasite Leishmania that causes devastating human diseases termed leishmaniases. Leishmania parasites lack transcriptional control and instead exploit genome instability to adapt to their host environment. Analyzing in vitro adaptation of hamster-derived parasites via gene copy number (genomic level) and gene expression changes (transcriptomic and proteomic levels), we show that these parasites likely exploit small nucleolar RNAs (snoRNAs) to mitigate toxic effects of genome instability by post-transcriptional regulation and the establishment of modified ribosomes. Our findings propose non-coding RNAs as potential novel biomarkers with diagnostic and prognostic value that may be linked to changes in parasite tissue tropism or drug susceptibility. This novel insight into Leishmania adaptation will be likely applicable to other fast evolving eukaryotic systems with unstable genomes, such as fungi or cancer cells.
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Affiliation(s)
- Laura Piel
- Institut Pasteur, Université de Paris, INSERM U1201, Unité de Parasitologie moléculaire et Signalisation, Paris, France
| | - K. Shanmugha Rajan
- The Mina and Everard Goodman Faculty of Life Sciences and Advanced Materials and Nanotechnology Institute, Bar-Ilan University, Ramat-Gan, Israel
| | - Giovanni Bussotti
- Institut Pasteur, Université de Paris, INSERM U1201, Unité de Parasitologie moléculaire et Signalisation, Paris, France
- Institut Pasteur, Bioinformatics and Biostatistics Hub, Department of Computational Biology, USR 3756 IP CNRS, Paris, France
| | - Hugo Varet
- Institut Pasteur, Bioinformatics and Biostatistics Hub, Department of Computational Biology, USR 3756 IP CNRS, Paris, France
- Institut Pasteur, Biomics, Paris, France; Institut Pasteur, UTechS MSBio, Paris, France
| | - Rachel Legendre
- Institut Pasteur, Bioinformatics and Biostatistics Hub, Department of Computational Biology, USR 3756 IP CNRS, Paris, France
- Institut Pasteur, Biomics, Paris, France; Institut Pasteur, UTechS MSBio, Paris, France
| | - Caroline Proux
- Institut Pasteur, Biomics, Paris, France; Institut Pasteur, UTechS MSBio, Paris, France
| | - Thibaut Douché
- Institut Pasteur, Proteomics Platform Mass Spectrometry for Biology UTechS, C2RT, USR2000 CNRS, Paris, France
| | - Quentin Giai-Gianetto
- Institut Pasteur, Bioinformatics and Biostatistics Hub, Department of Computational Biology, USR 3756 IP CNRS, Paris, France
- Institut Pasteur, Proteomics Platform Mass Spectrometry for Biology UTechS, C2RT, USR2000 CNRS, Paris, France
| | - Thibault Chaze
- Institut Pasteur, Proteomics Platform Mass Spectrometry for Biology UTechS, C2RT, USR2000 CNRS, Paris, France
| | - Thomas Cokelaer
- Institut Pasteur, Bioinformatics and Biostatistics Hub, Department of Computational Biology, USR 3756 IP CNRS, Paris, France
- Institut Pasteur, Biomics, Paris, France; Institut Pasteur, UTechS MSBio, Paris, France
| | - Barbora Vojtkova
- Department of Parasitology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Nadav Gordon-Bar
- The Mina and Everard Goodman Faculty of Life Sciences and Advanced Materials and Nanotechnology Institute, Bar-Ilan University, Ramat-Gan, Israel
| | - Tirza Doniger
- The Mina and Everard Goodman Faculty of Life Sciences and Advanced Materials and Nanotechnology Institute, Bar-Ilan University, Ramat-Gan, Israel
| | - Smadar Cohen-Chalamish
- The Mina and Everard Goodman Faculty of Life Sciences and Advanced Materials and Nanotechnology Institute, Bar-Ilan University, Ramat-Gan, Israel
| | - Praveenkumar Rengaraj
- The Mina and Everard Goodman Faculty of Life Sciences and Advanced Materials and Nanotechnology Institute, Bar-Ilan University, Ramat-Gan, Israel
| | - Céline Besse
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine, Evry, France
| | - Anne Boland
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine, Evry, France
| | - Jovana Sadlova
- Department of Parasitology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Jean-François Deleuze
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine, Evry, France
| | - Mariette Matondo
- Institut Pasteur, Proteomics Platform Mass Spectrometry for Biology UTechS, C2RT, USR2000 CNRS, Paris, France
| | - Ron Unger
- The Mina and Everard Goodman Faculty of Life Sciences and Advanced Materials and Nanotechnology Institute, Bar-Ilan University, Ramat-Gan, Israel
| | - Petr Volf
- Department of Parasitology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Shulamit Michaeli
- The Mina and Everard Goodman Faculty of Life Sciences and Advanced Materials and Nanotechnology Institute, Bar-Ilan University, Ramat-Gan, Israel
| | - Pascale Pescher
- Institut Pasteur, Université de Paris, INSERM U1201, Unité de Parasitologie moléculaire et Signalisation, Paris, France
- * E-mail: (PP); (GS)
| | - Gerald F. Späth
- Institut Pasteur, Université de Paris, INSERM U1201, Unité de Parasitologie moléculaire et Signalisation, Paris, France
- * E-mail: (PP); (GS)
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Functional characterization of 5' UTR cis-acting sequence elements that modulate translational efficiency in Plasmodium falciparum and humans. Malar J 2022; 21:15. [PMID: 34991611 PMCID: PMC8739713 DOI: 10.1186/s12936-021-04024-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 12/14/2021] [Indexed: 11/10/2022] Open
Abstract
Background The eukaryotic parasite Plasmodium falciparum causes millions of malarial infections annually while drug resistance to common anti-malarials is further confounding eradication efforts. Translation is an attractive therapeutic target that will benefit from a deeper mechanistic understanding. As the rate limiting step of translation, initiation is a primary driver of translational efficiency. It is a complex process regulated by both cis and trans acting factors, providing numerous potential targets. Relative to model organisms and humans, P. falciparum mRNAs feature unusual 5′ untranslated regions suggesting cis-acting sequence complexity in this parasite may act to tune levels of protein synthesis through their effects on translational efficiency. Methods Here, in vitro translation is deployed to compare the role of cis-acting regulatory sequences in P. falciparum and humans. Using parasite mRNAs with high or low translational efficiency, the presence, position, and termination status of upstream “AUG”s, in addition to the base composition of the 5′ untranslated regions, were characterized. Results The density of upstream “AUG”s differed significantly among the most and least efficiently translated genes in P. falciparum, as did the average “GC” content of the 5′ untranslated regions. Using exemplars from highly translated and poorly translated mRNAs, multiple putative upstream elements were interrogated for impact on translational efficiency. Upstream “AUG”s were found to repress translation to varying degrees, depending on their position and context, while combinations of upstream “AUG”s had non-additive effects. The base composition of the 5′ untranslated regions also impacted translation, but to a lesser degree. Surprisingly, the effects of cis-acting sequences were remarkably conserved between P. falciparum and humans. Conclusions While translational regulation is inherently complex, this work contributes toward a more comprehensive understanding of parasite and human translational regulation by examining the impact of discrete cis-acting features, acting alone or in context. Supplementary Information The online version contains supplementary material available at 10.1186/s12936-021-04024-2.
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Yap NJ, Hossain H, Nada-Raja T, Ngui R, Muslim A, Hoh BP, Khaw LT, Kadir KA, Simon Divis PC, Vythilingam I, Singh B, Lim YAL. Natural Human Infections with Plasmodium cynomolgi, P. inui, and 4 other Simian Malaria Parasites, Malaysia. Emerg Infect Dis 2021; 27:2187-2191. [PMID: 34287122 PMCID: PMC8314832 DOI: 10.3201/eid2708.204502] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
We detected the simian malaria parasites Plasmodium knowlesi, P. cynomolgi, P. inui, P. coatneyi, P. inui–like, and P. simiovale among forest fringe–living indigenous communities from various locations in Malaysia. Our findings underscore the importance of using molecular tools to identify newly emergent malaria parasites in humans.
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Asali S, Raz A, Turki H, Mafakher L, Razmjou E, Solaymani-Mohammadi S. Restricted genetic heterogeneity of the Plasmodium vivax transmission-blocking vaccine (TBV) candidate Pvs48/45 in a low transmission setting: Implications for the Plasmodium vivax malaria vaccine development. INFECTION GENETICS AND EVOLUTION 2021; 89:104710. [PMID: 33421653 DOI: 10.1016/j.meegid.2021.104710] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Revised: 12/28/2020] [Accepted: 01/04/2021] [Indexed: 12/14/2022]
Abstract
Plasmodium vivax is the most widespread malaria species parasitizing humans outside Africa, with approximately 100 million cases reported per year. Most human cases of P. vivax are asymptomatic with low parasitemia, making active case detection-based elimination programme challenging and less effective. Despite the widespread distribution of P. vivax, no effective vaccines are currently available. Transmission blocking vaccines have recently emerged as potential vaccine candidates to reduce transmission rates to below the essential levels required for the maintenance of the parasite life cycle. Here, we demonstrated that P. vivax was the predominant species found in a malaria-endemic area, although P. vivax/P. falciparum co-infections were also common. Through genomic sequence analysis and neighbor-joining algorithms, we demonstrated limited genetic heterogeneity in the P. vivax transmission-blocking vaccine candidate Pvs48/45 among clinical isolates of P. vivax. Restricted genetic polymorphism occurred at both nucleotide and amino acid levels. The most frequent mutation was A → G at nucleotide position 77 (46.7%), whereas the least frequent was C → T at nucleotide position 1230 (3.3%). The occurrence of single nucleotide polymorphisms (SNPs) distribution at 6/8 positions (75%) led to changes in amino acid sequences in the Pvs48/45 loci, whereas 2/8 (25%) of SNPs resulted in no amino acid sequence variations. Consistently, the nucleotide diversity in the Pvs48/45 locus among the P. vivax population studied was extremely low (π = 0.000525). Changes in amino acid sequences in the Pvs48/45 protein did not result in substantial conformational modifications in the tertiary structures of these proteins. Unveiling the population genetic structure and genetic heterogeneity of vaccine target antigens are necessary for rational design of transmission-blocking antibody vaccines and to monitor the vaccine efficacy in clinical trials in endemic areas for malaria.
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Affiliation(s)
- Soheila Asali
- Department of Parasitology and Mycology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Abbasali Raz
- Malaria and Vector Research Group, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Habibollah Turki
- Infectious and Tropical Diseases Research Center, Hormozgan Health Institute, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Ladan Mafakher
- Medicinal Plant Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Elham Razmjou
- Department of Parasitology and Mycology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran; Microbial Biotechnology Research Center (MBiRC), Iran University of Medical Sciences, Tehran, Iran.
| | - Shahram Solaymani-Mohammadi
- Laboratory of Mucosal Immunology, Department of Biomedical Sciences, School of Medicine and Health Sciences, University of North Dakota, Grand Forks, ND, United States.
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Wahab A, Shaukat A, Ali Q, Hussain M, Khan TA, Khan MAU, Rashid I, Saleem MA, Evans M, Sargison ND, Chaudhry U. A novel metabarcoded 18S ribosomal DNA sequencing tool for the detection of Plasmodium species in malaria positive patients. INFECTION GENETICS AND EVOLUTION 2020; 82:104305. [PMID: 32247865 DOI: 10.1016/j.meegid.2020.104305] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 03/13/2020] [Accepted: 03/26/2020] [Indexed: 02/07/2023]
Abstract
Various PCR based methods have been described for the diagnosis of malaria, but most depend on the use of Plasmodium species-specific probes and primers; hence only the tested species are identified and there is limited available data on the true circulating species diversity. Sensitive diagnostic tools and platforms for their use are needed to detect Plasmodium species in both clinical cases and asymptomatic infections that contribute to disease transmission. We have recently developed for the first time a novel high throughput 'haemoprotobiome' metabarcoded DNA sequencing method and applied it for the quantification of haemoprotozoan parasites (Theleria and Babesia) of livestock. Here, we describe a novel, high throughput method using an Illumina MiSeq platform to demonstrate the proportions of Plasmodium species in metabarcoded DNA samples derived from human malaria patients. Plasmodium falciparum and Plasmodium vivax positive control gDNA was used to prepare mock DNA pools of parasites to evaluate the detection threshold of the assay for each of the two species. The different mock pools demonstrate the accurate detection ability and to show the proportions of each of the species being present. We then applied the assay to malaria-positive human samples to show the species composition of Plasmodium communities in the Punjab province of Pakistan and in the Afghanistan-Pakistan tribal areas. The diagnostic performance of the deep amplicon sequencing method was compared to an immunochromatographic assay that is widely used in the region. The deep amplicon sequencing showed that P. vivax was present in 69.8%, P. falciparum in 29.5% and mixed infection in 0.7% patients examined. The immunochromatographic assay showed that P. vivax was present in 65.6%, P. falciparum in 27.4%, mixed infection 0.7% patients and 6.32% malaria-positive cases were negative in immunochromatographic assay, but positive in the deep amplicon sequencing. Overall, metabarcoded DNA sequencing demonstrates better diagnostic performance, greatly increasing the estimated prevalence of Plasmodium infection. The next-generation sequencing method using metabarcoded DNA has potential applications in the diagnosis, surveillance, treatment, and control of Plasmodium infections, as well as to study the parasite biology.
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Affiliation(s)
- Abdul Wahab
- University of Science and Technology, Kohat, Khyber Pakhtunkhwa, Pakistan
| | - Ayaz Shaukat
- University of Central Punjab, Lahore, Punjab, Pakistan
| | - Qasim Ali
- Gomal University, Dera Ismail Khan, Khyber Pakhtunkhwa, Pakistan
| | - Mubashir Hussain
- University of Science and Technology, Kohat, Khyber Pakhtunkhwa, Pakistan
| | - Taj Ali Khan
- University of Science and Technology, Kohat, Khyber Pakhtunkhwa, Pakistan
| | | | - Imran Rashid
- University of Veterinary and Animal Sciences, Lahore, Punjab, Pakistan
| | | | - Mike Evans
- Royal Dick School of Veterinary Studies, University of Edinburgh, UK
| | - Neil D Sargison
- Royal Dick School of Veterinary Studies, University of Edinburgh, UK.
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González-Cerón L, Rodríguez MH, Ovilla-Muñoz MT, Santillán-Valenzuela F, Hernández-Ávila JE, Rodríguez MC, Martínez-Barnetche J, Villarreal-Treviño C. Ookinete-Specific Genes and 18S SSU rRNA Evidenced in Plasmodium vivax Selection and Adaptation by Sympatric Vectors. Front Genet 2020; 10:1362. [PMID: 32153625 PMCID: PMC7047961 DOI: 10.3389/fgene.2019.01362] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Accepted: 12/12/2019] [Indexed: 01/26/2023] Open
Abstract
In the southern Pacific coast of Chiapas, Mexico (SM), the two most abundant vector species, Nyssorhynchus albimanus and Anopheles pseudopunctipennis, were susceptible to different Plasmodium vivax Pvs25/28 haplotypes. To broaden our understanding of the existing P. vivax in the area, genes encoding proteins relevant for ookinete development and the 18S rRNA were studied. P. vivax infectivity (percentage of infected mosquitoes and oocyst numbers) was evaluated by simultaneously feeding infected blood samples from patients to Ny. albimanus and An. pseudopunctipennis female mosquitoes. Three infectivity patterns were identified: one group of parasites were more infective to An. pseudopunctipennis than to Ny. albimanus, another group was more infective to Ny. albimanus, while a third group infected both vectors similarly. In 29 parasite isolates, the molecular variations of ookinete-specific genes and the 18S rRNA-type S were analyzed. Using concatenated sequences, phylogenetic trees, and Structure analysis, parasite clustering within SM isolates and between these and those from other geographical origins were investigated. A ML phylogenetic tree resolved two parasite lineages: PvSM-A and PvSM-B. They were associated to a different 18S rRNA variant. PvSM-A parasites had 18S rRNA variant rV2 and correspond to parasites causing high oocyst infection in Ny. albimanus. A new ML tree and Structure analysis, both comprising global sequences, showed PvSM-A clustered with Latin American parasites. Meanwhile, all isolates of PvSM-B had 18S rRNA variant rV1 and remained as unique genetic cluster comprising two subgroups: PvSM-Ba, producing high infection in An. pseudopunctipennis, and PvSM-Bb, causing similar oocyst infection in both vector species. PvSM-A parasites were genetically similar to parasites from South America. Meanwhile, PvSM-B were exclusive to southern Mexico and share ancestry with Asian parasites. The results suggest that these lineages evolved separately, likely by geographic and vector restriction.
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Affiliation(s)
- Lilia González-Cerón
- Regional Center of Research in Public Health, National Institute of Public Health, Ministry of Health, Tapachula, Mexico
| | - Mario H Rodríguez
- Vector Borne Diseases, Center for Research on Infectious Diseases, National Institute of Public Health, Ministry of Health, Cuernavaca, Mexico
| | - Marbella T Ovilla-Muñoz
- Chronic Infections and Cancer, Center for Research on Infectious Diseases, National Institute of Public Health, Ministry of Health, Cuernavaca, Mexico
| | - Frida Santillán-Valenzuela
- Regional Center of Research in Public Health, National Institute of Public Health, Ministry of Health, Tapachula, Mexico
| | - Juan E Hernández-Ávila
- Center of Information for Public Health Decisions, National Institute of Public Health, Ministry of Health, Mexico City, Mexico
| | - María Carmen Rodríguez
- Vector Borne Diseases, Center for Research on Infectious Diseases, National Institute of Public Health, Ministry of Health, Cuernavaca, Mexico
| | - Jesús Martínez-Barnetche
- Chronic Infections and Cancer, Center for Research on Infectious Diseases, National Institute of Public Health, Ministry of Health, Cuernavaca, Mexico
| | - Cuauhtémoc Villarreal-Treviño
- Regional Center of Research in Public Health, National Institute of Public Health, Ministry of Health, Tapachula, Mexico
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Erath J, Djuranovic S, Djuranovic SP. Adaptation of Translational Machinery in Malaria Parasites to Accommodate Translation of Poly-Adenosine Stretches Throughout Its Life Cycle. Front Microbiol 2019; 10:2823. [PMID: 31866984 PMCID: PMC6908487 DOI: 10.3389/fmicb.2019.02823] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 11/21/2019] [Indexed: 11/13/2022] Open
Abstract
Malaria is caused by unicellular apicomplexan parasites of the genus Plasmodium, which includes the major human parasite Plasmodium falciparum. The complex cycle of the malaria parasite in both mosquito and human hosts has been studied extensively. There is tight control of gene expression in each developmental stage, and at every level of gene synthesis: from RNA transcription, to its subsequent translation, and finally post-translational modifications of the resulting protein. Whole-genome sequencing of P. falciparum has laid the foundation for significant biological advances by revealing surprising genomic information. The P. falciparum genome is extremely AT-rich (∼80%), with a substantial portion of genes encoding intragenic polyadenosine (polyA) tracks being expressed throughout the entire parasite life cycle. In most eukaryotes, intragenic polyA runs act as negative regulators of gene expression. Recent studies have shown that translation of mRNAs containing 12 or more consecutive adenosines results in ribosomal stalling and frameshifting; activating mRNA surveillance mechanisms. In contrast, P. falciparum translational machinery can efficiently and accurately translate polyA tracks without activating mRNA surveillance pathways. This unique feature of P. falciparum raises interesting questions: (1) How is P. falciparum able to efficiently and correctly translate polyA track transcripts, and (2) What are the specifics of the translational machinery and mRNA surveillance mechanisms that separate P. falciparum from other organisms? In this review, we analyze possible evolutionary shifts in P. falciparum protein synthesis machinery that allow efficient translation of an AU rich-transcriptome. We focus on physiological and structural differences of P. falciparum stage specific ribosomes, ribosome-associated proteins, and changes in mRNA surveillance mechanisms throughout the complete parasite life cycle, with an emphasis on the mosquito and liver stages.
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Affiliation(s)
| | - Sergej Djuranovic
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO, United States
| | - Slavica Pavlovic Djuranovic
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO, United States
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Mohon AN, Getie S, Jahan N, Alam MS, Pillai DR. Ultrasensitive loop mediated isothermal amplification (US-LAMP) to detect malaria for elimination. Malar J 2019; 18:350. [PMID: 31619258 PMCID: PMC6796404 DOI: 10.1186/s12936-019-2979-4] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2019] [Accepted: 09/26/2019] [Indexed: 11/13/2022] Open
Abstract
Background Malaria elimination requires diagnostic methods able to detect parasite levels well below what is currently possible with microscopy and rapid diagnostic tests. This is particularly true in surveillance of malaria at the population level that includes so-called “asymptomatic” individuals. Methods The development of the first ultrasensitive loop mediated amplification method capable of detecting malaria from both whole blood and dried blood spots (DBS) is described. The 18S rRNA and corresponding genes that remain stable on DBS for up to 5 months are targeted. Results In the case of Plasmodium falciparum, lower limits of detection of 25 parasite/mL and 50–100 parasite/mL from whole blood and DBS were obtained, respectively. A sensitivity of 97.0% (95% CI 82.5–99.8) and specificity of 99.1% (95% CI 97.6–99.7) was obtained for the detection of all species in asymptomatic individuals from Africa and Asia (n = 494). Conclusion This tool is ideally suited for low middle-income countries where malaria is endemic and ultrasensitive surveillance of malaria is highly desirable for elimination.
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Affiliation(s)
- Abu Naser Mohon
- Department of Microbiology and Infectious Disease, Cumming School of Medicine, University of Calgary, Alberta, T2N 4N1, Canada.,Department of Pathology and Laboratory Medicine, Cumming School of Medicine, University of Calgary, 9-3535 Research Road NW, 1 W-416, Calgary, AB, T2L2K8, Canada
| | - Sisay Getie
- Department of Medical Parasitology, School of Biomedical and Laboratory Science, College of Medicine and Health Sciences, University of Gondar, P. O. Box: 196, Gondar, Ethiopia
| | - Nusrat Jahan
- Emerging Infections and Parasitology Laboratory, International Center for Diarrheal Disease Research, Bangladesh (icddr,b), Dhaka, 1212, Bangladesh
| | - Mohammad Shafiul Alam
- Emerging Infections and Parasitology Laboratory, International Center for Diarrheal Disease Research, Bangladesh (icddr,b), Dhaka, 1212, Bangladesh
| | - Dylan R Pillai
- Department of Microbiology and Infectious Disease, Cumming School of Medicine, University of Calgary, Alberta, T2N 4N1, Canada. .,Department of Pathology and Laboratory Medicine, Cumming School of Medicine, University of Calgary, 9-3535 Research Road NW, 1 W-416, Calgary, AB, T2L2K8, Canada. .,Department of Medicine, Cumming School of Medicine, University of Calgary, Alberta, T2N 4N1, Canada.
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11
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Harl J, Himmel T, Valkiūnas G, Weissenböck H. The nuclear 18S ribosomal DNAs of avian haemosporidian parasites. Malar J 2019; 18:305. [PMID: 31481072 PMCID: PMC6724295 DOI: 10.1186/s12936-019-2940-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Accepted: 08/27/2019] [Indexed: 01/19/2023] Open
Abstract
Background Plasmodium species feature only four to eight nuclear ribosomal units on different chromosomes, which are assumed to evolve independently according to a birth-and-death model, in which new variants originate by duplication and others are deleted throughout time. Moreover, distinct ribosomal units were shown to be expressed during different developmental stages in the vertebrate and mosquito hosts. Here, the 18S rDNA sequences of 32 species of avian haemosporidian parasites are reported and compared to those of simian and rodent Plasmodium species. Methods Almost the entire 18S rDNAs of avian haemosporidians belonging to the genera Plasmodium (7), Haemoproteus (9), and Leucocytozoon (16) were obtained by PCR, molecular cloning, and sequencing ten clones each. Phylogenetic trees were calculated and sequence patterns were analysed and compared to those of simian and rodent malaria species. A section of the mitochondrial CytB was also sequenced. Results Sequence patterns in most avian Plasmodium species were similar to those in the mammalian parasites with most species featuring two distinct 18S rDNA sequence clusters. Distinct 18S variants were also found in Haemoproteus tartakovskyi and the three Leucocytozoon species, whereas the other species featured sets of similar haplotypes. The 18S rDNA GC-contents of the Leucocytozoon toddi complex and the subgenus Parahaemoproteus were extremely high with 49.3% and 44.9%, respectively. The 18S sequences of several species from all three genera showed chimeric features, thus indicating recombination. Conclusion Gene duplication events leading to two diverged main sequence clusters happened independently in at least six out of seven avian Plasmodium species, thus supporting evolution according to a birth-and-death model like proposed for the ribosomal units of simian and rodent Plasmodium species. Patterns were similar in the 18S rDNAs of the Leucocytozoon toddi complex and Haemoproteus tartakovskyi. However, the 18S rDNAs of the other species seem to evolve in concerted fashion like in most eukaryotes, but the presence of chimeric variants indicates that the ribosomal units rather evolve in a semi-concerted manner. The new data may provide a basis for studies testing whether differential expression of distinct 18S rDNA also occurs in avian Plasmodium species and related haemosporidian parasites.
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Affiliation(s)
- Josef Harl
- Department of Pathobiology, Institute of Pathology, University of Veterinary Medicine, Veterinaerplatz 1, 1210, Vienna, Austria
| | - Tanja Himmel
- Department of Pathobiology, Institute of Pathology, University of Veterinary Medicine, Veterinaerplatz 1, 1210, Vienna, Austria
| | | | - Herbert Weissenböck
- Department of Pathobiology, Institute of Pathology, University of Veterinary Medicine, Veterinaerplatz 1, 1210, Vienna, Austria.
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12
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Specialized ribosomes and the control of translation. Biochem Soc Trans 2018; 46:855-869. [PMID: 29986937 DOI: 10.1042/bst20160426] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Revised: 05/21/2018] [Accepted: 05/24/2018] [Indexed: 11/17/2022]
Abstract
The control of translation is increasingly recognized as a major factor in determining protein levels in the cell. The ribosome - the cellular machine that mediates protein synthesis - is typically seen as a key, but invariant, player in this process. This is because translational control is thought to be mediated by other auxiliary factors while ribosome recruitment is seen as the end-point of regulation. However, recent developments have made it clear that heterogeneous ribosome types can exist in different tissues, and more importantly, that these ribosomes can preferentially translate different subsets of mRNAs. In so doing, heterogeneous ribosomes could be key regulatory players in differentiation and development. Here, we examine current evidence for the existence of different ribosome types and how they might arise. In particular, we will take a close look at the mechanisms through which these ribosomes might mediate selective mRNA translation. We also summarize recently developed techniques/approaches that will aid in our understanding of the functions of such specialized ribosomes.
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13
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Gruenberg M, Moniz CA, Hofmann NE, Wampfler R, Koepfli C, Mueller I, Monteiro WM, Lacerda M, de Melo GC, Kuehn A, Siqueira AM, Felger I. Plasmodium vivax molecular diagnostics in community surveys: pitfalls and solutions. Malar J 2018; 17:55. [PMID: 29378609 PMCID: PMC5789620 DOI: 10.1186/s12936-018-2201-0] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 01/20/2018] [Indexed: 11/10/2022] Open
Abstract
A distinctive feature of Plasmodium vivax infections is the overall low parasite density in peripheral blood. Thus, identifying asymptomatic infected individuals in endemic communities requires diagnostic tests with high sensitivity. The detection limits of molecular diagnostic tests are primarily defined by the volume of blood analysed and by the copy number of the amplified molecular marker serving as the template for amplification. By using mitochondrial DNA as the multi-copy template, the detection limit can be improved more than tenfold, compared to standard 18S rRNA targets, thereby allowing detection of lower parasite densities. In a very low transmission area in Brazil, application of a mitochondrial DNA-based assay increased prevalence from 4.9 to 6.5%. The usefulness of molecular tests in malaria epidemiological studies is widely recognized, especially when precise prevalence rates are desired. Of concern, however, is the challenge of demonstrating test accuracy and quality control for samples with very low parasite densities. In this case, chance effects in template distribution around the detection limit constrain reproducibility. Rigorous assessment of false positive and false negative test results is, therefore, required to prevent over- or under-estimation of parasite prevalence in epidemiological studies or when monitoring interventions.
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Affiliation(s)
- Maria Gruenberg
- Swiss Tropical and Public Health Institute, Socinstrasse 57, 4002, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Clara Antunes Moniz
- Swiss Tropical and Public Health Institute, Socinstrasse 57, 4002, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Natalie Ellen Hofmann
- Swiss Tropical and Public Health Institute, Socinstrasse 57, 4002, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Rahel Wampfler
- Swiss Tropical and Public Health Institute, Socinstrasse 57, 4002, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Cristian Koepfli
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Ivo Mueller
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | | | - Marcus Lacerda
- Fundação de Medicina Tropical Dr. Heitor Vieira Dourado (FMT-HVD), Manaus, Brazil.,Universidade do Estado do Amazonas, Manaus, Brazil
| | - Gisely Cardoso de Melo
- Fundação de Medicina Tropical Dr. Heitor Vieira Dourado (FMT-HVD), Manaus, Brazil.,Universidade do Estado do Amazonas, Manaus, Brazil
| | - Andrea Kuehn
- Fundação de Medicina Tropical Dr. Heitor Vieira Dourado (FMT-HVD), Manaus, Brazil
| | - Andre M Siqueira
- Fundação de Medicina Tropical Dr. Heitor Vieira Dourado (FMT-HVD), Manaus, Brazil.,Instituto Nacional de Infectologia, Evandro Chagas, Fiocruz, Rio de Janeiro, Brazil
| | - Ingrid Felger
- Swiss Tropical and Public Health Institute, Socinstrasse 57, 4002, Basel, Switzerland. .,University of Basel, Basel, Switzerland.
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14
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Siner A, Liew ST, Kadir KA, Mohamad DSA, Thomas FK, Zulkarnaen M, Singh B. Absence of Plasmodium inui and Plasmodium cynomolgi, but detection of Plasmodium knowlesi and Plasmodium vivax infections in asymptomatic humans in the Betong division of Sarawak, Malaysian Borneo. Malar J 2017; 16:417. [PMID: 29041929 PMCID: PMC5645983 DOI: 10.1186/s12936-017-2064-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2017] [Accepted: 10/11/2017] [Indexed: 01/01/2023] Open
Abstract
Background Plasmodium knowlesi, a simian malaria parasite, has become the main cause of malaria in Sarawak, Malaysian Borneo. Epidemiological data on malaria for Sarawak has been derived solely from hospitalized patients, and more accurate epidemiological data on malaria is necessary. Therefore, a longitudinal study of communities affected by knowlesi malaria was undertaken. Methods A total of 3002 blood samples on filter paper were collected from 555 inhabitants of 8 longhouses with recently reported knowlesi malaria cases in the Betong Division of Sarawak, Malaysian Borneo. Each longhouse was visited bimonthly for a total of 10 times during a 21-month study period (Jan 2014–Oct 2015). DNA extracted from blood spots were examined by a nested PCR assay for Plasmodium and positive samples were then examined by nested PCR assays for Plasmodium falciparum, Plasmodium vivax, Plasmodium malariae, Plasmodium ovale, Plasmodium knowlesi, Plasmodium cynomolgi and Plasmodium inui. Blood films of samples positive by PCR were also examined by microscopy. Results Genus-specific PCR assay detected Plasmodium DNA in 9 out of 3002 samples. Species-specific PCR identified 7 P. knowlesi and one P. vivax. Malaria parasites were observed in 5 thick blood films of the PCR positive samples. No parasites were observed in blood films from one knowlesi-, one vivax- and the genus-positive samples. Only one of 7 P. knowlesi-infected individual was febrile and had sought medical treatment at Betong Hospital the day after sampling. The 6 knowlesi-, one vivax- and one Plasmodium-infected individuals were afebrile and did not seek any medical treatment. Conclusions Asymptomatic human P. knowlesi and P. vivax malaria infections, but not P. cynomolgi and P. inui infections, are occurring within communities affected with malaria.
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Affiliation(s)
- Angela Siner
- Malaria Research Centre, Faculty of Medicine and Health Sciences, Universiti Malaysia Sarawak, 94300, Kota Samarahan, Sarawak, Malaysia.
| | - Sze-Tze Liew
- Malaria Research Centre, Faculty of Medicine and Health Sciences, Universiti Malaysia Sarawak, 94300, Kota Samarahan, Sarawak, Malaysia
| | - Khamisah Abdul Kadir
- Malaria Research Centre, Faculty of Medicine and Health Sciences, Universiti Malaysia Sarawak, 94300, Kota Samarahan, Sarawak, Malaysia
| | - Dayang Shuaisah Awang Mohamad
- Malaria Research Centre, Faculty of Medicine and Health Sciences, Universiti Malaysia Sarawak, 94300, Kota Samarahan, Sarawak, Malaysia
| | - Felicia Kavita Thomas
- Malaria Research Centre, Faculty of Medicine and Health Sciences, Universiti Malaysia Sarawak, 94300, Kota Samarahan, Sarawak, Malaysia
| | - Mohammad Zulkarnaen
- Malaria Research Centre, Faculty of Medicine and Health Sciences, Universiti Malaysia Sarawak, 94300, Kota Samarahan, Sarawak, Malaysia
| | - Balbir Singh
- Malaria Research Centre, Faculty of Medicine and Health Sciences, Universiti Malaysia Sarawak, 94300, Kota Samarahan, Sarawak, Malaysia.
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15
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Megía-Palma R, Martínez J, Paranjpe D, D’Amico V, Aguilar R, Palacios MG, Cooper R, Ferri-Yáñez F, Sinervo B, Merino S. Phylogenetic analyses reveal that Schellackia parasites (Apicomplexa) detected in American lizards are closely related to the genus Lankesterella: is the range of Schellackia restricted to the Old World? Parasit Vectors 2017; 10:470. [PMID: 29017602 PMCID: PMC5633878 DOI: 10.1186/s13071-017-2405-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Accepted: 09/26/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Species of Schellackia Reichenow, 1919 have been described from the blood of reptiles distributed worldwide. Recently, Schellackia spp. detected in European and Asian lizards have been molecularly characterised. However, parasites detected in American lizard hosts remain uncharacterised. Thus, phylogenetic affinities between the Old and New World parasite species are unknown. METHODS In the present study, we characterised morphologically and molecularly the hemococcidian parasites (sporozoites) that infect three lizard hosts from North America and two from South America. RESULTS In total, we generated 12 new 18S rRNA gene sequences of hemococcidian parasites infecting New World lizard hosts. By the microscopic examination of the smears we identified Schellackia golvani Rogier & Landau, 1975 (ex Anolis carolinensis Voigt) and Schellackia occidentalis Bonorris & Ball, 1955 (ex Uta stansburiana Baird & Girard and Sceloporus occidentalis Baird & Girard) in some samples, but the phylogenetic analysis indicated that all 18S rDNA sequences are distant from Schellackia species found in Old World lizards. In fact, the hemococcidian parasites detected in the New World lizards (including S. occidentalis and S. golvani) were closely related to the genus Lankesterella Labbé, 1899. Consequently, we suggest these two species to be included within the genus Lankesterella. CONCLUSIONS Life history traits of hemococcidian parasites such as the type of host blood cells infected, host species or number of refractile bodies are not valid diagnostic characteristics to differentiate the parasites between the genera Schellackia and Lankesterella. Indeed, lankesterellid parasites with a different number of refractile bodies had a close phylogenetic origin. Based on the phylogenetic results we provide a systematic revision of the North American hemococcidians. Our recommendation is to include the species formerly described in the genus Schellackia that infect American lizards into Lankesterella (Lankesterellidae) as Lankesterella golvani (Rogier & Landau, 1975) n. comb and L. occidentalis (Bonorris & Ball, 1955) n. comb.
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Affiliation(s)
- Rodrigo Megía-Palma
- Departamento de Ecología Evolutiva, Museo Nacional de Ciencias Naturales-CSIC, Madrid, Spain
| | - Javier Martínez
- Departamento de Biomedicina y Biotecnología, Área de Parasitología, Universidad de Alcalá de Henares, Alcalá de Henares, Spain
| | - Dhanashree Paranjpe
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, California 95064 USA
- Department of Biodiversity, Abasaheb Garware College, Pune, India
| | - Verónica D’Amico
- Grupo de Ecofisiología Aplicada al Manejo y Conservación de la Fauna Silvestre, Centro para el Estudio de Sistemas Marinos, Centro Nacional Patagónico, Puerto Madryn, Chubut Argentina
| | - Rocío Aguilar
- Instituto Argentino de Zonas Áridas, Grupo de Investigaciones de la Biodiversidad CONICET MENDOZA, Mendoza, Argentina
- School of Biosciences, The University of Melbourne, Melbourne, VIC Australia
| | - María Gabriela Palacios
- Grupo de Ecofisiología Aplicada al Manejo y Conservación de la Fauna Silvestre, Centro para el Estudio de Sistemas Marinos, Centro Nacional Patagónico, Puerto Madryn, Chubut Argentina
| | - Robert Cooper
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, California 95064 USA
| | - Francisco Ferri-Yáñez
- Departamento de Biogeografía y Cambio Global, Museo Nacional de Ciencias Naturales-CSIC, Madrid, Spain
| | - Barry Sinervo
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, California 95064 USA
| | - Santiago Merino
- Departamento de Ecología Evolutiva, Museo Nacional de Ciencias Naturales-CSIC, Madrid, Spain
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16
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Ogedengbe ME, El-Sherry S, Ogedengbe JD, Chapman HD, Barta JR. Phylogenies based on combined mitochondrial and nuclear sequences conflict with morphologically defined genera in the eimeriid coccidia (Apicomplexa). Int J Parasitol 2017; 48:59-69. [PMID: 28989067 DOI: 10.1016/j.ijpara.2017.07.008] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Revised: 07/24/2017] [Accepted: 07/25/2017] [Indexed: 10/18/2022]
Abstract
Partial mitochondrial (mt) cytochrome c oxidase subunit I (COI) and near-complete nuclear (nu) 18S rDNA sequences were obtained from various eimeriid coccidia infecting vertebrates. New and published sequences were used in phylogenetic reconstructions based on nu 18S rDNA, mt COI and concatenated sequence datasets. Bayesian analyses of nu 18S rDNA sequences used secondary structure-based alignments with a doublet nucleotide substitution model; the codon nucleotide substitution model was applied to COI sequences. Although alignment of the mt COI sequences was unambiguous, substitution saturation was evident for comparisons of COI sequences between ingroup (eimeriid) and outgroup (sarcocystid) taxa. Consequently, a combined dataset applying partition-specific analytical and alignment improvements was used to generate a robust molecular phylogeny. Most eimeriid parasites that infect closely related definitive hosts were found in close proximity on the resulting tree, frequently in a single clade. Whether this represents coevolution or co-accommodation or a combination remains an open point. Unlike host associations, basic oocyst configuration (number of sporocysts per oocyst and sporozoites per sporocyst) was not correlated with phylogeny. Neither 'Eimeria-type' nor 'Isospora-type' oocyst morphotypes formed monophyletic groups. In the combined dataset tree (representing only a tiny fraction of described eimeriid coccidia), at least 10 clades of Eimeria spp. would need to be re-assigned to nine distinct genera to resolve their paraphyly. The apparent lack of congruence between morphotype and genotype will require taxonomists to balance nomenclatural stability and diagnostic ease against the ideal of monophyletic genera. For now, recognition of paraphyletic eimeriid genera defined by basic oocyst configuration may be necessary for reasons of taxonomic stability and diagnostic utility. Future taxonomic revisions to produce monophyletic eimeriid genera will ultimately require the identification of reliable phenotypic characters that agree with the molecular phylogeny of these parasites or, less optimally, acceptance that genotyping may be needed to support monophyletic supraspecific taxonomic groups.
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Affiliation(s)
- Mosun E Ogedengbe
- Department of Pathobiology, University of Guelph, Guelph, ON, Canada
| | - Shiem El-Sherry
- Department of Pathobiology, University of Guelph, Guelph, ON, Canada; Department of Poultry Diseases, Faculty of Veterinary Medicine, Assiut University, Egypt
| | | | - H David Chapman
- Department of Poultry Science, University of Arkansas, Fayetteville, USA
| | - John R Barta
- Department of Pathobiology, University of Guelph, Guelph, ON, Canada.
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17
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Kim A, Popovici J, Vantaux A, Samreth R, Bin S, Kim S, Roesch C, Liang L, Davies H, Felgner P, Herrera S, Arévalo-Herrera M, Ménard D, Serre D. Characterization of P. vivax blood stage transcriptomes from field isolates reveals similarities among infections and complex gene isoforms. Sci Rep 2017; 7:7761. [PMID: 28798400 PMCID: PMC5552866 DOI: 10.1038/s41598-017-07275-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 06/23/2017] [Indexed: 01/19/2023] Open
Abstract
Our understanding of the structure and regulation of Plasmodium vivax genes is limited by our inability to grow the parasites in long-term in vitro cultures. Most P. vivax studies must therefore rely on patient samples, which typically display a low proportion of parasites and asynchronous parasites. Here, we present stranded RNA-seq data generated directly from a small volume of blood from three Cambodian vivax malaria patients collected before treatment. Our analyses show surprising similarities of the parasite gene expression patterns across infections, despite extensive variations in parasite stage proportion. These similarities contrast with the unique gene expression patterns observed in sporozoites isolated from salivary glands of infected Colombian mosquitoes. Our analyses also indicate that more than 10% of P. vivax genes encode multiple, often undescribed, protein-coding sequences, potentially increasing the diversity of proteins synthesized by blood stage parasites. These data also greatly improve the annotations of P. vivax gene untranslated regions, providing an important resource for future studies of specific genes.
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Affiliation(s)
- Adam Kim
- Institute for Genome Sciences, University of Maryland, Baltimore, Maryland, USA
| | - Jean Popovici
- Malaria Molecular Epidemiology Unit, Institut Pasteur in Cambodia, Phnom Penh, Cambodia
| | - Amélie Vantaux
- Malaria Molecular Epidemiology Unit, Institut Pasteur in Cambodia, Phnom Penh, Cambodia
| | - Reingsey Samreth
- Malaria Molecular Epidemiology Unit, Institut Pasteur in Cambodia, Phnom Penh, Cambodia
| | - Sophalai Bin
- Malaria Molecular Epidemiology Unit, Institut Pasteur in Cambodia, Phnom Penh, Cambodia
| | - Saorin Kim
- Malaria Molecular Epidemiology Unit, Institut Pasteur in Cambodia, Phnom Penh, Cambodia
| | - Camille Roesch
- Malaria Molecular Epidemiology Unit, Institut Pasteur in Cambodia, Phnom Penh, Cambodia
| | - Li Liang
- Division of Infectious Diseases, University of California Irvine, Irvine, California, USA
| | - Huw Davies
- Division of Infectious Diseases, University of California Irvine, Irvine, California, USA
| | - Philip Felgner
- Division of Infectious Diseases, University of California Irvine, Irvine, California, USA
| | | | - Myriam Arévalo-Herrera
- Caucaseco Scientific Research Center, Cali, Colombia.,School of Health, University of Valle, Cali, Colombia
| | - Didier Ménard
- Malaria Molecular Epidemiology Unit, Institut Pasteur in Cambodia, Phnom Penh, Cambodia. .,Unité Biologie des Interactions Hôte-Parasite, Institut Pasteur, Paris, France. .,Inserm U1016, CNRS UMR8104, Institut Cochin, Paris, France.
| | - David Serre
- Institute for Genome Sciences, University of Maryland, Baltimore, Maryland, USA.
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18
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Abstract
The nuclear ribosomal DNA (rDNA) is considered as a paradigm of concerted evolution. Components of the rDNA tandem repeats (45S) are widely used in phylogenetic studies of different organisms and the internal transcribed spacer (ITS) region was recently selected as a fungal DNA bar code. However, rRNA pseudogenes, as one kind of escape from concerted evolution, were reported in a wide range of organisms, especially in plants and animals. Moreover, large numbers of 5S rRNA pseudogenes were identified in several filamentous ascomycetes. To study whether rDNA evolves in a strict concerted manner and test whether rRNA pseudogenes exist in more species of ascomycetes, intragenomic rDNA polymorphisms were analyzed using whole genome sequences. Divergent rDNA paralogs were found to coexist within a single genome in seven filamentous ascomycetes examined. A great number of paralogs were identified as pseudogenes according to the mutation and secondary structure analyses. Phylogenetic analyses of the three rRNA coding regions of the 45S rDNA repeats, i.e., 18S, 5.8S, and 28S, revealed an interspecies clustering pattern of those different rDNA paralogs. The identified rRNA pseudogenic sequences were validated using specific primers designed. Mutation analyses revealed that the repeat-induced point (RIP) mutation was probably responsible for the formation of those rRNA pseudogenes.
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19
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Sumari D, Mwingira F, Selemani M, Mugasa J, Mugittu K, Gwakisa P. Malaria prevalence in asymptomatic and symptomatic children in Kiwangwa, Bagamoyo district, Tanzania. Malar J 2017; 16:222. [PMID: 28545457 PMCID: PMC5445421 DOI: 10.1186/s12936-017-1870-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 05/18/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Malaria prevalence continues to decline across sub-Saharan Africa as a result of various intervention strategies. However, the diseases still poses a public health concern in the region. While symptomatic malaria is recognized and treated, asymptomatic infections become increasingly important for interrupting transmission. A cross-sectional survey was conducted to assess malaria prevalence in symptomatic and asymptomatic children in Kiwangwa ward in Bagamoyo District in Tanzania. METHODS Four hundred school-aged children in Kiwanga ward were recruited in the study; 200 from Kiwangwa dispensary and 200 from nearby schools. Primary health parameters were examined and blood samples collected and examined for Plasmodium falciparum prevalence using rapid diagnostic test (RDT), light microscopy (LM) and reverse transcription quantitative PCR (RT-qPCR) targeting transcripts of A-type 18s rRNA of P. falciparum. Gametocytes were detected by LM and RT-qPCR targeting transcripts of gametocyte specific marker, Pfs25. RESULTS Overall P. falciparum prevalence was 73.3, 40.8 and 36.3% by RT-qPCR, RDT and LM in the study area, respectively (P < 0.001). As expected symptomatic children had a significantly higher prevalence of 89, 67.5 and 64.5% by qPCR, RDT and LM, compared to 57.5, 14 and 8% in the asymptomatic group, respectively. However, gametocyte prevalence in asymptomatic individuals was higher by both LM (2%) and qPCR (14%) than in symptomatic individuals LM (0.5%) and qPCR (3%). CONCLUSIONS A substantial difference in prevalence of symptomatic and asymptomatic infections observed in Kiwangwa ward underpins the use of molecular tools in malaria surveillance aiming at estimating prevalence and transmission. Notably, the higher gametocytaemia observed in asymptomatic children indicates the reservoir infections and points to the need for detection and treatment of both asymptomatic and symptomatic malaria.
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Affiliation(s)
- Deborah Sumari
- Intervention and Clinical Trials Department, Ifakara Health Institute, Bagamoyo, Tanzania
- School of Life Sciences and Bioengineering, The Nelson Mandela African Institution for Science and Technology, Arusha, Tanzania
| | - Felista Mwingira
- Biological Sciences Department, Dar es Salaam University College of Education, P. O. Box 2329, Dar es Salaam, Tanzania
| | - Majige Selemani
- Intervention and Clinical Trials Department, Ifakara Health Institute, Bagamoyo, Tanzania
- Department of Statistics, University of Dar es Salaam, P. O. Box 35047, Dar es Salaam, Tanzania
| | - Joseph Mugasa
- National Institute for Medical Research, Amani Medical Research Centre, P. O. Box 81, Muheza, Tanga, Tanzania
| | - Kefas Mugittu
- Muvek Laboratories, P. O. Box 105270, Dar es Salaam, Tanzania
| | - Paul Gwakisa
- School of Life Sciences and Bioengineering, The Nelson Mandela African Institution for Science and Technology, Arusha, Tanzania
- Genome Sciences Centre and Department of Microbiology, Parasitology and Immunology, College of Veterinary and Medical Sciences, Sokoine University of Agriculture, P. O. Box 3019, Morogoro, Tanzania
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Vembar SS, Droll D, Scherf A. Translational regulation in blood stages of the malaria parasite Plasmodium spp.: systems-wide studies pave the way. WILEY INTERDISCIPLINARY REVIEWS-RNA 2016; 7:772-792. [PMID: 27230797 PMCID: PMC5111744 DOI: 10.1002/wrna.1365] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Revised: 04/21/2016] [Accepted: 04/26/2016] [Indexed: 11/10/2022]
Abstract
The malaria parasite Plasmodium spp. varies the expression profile of its genes depending on the host it resides in and its developmental stage. Virtually all messenger RNA (mRNA) is expressed in a monocistronic manner, with transcriptional activation regulated at the epigenetic level and by specialized transcription factors. Furthermore, recent systems-wide studies have identified distinct mechanisms of post-transcriptional and translational control at various points of the parasite lifecycle. Taken together, it is evident that 'just-in-time' transcription and translation strategies coexist and coordinate protein expression during Plasmodium development, some of which we review here. In particular, we discuss global and specific mechanisms that control protein translation in blood stages of the human malaria parasite Plasmodium falciparum, once a cytoplasmic mRNA has been generated, and its crosstalk with mRNA decay and storage. We also focus on the widespread translational delay observed during the 48-hour blood stage lifecycle of P. falciparum-for over 30% of transcribed genes, including virulence factors required to invade erythrocytes-and its regulation by cis-elements in the mRNA, RNA-processing enzymes and RNA-binding proteins; the first-characterized amongst these are the DNA- and RNA-binding Alba proteins. More generally, we conclude that translational regulation is an emerging research field in malaria parasites and propose that its elucidation will not only shed light on the complex developmental program of this parasite, but may also reveal mechanisms contributing to drug resistance and define new targets for malaria intervention strategies. WIREs RNA 2016, 7:772-792. doi: 10.1002/wrna.1365 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Shruthi Sridhar Vembar
- Unité Biologie des Interactions Hôte-Parasite, Département de Parasites et Insectes Vecteurs, Institut Pasteur, Paris, France.
| | - Dorothea Droll
- Unité Biologie des Interactions Hôte-Parasite, Département de Parasites et Insectes Vecteurs, Institut Pasteur, Paris, France
| | - Artur Scherf
- Unité Biologie des Interactions Hôte-Parasite, Département de Parasites et Insectes Vecteurs, Institut Pasteur, Paris, France
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Molecular phylogenetic analyses of tissue coccidia (sarcocystidae; apicomplexa) based on nuclear 18s RDNA and mitochondrial COI sequences confirms the paraphyly of the genus Hammondia. ACTA ACUST UNITED AC 2016. [DOI: 10.1017/pao.2015.7] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
SUMMARYPartial mitochondrial cytochromecoxidase subunit I (mt COI) sequences were generated from:Toxoplasma gondii(strains CTG, GTI, MAS, ME49, PTG, TgCatBr5, TgCat, Br64, TgCgCal, TgToucan);Neospora caninum(Strain NC1);Hammondia hammondi(Strain H.H–20);H. heydorni; H. cf.triffittae; Cystoisospora felis; C. suis; C. canis; C. rivolta; C. cf.ohioensis; Caryospora bigenetica; Sarcocystis rileyi; andS. neurona. Nuclear 18S rDNA sequences were generated forH. heydorni, H. hammondi, C. suis, C. canis, C. felis, C. rivolta, C. cf.ohioensis, S. neurona, andS. rileyi. Aligned, concatenated 18S rDNA and COI sequences were Bayesian analysed using partitioned nucleotide substitution models [HKY + I + G for 18S; GTR + I + G codon (code = metmt) for COI]. Phylogenetic hypotheses supported a monophyletic Sarcocystidae and its subfamilie with two major clades within the Toxoplasmatinae: (1) a monophyletic clade ofCystoisosporaspp. withNephroisospora eptesici; and (2) a clade ofToxoplasma, NeosporaandHammondia. Within the latter,Hammondiawas shown to be paraphyletic;H. heydorniandH. triffittaewere monophyletic withN. caninum[canine definitive hosts (DHs)], whereasH. hammondiwas monophyletic withT. gondii(feline DHs). A new genus is erected to resolve the paraphyly of the genusHammondiaconfirmed using mt COI and combined 18S/COI sequence datasets.
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Molecular Approaches for Diagnosis of Malaria and the Characterization of Genetic Markers for Drug Resistance. Mol Microbiol 2016. [DOI: 10.1128/9781555819071.ch37] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Molecular phylogenetics of eimeriid coccidia (Eimeriidae, Eimeriorina, Apicomplexa, Alveolata): A preliminary multi-gene and multi-genome approach. Parasitol Res 2015; 114:4149-60. [PMID: 26319519 DOI: 10.1007/s00436-015-4646-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Accepted: 07/23/2015] [Indexed: 10/23/2022]
Abstract
Coccidia possess three distinct genomes: nuclear, mitochondrial, and plastid. Sequences from five genes located on these three genomes were used to reconstruct the phylogenetic relationships of members of the phylum Apicomplexa: 18S rDNA sequences from the nuclear (nu) genome, partial cytochrome c oxidase subunit I sequences from the mitochondrial (mt) genome, and partial 16S and 23S rDNA sequences and RNA polymerase B sequences from plastid (pl) genomes. Maximum parsimony, maximum likelihood, and Bayesian inference were used in conjunction with nuclear substitution models generated from data subsets in the analyses. Major groups within the Apicomplexa were well supported with the mitochondrial, nuclear, and a combination of mitochondrial, nuclear and concatenated plastid gene sequences. However, the genus Eimeria was paraphyletic in phylogenetic trees based on the nuclear gene. Analyses using the individual genes (18S rDNA and cytochrome c oxidase subunit I) resolved the various apicomplexan groups with high Bayesian posterior probabilities. The multi-gene, multi-genome analyses based on concatenated nu 18S rDNA, pl 16S, pl 23S, pl rPoB, pl rPoB1, and mt COI sequences appeared useful in resolving phylogenetic relationships within the phylum Apicomplexa. Genus-level relationships, or higher, appear best supported by 18S rDNA analyses, and species-level analyses are best investigated using mt COI sequences; for parasites for which both loci are available, nuclear 18S rDNA sequences combined with mitochondrial COI sequences provide a compact and informative molecular dataset for inferring the evolutionary relationships taxa in the Apicomplexa.
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Sinden RE. The cell biology of malaria infection of mosquito: advances and opportunities. Cell Microbiol 2015; 17:451-66. [PMID: 25557077 PMCID: PMC4409862 DOI: 10.1111/cmi.12413] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Revised: 12/12/2014] [Accepted: 12/24/2014] [Indexed: 01/01/2023]
Abstract
Recent reviews (Feachem et al.; Alonso et al.) have concluded that in order to have a sustainable impact on the global burden of malaria, it is essential that we knowingly reduce the global incidence of infected persons. To achieve this we must reduce the basic reproductive rate of the parasites to < 1 in diverse epidemiological settings. This can be achieved by impacting combinations of the following parameters: the number of mosquitoes relative to the number of persons, the mosquito/human biting rate, the proportion of mosquitoes carrying infectious sporozoites, the daily survival rate of the infectious mosquito and the ability of malaria-infected persons to infect mosquito vectors. This paper focuses on our understanding of parasite biology underpinning the last of these terms: infection of the mosquito. The article attempts to highlight central issues that require further study to assist in the discovery of useful transmission-blocking measures.
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Affiliation(s)
- R E Sinden
- Department of Life Sciences, Imperial College London and the Jenner Institute, The University of Oxford, Oxford, UK
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Cui L, Lindner S, Miao J. Translational regulation during stage transitions in malaria parasites. Ann N Y Acad Sci 2014; 1342:1-9. [PMID: 25387887 DOI: 10.1111/nyas.12573] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The complicated life cycle of the malaria parasite involves a vertebrate host and a mosquito vector, and translational regulation plays a prominent role in orchestrating the developmental events in the two transition stages: gametocytes and sporozoites. Translational regulation is executed in both global and transcript-specific manners. Plasmodium uses a conserved mechanism involving phosphorylation of eIF2α to repress global protein synthesis during the latent period of sporozoite development in the mosquito salivary glands. Transcript-specific translational regulation is achieved by a network of RNA-binding proteins (RBPs), among which the Dhh1 RNA helicase DOZI and Puf family RBPs are by far the best studied in Plasmodium. While the DOZI complex defines a new P granule with a role in protecting certain gametocyte mRNAs from degradation, the Puf proteins appear to repress expression of mRNAs in both gametocytes and sporozoites. These examples underscore the significance of translational regulation in Plasmodium development.
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Li M, Xia Z, Yan H. New type of SSUrDNA sequence was detected from both Plasmodium ovale curtisi and Plasmodium ovale wallikeri samples. Malar J 2014; 13:216. [PMID: 24893846 PMCID: PMC4049480 DOI: 10.1186/1475-2875-13-216] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2014] [Accepted: 05/21/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Plasmodium ovale is relatively unfamiliar to Chinese staff engaged in malaria diagnosis. In 2013, dried blood spots of four unidentified but suspected ovale malaria samples were sent to the National Malaria Reference Laboratory (NMRL) for reconfirmation. METHODS Partial and complete, small, subunit ribosomal DNA (SSU rDNA) sequences of four samples were obtained with PCR-cloning-sequencing method. Obtained sequences were analyzed by aligning with each other and with nine SSU rDNA sequences of six known Plasmodium parasites. A phylogenetic tree was constructed based on complete SSU rDNA sequences and 12 same gene sequences derived from six known Plasmodium parasites and three Babesia parasites. Primary structure of conservative and variable regions of variant sequences was determined also by comparing them with those of six known Plasmodium parasites. To confirm their existence in genome, they were redetected with primers matching their variable regions. PCR systems aimed to roughly detect any eukaryotes and prokaryotes respectively were also applied to search for other pathogens in one of four patients. RESULTS Totally, 19 partial and 23 complete SSU rDNA sequences obtained from four samples. Except eight variant sequences, similarities among sequences from same DNA sample were in general high (more than 98%). The phylogenetic analysis revealed that three cases were infected by P. ovale wallikeri and one by P. ovale curtisi. Four of the variant sequences which obtained from four samples relatively showed high similarities with each other (98.5%-100%). Identical variant sequences actually could be re-obtained from each DNA sample. Their primary structure of conservative and variable regions showed quite fit with that of six known Plasmodium parasites. The test for prokaryote pathogens showed negative and the tests for eukaryotes only found DNA sequences of Human and P. ovale parasites. CONCLUSION Both P. ovale wallikeri and P. ovale curtisi infections are present in imported malaria cases of China. New type of partial SSU rDNA sequence which assumed to express in a certain life stage of P. ovale was obtained from both P. ovale wallikeri and P. ovale curtisi samples. This discovery would supply information and clues to identify and understand P. ovale parasites more accurately.
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Affiliation(s)
- Mei Li
- National Institute of Parasitic Diseases, Chinese Centre for Diseases Control and Prevention, Key Laboratory of Parasite and Vector Biology, Ministry of Public Health, WHO Collaborating Centre for Malaria, Schistosomiasis and Filariasis, Shanghai 200025, People’s Republic of China
| | - Zhigui Xia
- National Institute of Parasitic Diseases, Chinese Centre for Diseases Control and Prevention, Key Laboratory of Parasite and Vector Biology, Ministry of Public Health, WHO Collaborating Centre for Malaria, Schistosomiasis and Filariasis, Shanghai 200025, People’s Republic of China
| | - He Yan
- National Institute of Parasitic Diseases, Chinese Centre for Diseases Control and Prevention, Key Laboratory of Parasite and Vector Biology, Ministry of Public Health, WHO Collaborating Centre for Malaria, Schistosomiasis and Filariasis, Shanghai 200025, People’s Republic of China
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Megía-Palma R, Martínez J, Merino S. Molecular characterization of haemococcidia genusSchellackia(Apicomplexa) reveals the polyphyletic origin of the family Lankesterellidae. ZOOL SCR 2014. [DOI: 10.1111/zsc.12050] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Rodrigo Megía-Palma
- Departamento de Ecología Evolutiva; Museo Nacional de Ciencias Naturales-CSIC; J. Gutiérrez Abascal, 2 Madrid E-28006 Spain
| | - Javier Martínez
- Departamento de Microbiología y Parasitología; Facultad de Farmacia; Universidad de Alcalá de Henares; Alcalá de Henares Madrid E-28871 Spain
| | - Santiago Merino
- Departamento de Ecología Evolutiva; Museo Nacional de Ciencias Naturales-CSIC; J. Gutiérrez Abascal, 2 Madrid E-28006 Spain
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Pakalapati D, Garg S, Middha S, Acharya J, Subudhi AK, Boopathi AP, Saxena V, Kochar SK, Kochar DK, Das A. Development and evaluation of a 28S rRNA gene-based nested PCR assay for P. falciparum and P. vivax. Pathog Glob Health 2014; 107:180-8. [PMID: 23816509 DOI: 10.1179/2047773213y.0000000090] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
The 28S rRNA gene was amplified and sequenced from P. falciparum and P. vivax isolates collected from northwest India. Based upon the sequence diversity of the Plasmodium 28SrRNA gene in comparison with its human counterpart, various nested polymerase chain reaction (PCR) primers were designed from the 3R region of the 28SrRNA gene and evaluated on field isolates. This is the first report demonstrating the utility of this gene for species-specific diagnosis of malaria for these two species, prevalent in India. The initial evaluation on 363 clinical isolates indicated that, in comparison with microscopy, which showed sensitivity and specificity of 85·39% and 100% respectively, the sensitivity and specificity of the nested PCR assay was found to be 99·08% and 100% respectively. This assay was also successful in detecting mixed infections that are undetected by microscopy. Our results demonstrate the utility of the 28S rRNA gene as a diagnostic target for the detection of the major plasmodial species infecting humans.
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Affiliation(s)
- Deepak Pakalapati
- Department of Biological Sciences, Birla Institute of Technology and Science, Pilani, Rajasthan, India
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Wampfler R, Mwingira F, Javati S, Robinson L, Betuela I, Siba P, Beck HP, Mueller I, Felger I. Strategies for detection of Plasmodium species gametocytes. PLoS One 2013; 8:e76316. [PMID: 24312682 PMCID: PMC3848260 DOI: 10.1371/journal.pone.0076316] [Citation(s) in RCA: 165] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2013] [Accepted: 08/23/2013] [Indexed: 11/26/2022] Open
Abstract
Carriage and density of gametocytes, the transmission stages of malaria parasites, are determined for predicting the infectiousness of humans to mosquitoes. This measure is used for evaluating interventions that aim at reducing malaria transmission. Gametocytes need to be detected by amplification of stage-specific transcripts, which requires RNA-preserving blood sampling. For simultaneous, highly sensitive quantification of both, blood stages and gametocytes, we have compared and optimized different strategies for field and laboratory procedures in a cross sectional survey in 315 5-9 yr old children from Papua New Guinea. qRT-PCR was performed for gametocyte markers pfs25 and pvs25, Plasmodium species prevalence was determined by targeting both, 18S rRNA genes and transcripts. RNA-based parasite detection resulted in a P. falciparum positivity of 24.1%; of these 40.8% carried gametocytes. P. vivax positivity was 38.4%, with 38.0% of these carrying gametocytes. Sensitivity of DNA-based parasite detection was substantially lower with 14.1% for P. falciparum and 19.6% for P. vivax. Using the lower DNA-based prevalence of asexual stages as a denominator increased the percentage of gametocyte-positive infections to 59.1% for P. falciparum and 52.4% for P. vivax. For studies requiring highly sensitive and simultaneous quantification of sexual and asexual parasite stages, 18S rRNA transcript-based detection saves efforts and costs. RNA-based positivity is considerably higher than other methods. On the other hand, DNA-based parasite quantification is robust and permits comparison with other globally generated molecular prevalence data. Molecular monitoring of low density asexual and sexual parasitaemia will support the evaluation of effects of up-scaled antimalarial intervention programs and can also inform about small scale spatial variability in transmission intensity.
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Affiliation(s)
- Rahel Wampfler
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Felistas Mwingira
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Sarah Javati
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
- Papua New Guinea Institute of Medical Research, Goroka, Papua New Guinea
| | - Leanne Robinson
- Papua New Guinea Institute of Medical Research, Goroka, Papua New Guinea
| | - Inoni Betuela
- Papua New Guinea Institute of Medical Research, Goroka, Papua New Guinea
| | - Peter Siba
- Papua New Guinea Institute of Medical Research, Goroka, Papua New Guinea
| | - Hans-Peter Beck
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Ivo Mueller
- Papua New Guinea Institute of Medical Research, Goroka, Papua New Guinea
- Infection and Immunity Division, Walter and Eliza Hall Institute, Parkville, Victoria, Australia
| | - Ingrid Felger
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
- * E-mail:
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Divergent nuclear 18S rDNA paralogs in a turkey coccidium, Eimeria meleagrimitis, complicate molecular systematics and identification. Int J Parasitol 2013; 43:679-85. [DOI: 10.1016/j.ijpara.2013.03.005] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2012] [Revised: 03/19/2013] [Accepted: 03/20/2013] [Indexed: 11/18/2022]
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Starkey LA, Panciera RJ, Paras K, Allen KE, Reiskind MH, Reichard MV, Johnson EM, Little SE. Genetic Diversity ofHepatozoonspp. in Coyotes from the South-Central United States. J Parasitol 2013; 99:375-8. [DOI: 10.1645/ge-3104.1] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Bernabeu M, Gomez-Perez GP, Sissoko S, Niambélé MB, Haibala AA, Sanz A, Théra MA, Fernandez-Becerra C, Traoré K, Alonso PL, Bassat Q, Del Portillo HA, Doumbo O. Plasmodium vivax malaria in Mali: a study from three different regions. Malar J 2012; 11:405. [PMID: 23217064 PMCID: PMC3547733 DOI: 10.1186/1475-2875-11-405] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2012] [Accepted: 11/30/2012] [Indexed: 12/03/2022] Open
Abstract
Background Plasmodium vivax has traditionally been considered virtually absent from Western and Central Africa, due to the absence of the Duffy blood group in most of the population living in these areas. Recent reports, however, suggest the circulation of P. vivax in sub-Saharan Africa. Methods Giemsa/Field-stained smears from febrile patients recruited in five different cities (Goundam, Tombouctou, Gao, Bourem and Kidal) pertaining to three regions from Northern Mali were examined. Nested-PCR and DNA sequence analyses of selected samples were performed to fully confirm the presence of P. vivax infections. Results Results demonstrated the presence of P. vivax infections in close to 30% of the cases as detected by Giemsa/Field-stained smears and nested-PCR and DNA-sequence analyses of selected samples unequivocally confirmed the presence of P. vivax. Conclusions The diagnostics of this human malaria parasite should be taken into account in the context of malaria control and elimination efforts, not only in Mali, but also in sub-Saharan Africa.
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Affiliation(s)
- Maria Bernabeu
- Barcelona Centre for International Health Research, Hospital Clínic-Universitat de Barcelona, Barcelona, Spain.
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Van Wormhoudt A, Gaume B, Le Bras Y, Roussel V, Huchette S. Two different and functional nuclear rDNA genes in the abalone Haliotis tuberculata: tissue differential expression. Genetica 2011; 139:1217-27. [PMID: 22210151 DOI: 10.1007/s10709-011-9623-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2011] [Accepted: 12/20/2011] [Indexed: 12/22/2022]
Abstract
Analysis of the 18S rDNA sequences of Haliotis tuberculata tuberculata and H. t. coccinea subtaxa identified two different types of 18S rDNA genes and ITS1 regions. These two different genes were also detected in H. marmorata, H. rugosa and H. diversicolor that are separated from H. tuberculata by 5-65 mya. The mean divergence value between type I and type II sequences ranged from 7.25% for 18S to 80% for ITS1. ITS1 type II is homologous with the ITS1 consensus sequences published for many abalone species, whereas ITS1 type I presented only minor homology with a unique database entry for H. iris ITS1. A phylogenetic analysis makes a clear separation between type I and type II ITS1 sequences and supports grouping H. t. tuberculata, H. t. coccinea and H. marmorata together. The two subtaxa do not show any significant differences between the homologous 18S rDNA sequences. A general structure of the ITS1 transcript was proposed, with four major helices for the two types. The two genes were expressed and, for the first time, a putative differential expression of ITS1 type I was detected in the gills, digestive gland and gonads whereas ITS1 type II was expressed in all tissues.
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Affiliation(s)
- Alain Van Wormhoudt
- CNRS UMR 7208, Station de Biologie Marine du Muséum National d'Histoire Naturelle, 29900 Concarneau, France.
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Applied genomics: data mining reveals species-specific malaria diagnostic targets more sensitive than 18S rRNA. J Clin Microbiol 2011; 49:2411-8. [PMID: 21525225 DOI: 10.1128/jcm.02603-10] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Accurate and rapid diagnosis of malaria infections is crucial for implementing species-appropriate treatment and saving lives. Molecular diagnostic tools are the most accurate and sensitive method of detecting Plasmodium, differentiating between Plasmodium species, and detecting subclinical infections. Despite available whole-genome sequence data for Plasmodium falciparum and P. vivax, the majority of PCR-based methods still rely on the 18S rRNA gene targets. Historically, this gene has served as the best target for diagnostic assays. However, it is limited in its ability to detect mixed infections in multiplex assay platforms without the use of nested PCR. New diagnostic targets are needed. Ideal targets will be species specific, highly sensitive, and amenable to both single-step and multiplex PCRs. We have mined the genomes of P. falciparum and P. vivax to identify species-specific, repetitive sequences that serve as new PCR targets for the detection of malaria. We show that these targets (Pvr47 and Pfr364) exist in 14 to 41 copies and are more sensitive than 18S rRNA when utilized in a single-step PCR. Parasites are routinely detected at levels of 1 to 10 parasites/μl. The reaction can be multiplexed to detect both species in a single reaction. We have examined 7 P. falciparum strains and 91 P. falciparum clinical isolates from Tanzania and 10 P. vivax strains and 96 P. vivax clinical isolates from Venezuela, and we have verified a sensitivity and specificity of ∼100% for both targets compared with a nested 18S rRNA approach. We show that bioinformatics approaches can be successfully applied to identify novel diagnostic targets and improve molecular methods for pathogen detection. These novel targets provide a powerful alternative molecular diagnostic method for the detection of P. falciparum and P. vivax in conventional or multiplex PCR platforms.
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Al-Mekhlafi AM, Mahdy MA, A Azazy A, Fong MY. Molecular epidemiology of Plasmodium species prevalent in Yemen based on 18 s rRNA. Parasit Vectors 2010; 3:110. [PMID: 21092097 PMCID: PMC2997089 DOI: 10.1186/1756-3305-3-110] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2010] [Accepted: 11/19/2010] [Indexed: 11/12/2022] Open
Abstract
Background Malaria is an endemic disease in Yemen and is responsible for 4.9 deaths per 100,000 population per year and 43,000 disability adjusted life years lost. Although malaria in Yemen is caused mainly by Plasmodium falciparum and Plasmodium vivax, there are no sequence data available on the two species. This study was conducted to investigate the distribution of the Plasmodium species based on the molecular detection and to study the molecular phylogeny of these parasites. Methods Blood samples from 511 febrile patients were collected and a partial region of the 18 s ribosomal RNA (18 s rRNA) gene was amplified using nested PCR. From the 86 positive blood samples, 13 Plasmodium falciparum and 4 Plasmodium vivax were selected and underwent cloning and, subsequently, sequencing and the sequences were subjected to phylogenetic analysis using the neighbor-joining and maximum parsimony methods. Results Malaria was detected by PCR in 86 samples (16.8%). The majority of the single infections were caused by P. falciparum (80.3%), followed by P. vivax (5.8%). Mixed infection rates of P. falciparum + P. vivax and P. falciparum + P. malariae were 11.6% and 2.3%, respectively. All P. falciparum isolates were grouped with the strain 3D7, while P. vivax isolates were grouped with the strain Salvador1. Phylogenetic trees based on 18 s rRNA placed the P. falciparum isolates into three sub-clusters and P. vivax into one cluster. Sequence alignment analysis showed 5-14.8% SNP in the partial sequences of the 18 s rRNA of P. falciparum. Conclusions Although P. falciparum is predominant, P. vivax, P. malariae and mixed infections are more prevalent than has been revealed by microscopy. This overlooked distribution should be considered by malaria control strategy makers. The genetic polymorphisms warrant further investigation.
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Affiliation(s)
- Abdulsalam Mq Al-Mekhlafi
- Department of Parasitology, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia.
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Hughes KR, Philip N, Lucas Starnes G, Taylor S, Waters AP. From cradle to grave: RNA biology in malaria parasites. WILEY INTERDISCIPLINARY REVIEWS-RNA 2010; 1:287-303. [DOI: 10.1002/wrna.30] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Katie R. Hughes
- Division of Infection and Immunity, Faculty of Biomedical Life Sciences, Glasgow Biomedical Research Centre, University of Glasgow, 120 University Place, Glasgow G12 8TA, Scotland, UK
- Wellcome Centre for Molecular Parasitology, Glasgow Biomedical Research Centre, University of Glasgow, 120 University Place, Glasgow G12 8TA, Scotland, UK
| | - Nisha Philip
- Division of Infection and Immunity, Faculty of Biomedical Life Sciences, Glasgow Biomedical Research Centre, University of Glasgow, 120 University Place, Glasgow G12 8TA, Scotland, UK
- Wellcome Centre for Molecular Parasitology, Glasgow Biomedical Research Centre, University of Glasgow, 120 University Place, Glasgow G12 8TA, Scotland, UK
| | - G. Lucas Starnes
- Division of Infection and Immunity, Faculty of Biomedical Life Sciences, Glasgow Biomedical Research Centre, University of Glasgow, 120 University Place, Glasgow G12 8TA, Scotland, UK
- Wellcome Centre for Molecular Parasitology, Glasgow Biomedical Research Centre, University of Glasgow, 120 University Place, Glasgow G12 8TA, Scotland, UK
| | - Sonya Taylor
- Division of Infection and Immunity, Faculty of Biomedical Life Sciences, Glasgow Biomedical Research Centre, University of Glasgow, 120 University Place, Glasgow G12 8TA, Scotland, UK
- Wellcome Centre for Molecular Parasitology, Glasgow Biomedical Research Centre, University of Glasgow, 120 University Place, Glasgow G12 8TA, Scotland, UK
| | - Andrew P. Waters
- Division of Infection and Immunity, Faculty of Biomedical Life Sciences, Glasgow Biomedical Research Centre, University of Glasgow, 120 University Place, Glasgow G12 8TA, Scotland, UK
- Wellcome Centre for Molecular Parasitology, Glasgow Biomedical Research Centre, University of Glasgow, 120 University Place, Glasgow G12 8TA, Scotland, UK
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Singh B, Simon Divis PC. Orangutans not infected with Plasmodium vivax or P. cynomolgi, Indonesia. Emerg Infect Dis 2010; 15:1657-8. [PMID: 19861067 PMCID: PMC2866404 DOI: 10.3201/eid1510.090364] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
After orangutans in Indonesia were reported as infected with Plasmodium cynomolgi and P. vivax, we conducted phylogenetic analyses of small subunit ribosomal RNA gene sequences of Plasmodium spp. We found that these orangutans are not hosts of P. cynomolgi and P. vivax. Analysis of >1 genes is needed to identify Plasmodium spp. infecting orangutans.
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Affiliation(s)
- Balbir Singh
- Malaria Research Centre, Universiti Malaysia Sarawak, Sarawak, Malaysia.
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Jacobs-Lorena VY, Mikolajczak SA, Labaied M, Vaughan AM, Kappe SHI. A dispensable Plasmodium locus for stable transgene expression. Mol Biochem Parasitol 2010; 171:40-4. [PMID: 20045029 DOI: 10.1016/j.molbiopara.2009.12.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2009] [Revised: 12/17/2009] [Accepted: 12/21/2009] [Indexed: 10/20/2022]
Abstract
The ribosomal small subunit locus has been used for transgene expression in the rodent malaria parasites, Plasmodium berghei and Plasmodium yoelii, but this strategy utilizes single crossover integration and is thus prone to reversion by plasmid excision. Targeting of the ribosomal subunit locus may also have a negative effect on oocyst development in the mosquito. In P. berghei, the p230 paralog locus has been used for transgene expression. Here, we show that the P. yoelii S1 locus (sporozoite expressed gene 1) (PY05712) is dispensable and can be used for stable transgene expression throughout the parasite life cycle. P. yoelii s1(-) parasites show no defect in blood stage replication, oocyst formation, sporozoite production, or liver stage development when compared to P. yoelii wildtype parasites. Further, we show that a fluorescent transgene can be stably expressed from this site. This demonstrates that the S1 locus can be utilized for stable expression of heterologous genes in rodent malaria parasites.
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Torres-Machorro AL, Hernández R, Cevallos AM, López-Villaseñor I. Ribosomal RNA genes in eukaryotic microorganisms: witnesses of phylogeny? FEMS Microbiol Rev 2010; 34:59-86. [DOI: 10.1111/j.1574-6976.2009.00196.x] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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40
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Steenkeste N, Incardona S, Chy S, Duval L, Ekala MT, Lim P, Hewitt S, Sochantha T, Socheat D, Rogier C, Mercereau-Puijalon O, Fandeur T, Ariey F. Towards high-throughput molecular detection of Plasmodium: new approaches and molecular markers. Malar J 2009; 8:86. [PMID: 19402894 PMCID: PMC2686730 DOI: 10.1186/1475-2875-8-86] [Citation(s) in RCA: 99] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2008] [Accepted: 04/29/2009] [Indexed: 11/15/2022] Open
Abstract
Background Several strategies are currently deployed in many countries in the tropics to strengthen malaria control toward malaria elimination. To measure the impact of any intervention, there is a need to detect malaria properly. Mostly, decisions still rely on microscopy diagnosis. But sensitive diagnosis tools enabling to deal with a large number of samples are needed. The molecular detection approach offers a much higher sensitivity, and the flexibility to be automated and upgraded. Methods Two new molecular methods were developed: dot18S, a Plasmodium-specific nested PCR based on the 18S rRNA gene followed by dot-blot detection of species by using species-specific probes and CYTB, a Plasmodium-specific nested PCR based on cytochrome b gene followed by species detection using SNP analysis. The results were compared to those obtained with microscopic examination and the "standard" 18S rRNA gene based nested PCR using species specific primers. 337 samples were diagnosed. Results Compared to the microscopy the three molecular methods were more sensitive, greatly increasing the estimated prevalence of Plasmodium infection, including P. malariae and P. ovale. A high rate of mixed infections was uncovered with about one third of the villagers infected with more than one malaria parasite species. Dot18S and CYTB sensitivity outranged the "standard" nested PCR method, CYTB being the most sensitive. As a consequence, compared to the "standard" nested PCR method for the detection of Plasmodium spp., the sensitivity of dot18S and CYTB was respectively 95.3% and 97.3%. Consistent detection of Plasmodium spp. by the three molecular methods was obtained for 83% of tested isolates. Contradictory results were mostly related to detection of Plasmodium malariae and Plasmodium ovale in mixed infections, due to an "all-or-none" detection effect at low-level parasitaemia. Conclusion A large reservoir of asymptomatic infections was uncovered using the molecular methods. Dot18S and CYTB, the new methods reported herein are highly sensitive, allow parasite DNA extraction as well as genus- and species-specific diagnosis of several hundreds of samples, and are amenable to high-throughput scaling up for larger sample sizes. Such methods provide novel information on malaria prevalence and epidemiology and are suited for active malaria detection. The usefulness of such sensitive malaria diagnosis tools, especially in low endemic areas where eradication plans are now on-going, is discussed in this paper.
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Affiliation(s)
- Nicolas Steenkeste
- Institut Pasteur du Cambodge, Laboratoire d'Epidémiologie Moléculaire, Phnom Penh, Cambodia.
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41
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Unidentified Plasmodium species in Australian black swans (Cygnus atratus) hatched and raised in North America. J Zoo Wildl Med 2008; 39:216-20. [PMID: 18634212 DOI: 10.1638/2007-0110r.1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
A pair of Australian black swans (Cygnus atratus) with origins in Wakefield, Virginia, USA, was admitted to the quarantine area at the Baltimore Zoo for general health assessments before housing in the collections. During the quarantine period, no clinical signs of disease were manifest; however, upon examination of a blood smear, intraerythrocytic parasites were detected and initially determined to be Haemoproteus species. Diagnostic polymerase chain reaction (PCR) and sequencing results, however, indicated that the parasites were within the genus Plasmodium. Subclinical infections with Plasmodium species in birds may affect collection management, and transmission from refractory hosts to susceptible hosts should be considered when multispecies exhibits are used. In addition, changes in the dynamics of host-vector-parasite interactions might have significant impacts on wild or domesticated populations of birds.
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42
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Sherman IW. References. ADVANCES IN PARASITOLOGY 2008. [DOI: 10.1016/s0065-308x(08)00430-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Chakrabarti K, Pearson M, Grate L, Sterne-Weiler T, Deans J, Donohue JP, Ares M. Structural RNAs of known and unknown function identified in malaria parasites by comparative genomics and RNA analysis. RNA (NEW YORK, N.Y.) 2007; 13:1923-39. [PMID: 17901154 PMCID: PMC2040097 DOI: 10.1261/rna.751807] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
As the genomes of more eukaryotic pathogens are sequenced, understanding how molecular differences between parasite and host might be exploited to provide new therapies has become a major focus. Central to cell function are RNA-containing complexes involved in gene expression, such as the ribosome, the spliceosome, snoRNAs, RNase P, and telomerase, among others. In this article we identify by comparative genomics and validate by RNA analysis numerous previously unknown structural RNAs encoded by the Plasmodium falciparum genome, including the telomerase RNA, U3, 31 snoRNAs, as well as previously predicted spliceosomal snRNAs, SRP RNA, MRP RNA, and RNAse P RNA. Furthermore, we identify six new RNA coding genes of unknown function. To investigate the relationships of the RNA coding genes to other genomic features in related parasites, we developed a genome browser for P. falciparum (http://areslab.ucsc.edu/cgi-bin/hgGateway). Additional experiments provide evidence supporting the prediction that snoRNAs guide methylation of a specific position on U4 snRNA, as well as predicting an snRNA promoter element particular to Plasmodium sp. These findings should allow detailed structural comparisons between the RNA components of the gene expression machinery of the parasite and its vertebrate hosts.
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Affiliation(s)
- Kausik Chakrabarti
- Department of Molecular, Cell and Developmental Biology, Center for Molecular Biology of RNA, University of California at Santa Cruz, Santa Cruz, CA 95064, USA
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de Oliveira Lima AN, da Silva Santos S, Herrera HM, Gama C, Cupolillo E, Jansen AM, Fernandes O. Trypanosoma evansi: molecular homogeneity as inferred by phenetical analysis of ribosomal internal transcribed spacers DNA of an eclectic parasite. Exp Parasitol 2007; 118:402-7. [PMID: 18158150 DOI: 10.1016/j.exppara.2007.10.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2007] [Revised: 09/26/2007] [Accepted: 10/02/2007] [Indexed: 11/27/2022]
Abstract
The protozoan Trypanosoma evansi is described as presenting high morphological and genetic similarities among the isolates despite its biological heterogeneity and wide geographical distribution. PCR amplification of the internal transcribed spacers of the ribosomal gene in combination with the coding region of the 5.8S ribosomal subunit further submitted to restriction enzymes digestion were carried out in DNAs extracted from 41 T. evansi strains isolated from horses, dogs, coatis and capybaras from two distinct regions of the Brazilian Pantanal. We also used one T. evansi isolate from Africa, one from Asia and one isolate of T. b. brucei from Africa. Analysis of the RFLP profiles yielded a unique "riboprinting" that does not vary intraspecifically. These results provide insights on the ribosomal gene organization of T. evansi and showed that ITS analysis by RFLP show high genetic similarity of this locus among isolates of this protozoan parasite.
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Affiliation(s)
- Aneska Norek de Oliveira Lima
- Laboratory of Tripanosomatid Biology, Oswaldo Cruz Institute, FIOCRUZ, Av. Brasil 4365, CEP. 21040-360, Rio de Janeiro/RJ, Brazil
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Caraguel CGB, O'Kelly CJ, Legendre P, Frasca S, Gast RJ, Després BM, Cawthorn RJ, Greenwood SJ. Microheterogeneity and Coevolution: An Examination of rDNA Sequence Characteristics in Neoparamoeba pemaquidensis and Its Prokinetoplastid Endosymbiont. J Eukaryot Microbiol 2007; 54:418-26. [PMID: 17910686 DOI: 10.1111/j.1550-7408.2007.00281.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Neoparamoeba pemaquidensis, the etiological agent of amoebic gill disease, has shown surprising sequence variability among different copies of the 18S ribosomal RNA gene within an isolate. This intra-genomic microheterogeneity was confirmed and extended to an analysis of the internal transcribed spacer (ITS) region. High levels of intra-genomic nucleotide diversity (Pi=0.0201-0.0313) were found among sequenced ITS regions from individual host amoeba isolates. In contrast, the ITS region of its endosymbiont revealed significantly lower levels of intra-genomic nucleotide diversity (Pi=0.0028-0.0056) compared with the host N. pemaquidensis. Phylogenetic and ParaFit coevolution analyses involving N. pemaquidensis isolates and their respective endosymbionts confirmed a significant coevolutionary relationship between the two protists. The observation of non-shared microheterogeneity and coevolution emphasizes the complexity of the interactions between N. pemaquidensis and its obligate endosymbiont.
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Affiliation(s)
- Charles G B Caraguel
- AVC Lobster Science Centre, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, Prince Edward Island, C1A 4P3, Canada
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Abstract
Until around 1990, most multigene families were thought to be subject to concerted evolution, in which all member genes of a family evolve as a unit in concert. However, phylogenetic analysis of MHC and other immune system genes showed a quite different evolutionary pattern, and a new model called birth-and-death evolution was proposed. In this model, new genes are created by gene duplication and some duplicate genes stay in the genome for a long time, whereas others are inactivated or deleted from the genome. Later investigations have shown that most non-rRNA genes including highly conserved histone or ubiquitin genes are subject to this type of evolution. However, the controversy over the two models is still continuing because the distinction between the two models becomes difficult when sequence differences are small. Unlike concerted evolution, the model of birth-and-death evolution can give some insights into the origins of new genetic systems or new phenotypic characters.
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Affiliation(s)
- Masatoshi Nei
- Institute of Molecular Evolutionary Genetics and1 Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802;
| | - Alejandro P. Rooney
- U.S. Department of Agriculture, Agricultural Research Service, National Center for Agricultural Utilization Research, Peoria, Illinois 61604;
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Leclerc MC, Hugot JP, Durand P, Renaud F. Evolutionary relationships between 15 Plasmodium species from new and old world primates (including humans): an 18S rDNA cladistic analysis. Parasitology 2005; 129:677-84. [PMID: 15648690 DOI: 10.1017/s0031182004006146] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
We present a new phylogenetic analysis of 15 primate Plasmodium species based on 18S rDNA sequences including new sequences of Plasmodium coatneyi, P. fieldi, P. gonderi, P. hylobati and P. simium. The results are discussed in the context of the parasite host species and their geographical distribution. Contrary to other phylogenies constructed with this 18S rDNA molecule, we observed that the topology of phylogenetic trees was not affected either by the quality of the nucleotide matrices, or by the species present in the outgroup. This analysis showed the following. (1) The polyphyly of human Plasmodium is confirmed. (2) The monophyly of Plasmodium from Old World monkeys is confirmed by the new added sequences and P. gonderi, an African species, possibly could be at the root of this group. (3) The most parsimonious biogeographical hypothesis is that P. vivax originated in Asia; thus, its related species P. simium appears to be derived through a transfer from the human P. vivax to New World monkey species in South America. (4) Sampling efforts of non-human primate Plasmodium could permit improvement of the knowledge of primate Plasmodium phylogeny and also consideration of the risks of malaria emergence from monkey reservoirs.
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Affiliation(s)
- M C Leclerc
- Génétique et Evolution des Maladies Infectieuses, UMR CNRS/IRD 2724, IRD, Equipe 'Evolution des Systèmes Symbiotiques', 34394 Montpellier cedex 5, France.
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48
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Schaap D, Arts G, van Poppel NFJ, Vermeulen AN. De novo ribosome biosynthesis is transcriptionally regulated in Eimeria tenella, dependent on its life cycle stage. Mol Biochem Parasitol 2005; 139:239-48. [PMID: 15664658 DOI: 10.1016/j.molbiopara.2004.11.011] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2004] [Revised: 10/30/2004] [Accepted: 11/06/2004] [Indexed: 10/26/2022]
Abstract
Protozoan parasites go through various developmental stages during their parasitic life, which requires the expression of different genes. To identify stage specific gene products in Eimeria tenella, a differential screening was performed comparing the intracellular schizont stage with the extracellular oocyst stage. De novo transcripts of 18S-5.8S-26S rRNA transcription units and of two ribosomal proteins (RPL5 and RPL23) were specifically identified in schizonts and were undetectable in oocysts. The stage specific transcription of pre-rRNAs (prior to processing) was confirmed with Northern blot analysis. Since the E. tenella genome contains a repeated gene cluster with an estimated 140 large rRNA transcription units, they all might be similarly regulated. Specific expression of RPL5 and RPL23 in E. tenella schizonts was also confirmed by Northern blotting. Furthermore, an analysis of the E. tenella EST database with 26,705 ESTs showed that 9.5% of all merozoite ESTs and only 0.2% of the sporozoite ESTs encoded ribosomal proteins (RPs). These ESTs encoded 69 different RPs, suggesting that most and possibly all RPs are differentially transcribed in E. tenella. Analysis of EST data from other Coccidia, such as Toxoplasma gondii, indicated a similar stage dependent transcription of RP genes. We conclude that ribosome biosynthesis is transcriptionally regulated in E. tenella and other Coccidia, such that rapidly growing parasite stages utilize much of their resources to de novo biosynthesis of ribosomes, and that "dormant" oocyst stages do not synthesize new ribosomes. The 50- to 100-fold reduction in transcription of RPs together with the reduced rRNA transcription prevents that unnecessary new ribosomes are synthesized in oocysts.
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Affiliation(s)
- Dick Schaap
- Department of Parasitology, Intervet International BV, P.O. Box 31, 5830AA Boxmeer, The Netherlands.
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49
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Le Roch KG, Johnson JR, Florens L, Zhou Y, Santrosyan A, Grainger M, Yan SF, Williamson KC, Holder AA, Carucci DJ, Yates JR, Winzeler EA. Global analysis of transcript and protein levels across the Plasmodium falciparum life cycle. Genome Res 2005; 14:2308-18. [PMID: 15520293 PMCID: PMC525690 DOI: 10.1101/gr.2523904] [Citation(s) in RCA: 336] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
To investigate the role of post-transcriptional controls in the regulation of protein expression for the malaria parasite, Plasmodium falciparum, we have compared mRNA transcript and protein abundance levels for seven different stages of the parasite life cycle. A moderately high positive relationship between mRNA and protein abundance was observed for these stages; the most common discrepancy was a delay between mRNA and protein accumulation. Potentially post-transcriptionally regulated genes are identified, and families of functionally related genes were observed to share similar patterns of mRNA and protein accumulation.
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Affiliation(s)
- Karine G Le Roch
- Department of Cell Biology ICND202, the Scripps Research Institute, La Jolla, California 92037, USA
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McCutchan TF, Rathore D, Li J. Compensatory evolution in the human malaria parasite Plasmodium ovale. Genetics 2004; 166:637-40. [PMID: 15020451 PMCID: PMC1470707 DOI: 10.1534/genetics.166.1.637] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The fixation of neutral compensatory mutations in a population depends on the effective population size of the species, which can fluctuate dramatically within a few generations, the mutation rate, and the selection intensity associated with the individual mutations. We observe compensatory mutations and intermediate states in populations of the malaria parasite Plasmodium ovale. The appearance of compensatory mutations and intermediate states in P. ovale raises interesting questions about population structure that could have considerable impact on the control of the associated disease.
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Affiliation(s)
- Thomas F McCutchan
- Growth and Development Section, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892-0425, USA.
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