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Zhang H, Ehrenkaufer GM, Hall N, Singh U. Small RNA pyrosequencing in the protozoan parasite Entamoeba histolytica reveals strain-specific small RNAs that target virulence genes. BMC Genomics 2013; 14:53. [PMID: 23347563 PMCID: PMC3610107 DOI: 10.1186/1471-2164-14-53] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2012] [Accepted: 01/02/2013] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Small RNA mediated gene silencing is a well-conserved regulatory pathway. In the parasite Entamoeba histolytica an endogenous RNAi pathway exists, however, the depth and diversity of the small RNA population remains unknown. RESULTS To characterize the small RNA population that associates with E. histolytica Argonaute-2 (EhAGO2-2), we immunoprecipitated small RNAs that associate with it and performed one full pyrosequencing run. Data analysis revealed new features of the 27nt small RNAs including the 5'-G predominance, distinct small RNA distribution patterns on protein coding genes, small RNAs mapping to both introns and exon-exon junctions, and small RNA targeted genes that are clustered particularly in sections of genome duplication. Characterization of genomic loci to which both sense and antisense small RNAs mapped showed that both sets of small RNAs have 5'-polyphosphate termini; strand-specific RT-PCR detected transcripts in both directions at these loci suggesting that both transcripts may serve as template for small RNA generation. In order to determine whether small RNA abundance patterns account for strain-specific gene expression profiles of E. histolytica virulent and non-virulent strains, we sequenced small RNAs from a non-virulent strain and found that small RNAs mapped to genes in a manner consistent with their regulation of strain-specific virulence genes. CONCLUSIONS We provided a full spectrum analysis for E. histolytica AGO2-2 associated 27nt small RNAs. Additionally, comparative analysis of small RNA populations from virulent and non-virulent amebic strains indicates that small RNA populations may regulate virulence genes.
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Affiliation(s)
- Hanbang Zhang
- Division of Infectious Diseases, Department of Internal Medicine, Stanford University School of Medicine, Stanford, California 94305-5107, USA
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102
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Gargantini PR, Serradell MC, Torri A, Lujan HD. Putative SF2 helicases of the early-branching eukaryote Giardia lamblia are involved in antigenic variation and parasite differentiation into cysts. BMC Microbiol 2012. [PMID: 23190735 PMCID: PMC3566956 DOI: 10.1186/1471-2180-12-284] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Background Regulation of surface antigenic variation in Giardia lamblia is controlled post-transcriptionally by an RNA-interference (RNAi) pathway that includes a Dicer-like bidentate RNase III (gDicer). This enzyme, however, lacks the RNA helicase domain present in Dicer enzymes from higher eukaryotes. The participation of several RNA helicases in practically all organisms in which RNAi was studied suggests that RNA helicases are potentially involved in antigenic variation, as well as during Giardia differentiation into cysts. Results An extensive in silico analysis of the Giardia genome identified 32 putative Super Family 2 RNA helicases that contain almost all the conserved RNA helicase motifs. Phylogenetic studies and sequence analysis separated them into 22 DEAD-box, 6 DEAH-box and 4 Ski2p-box RNA helicases, some of which are homologs of well-characterized helicases from higher organisms. No Giardia putative helicase was found to have significant homology to the RNA helicase domain of Dicer enzymes. Additionally a series of up- and down-regulated putative RNA helicases were found during encystation and antigenic variation by qPCR experiments. Finally, we were able to recognize 14 additional putative helicases from three different families (RecQ family, Swi2/Snf2 and Rad3 family) that could be considered DNA helicases. Conclusions This is the first comprehensive analysis of the Super Family 2 helicases from the human intestinal parasite G. lamblia. The relative and variable expression of particular RNA helicases during both antigenic variation and encystation agrees with the proposed participation of these enzymes during both adaptive processes. The putatives RNA and DNA helicases identified in this early-branching eukaryote provide initial information regarding the biological role of these enzymes in cell adaptation and differentiation.
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Affiliation(s)
- Pablo R Gargantini
- Laboratory of Biochemistry and Molecular Biology, School of Medicine, Catholic University of Córdoba, Córdoba X5004ASK, Argentina.
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103
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Unusual chromatin structure associated with monoparalogous transcription of the Babesia bovis ves multigene family. Int J Parasitol 2012. [PMID: 23178996 DOI: 10.1016/j.ijpara.2012.10.018] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Rapid antigenic variation in Babesia bovis involves the variant erythrocyte surface antigen-1 (VESA1), a heterodimeric protein with subunits encoded by two branches of the ves multigene family. The ves1α and ves1β gene pair encoding VESA1a and 1b, respectively, are transcribed in a monoparalogous manner from a single locus of active ves transcription (LAT), just one of many quasi-palindromic ves loci. To determine whether this organization plays a role in transcriptional regulation, chromatin structure was first assessed. Limited treatment of isolated nuclei with micrococcal nuclease to assay nucleosomal patterning revealed a periodicity of 156-159 bp in both bulk chromatin and specific gene coding regions. This pattern also was maintained in the intergenic regions (IGr) of non-transcribed ves genes. In contrast, the LAT IGr adopts a unique pattern, yielding an apparent cluster of five closely-spaced hypersensitive sites flanked by regions of reduced nucleosomal occupancy. ves loci fall into three patterns of overall sensitivity to micrococcal nuclease or DNase I digestion, with only the LAT being consistently very sensitive. Non-transcribed ves genes are inconsistent in their sensitivity to the two enzymatic probes. Non-linear DNA structure in chromatin was investigated to determine whether unique structure arising as a result of the quasi-palindromic nature of the LAT may effect transcriptional control. The in vitro capacity of ves IGr sequences to adopt stable higher-order DNA structure is demonstrated here, but the presence of such structure in vivo was not supported. Based upon these results a working model is proposed for the chromatin structural remodeling responsible for the sequential expression of ves multigene family members from divergently-organized loci.
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104
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Li W, Saraiya AA, Wang CC. The profile of snoRNA-derived microRNAs that regulate expression of variant surface proteins in Giardia lamblia. Cell Microbiol 2012; 14:1455-73. [PMID: 22568619 PMCID: PMC3422372 DOI: 10.1111/j.1462-5822.2012.01811.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2012] [Accepted: 04/27/2012] [Indexed: 12/21/2022]
Abstract
In the current investigation, we analysed all the known small nucleolar RNAs (snoRNAs) in the deeply branching protozoan parasite Giardia lamblia for potential microRNAs (miRNAs) that might be derived from them. Two putative miRNAs have since been identified by Northern blot, primer extension, 3' RACE and co-immunoprecipitation with Giardia Argonaute (GlAgo), and designated miR6 and miR10. Giardia Dicer (GlDcr) is capable of processing the snoRNAs into the corresponding miRNAs in vitro. Potential miR6 and miR10 binding sites in Giardia genome were predicted bio-informatically. A miR6 binding site was found at the 3' untranslated regions (UTR) of 44 variant surface protein (vsp) genes, whereas a miR10 binding site was identified at the 3' end of 159 vsp open-reading frames. Thirty-three of these vsp genes turned out to contain binding sites for both miR6 and miR10. A reporter mRNA tagged with the 3' end of vsp1267, which contains the target sites for both miRNAs, was translationally repressed by both miRNAs in Giardia. Episomal expression of an N-terminal c-myc tagged VSP1267 was found significantly repressed by introducing either miR6 or miR10 into the cells and the repressive effects were additive. When the 2'-O-methyl antisense oligos (ASOs) of either miR6 or miR10 was introduced, however, there was an enhancement of tagged VSP1267 expression suggesting an inhibition of the repressive effects of endogenous miR6 or miR10 by the ASOs. Of the total 220 vsp genes in Giardia, we have now found 178 of them carrying putative binding sites for all the miRNAs that have been currently identified, suggesting that miRNAs are likely the regulators of VSP expression in Giardia.
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Affiliation(s)
- Wei Li
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158-2280
| | - Ashesh A. Saraiya
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158-2280
| | - Ching C. Wang
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158-2280
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105
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Religa AA, Waters AP. Sirtuins of parasitic protozoa: in search of function(s). Mol Biochem Parasitol 2012; 185:71-88. [PMID: 22906508 PMCID: PMC3484402 DOI: 10.1016/j.molbiopara.2012.08.003] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2012] [Revised: 08/01/2012] [Accepted: 08/02/2012] [Indexed: 01/09/2023]
Abstract
The SIR2 family of NAD+-dependent protein deacetylases, collectively called sirtuins, has been of central interest due to their proposed roles in life-span regulation and ageing. Sirtuins are one group of environment sensors of a cell interpreting external information and orchestrating internal responses at the sub-cellular level, through participation in gene regulation mechanisms. Remarkably conserved across all kingdoms of life SIR2 proteins in several protozoan parasites appear to have both conserved and intriguing unique functions. This review summarises our current knowledge of the members of the sirtuin families in Apicomplexa, including Plasmodium, and other protozoan parasites such as Trypanosoma and Leishmania. The wide diversity of processes regulated by SIR2 proteins makes them targets worthy of exploitation in anti-parasitic therapies.
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Affiliation(s)
- Agnieszka A Religa
- Wellcome Trust Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow G12 8TA, UK.
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106
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Abstract
The recent discovery of microRNAs (miRNAs) in unicellular eukaryotes, including miRNAs known previously only from animals or plants, implies that miRNAs have a deep evolutionary history among eukaryotes. This contrasts with the prevailing view that miRNAs evolved convergently in animals and plants. We re-evaluate the evidence and find that none of the 73 plant and animal miRNAs described from protists meet the required criteria for miRNA annotation and, by implication, animals and plants did not acquire any of their respective miRNA genes from the crown ancestor of eukaryotes. Furthermore, of the 159 novel miRNAs previously identified among the seven species of unicellular protists examined, only 28 from the algae Ectocarpus and Chlamydomonas, meet the criteria for miRNA annotation. Therefore, at present only five groups of eukaryotes are known to possess miRNAs, indicating that miRNAs have evolved independently within eukaryotes through exaptation of their shared inherited RNAi machinery.
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Affiliation(s)
- James E Tarver
- School of Earth Sciences, University of Bristol, Bristol, UK.
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107
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Ma E, Zhou K, Kidwell MA, Doudna JA. Coordinated activities of human dicer domains in regulatory RNA processing. J Mol Biol 2012; 422:466-76. [PMID: 22727743 DOI: 10.1016/j.jmb.2012.06.009] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2012] [Revised: 05/31/2012] [Accepted: 06/01/2012] [Indexed: 12/22/2022]
Abstract
The conserved ribonuclease Dicer generates microRNAs and short-interfering RNAs that guide gene silencing in eukaryotes. The specific contributions of human Dicer's structural domains to RNA product length and substrate preference are incompletely understood, due in part to the difficulties of Dicer purification. Here, we show that active forms of human Dicer can be assembled from recombinant polypeptides expressed in bacteria. Using this system, we find that three distinct modes of RNA recognition give rise to Dicer's fidelity and product length specificity. The first involves anchoring one end of a double-stranded RNA helix within the PAZ domain, which can assemble in trans with Dicer's catalytic domains to reconstitute an accurate but non-substrate-selective dicing activity. The second entails nonspecific RNA binding by the double-stranded RNA binding domain, an interaction that is essential for substrate recruitment in the absence of the PAZ domain. The third mode of recognition involves hairpin RNA loop recognition by the helicase domain, which ensures efficient processing of specific substrates. These results reveal distinct interactions of each Dicer domain with different RNA structural features and provide a facile system for investigating the molecular mechanisms of human microRNA biogenesis.
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Affiliation(s)
- Enbo Ma
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
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108
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Immunity to protozoan parasites. J Parasitol Res 2012; 2012:250793. [PMID: 22619699 PMCID: PMC3352617 DOI: 10.1155/2012/250793] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2012] [Accepted: 01/09/2012] [Indexed: 11/29/2022] Open
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109
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Ma’ayeh SY, Brook-Carter PT. Representational difference analysis identifies specific genes in the interaction of Giardia duodenalis with the murine intestinal epithelial cell line, IEC-6. Int J Parasitol 2012; 42:501-9. [DOI: 10.1016/j.ijpara.2012.04.004] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2012] [Revised: 03/30/2012] [Accepted: 04/02/2012] [Indexed: 10/28/2022]
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110
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Live imaging of mitosomes and hydrogenosomes by HaloTag technology. PLoS One 2012; 7:e36314. [PMID: 22558433 PMCID: PMC3338651 DOI: 10.1371/journal.pone.0036314] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2012] [Accepted: 04/02/2012] [Indexed: 12/27/2022] Open
Abstract
Hydrogenosomes and mitosomes represent remarkable mitochondrial adaptations in the anaerobic parasitic protists such as Trichomonas vaginalis and Giardia intestinalis, respectively. In order to provide a tool to study these organelles in the live cells, the HaloTag was fused to G. intestinalis IscU and T. vaginalis frataxin and expressed in the mitosomes and hydrogenosomes, respectively. The incubation of the parasites with the fluorescent Halo-ligand resulted in highly specific organellar labeling, allowing live imaging of the organelles. With the array of available ligands the HaloTag technology offers a new tool to study the dynamics of mitochondria-related compartments as well as other cellular components in these intriguing unicellular eukaryotes.
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111
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Hirt RP, de Miguel N, Nakjang S, Dessi D, Liu YC, Diaz N, Rappelli P, Acosta-Serrano A, Fiori PL, Mottram JC. Trichomonas vaginalis pathobiology new insights from the genome sequence. ADVANCES IN PARASITOLOGY 2012; 77:87-140. [PMID: 22137583 DOI: 10.1016/b978-0-12-391429-3.00006-x] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The draft genome of the common sexually transmitted pathogen Trichomonas vaginalis encodes one of the largest known proteome with 60,000 candidate proteins. This provides parasitologists and molecular cell biologists alike with exciting, yet challenging, opportunities to unravel the molecular features of the parasite's cellular systems and potentially the molecular basis of its pathobiology. Here, recent investigations addressing selected aspects of the parasite's molecular cell biology are discussed, including surface and secreted virulent factors, membrane trafficking, cell signalling, the degradome, and the potential role of RNA interference in the regulation of gene expression.
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Affiliation(s)
- Robert P Hirt
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, UK
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112
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Characterization of the unusual bidirectional ves promoters driving VESA1 expression and associated with antigenic variation in Babesia bovis. EUKARYOTIC CELL 2012; 11:260-9. [PMID: 22286091 DOI: 10.1128/ec.05318-11] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Rapid clonal antigenic variation in Babesia bovis involves the variant erythrocyte surface antigen-1 (VESA1) protein expressed on the infected-erythrocyte surface. Because of the significance of this heterodimeric protein for demonstrated mechanisms of parasite survival and virulence, there is a need to understand how expression of the ves multigene family encoding this protein is controlled. As an initial step toward this goal, we present here initial characterization of the ves promoter driving transcription of VESA1a and -1b subunits. A series of transfection constructs containing various sequence elements from the in vivo locus of active ves transcription (LAT) were used to drive expression of the firefly luciferase gene in a dual luciferase-normalized assay. The results of this approach reveal the presence of two bidirectional promoter activities within the 434-bp intergenic region (IGr), influenced by putative regulatory sequences embedded within the flanking ves1α and ves1β genes. Repressor-like effects on the apposing gene were observed for intron 1 of both ves1α and ves1β. This effect is apparently not dependent upon intronic promoter activity and acts only in cis. The expression of genes within the ves family is likely modulated by local elements embedded within ves coding sequences outside the intergenic promoter region in concert with chromatin modifications. These results provide a framework to help us begin to understand gene regulation during antigenic variation in B. bovis.
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113
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Müller A, Klöppel C, Smith-Valentine M, Van Houten J, Simon M. Selective and programmed cleavage of GPI-anchored proteins from the surface membrane by phospholipase C. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2012; 1818:117-24. [DOI: 10.1016/j.bbamem.2011.10.009] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2011] [Revised: 10/06/2011] [Accepted: 10/07/2011] [Indexed: 01/22/2023]
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114
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Giardiasis: a review on assemblage distribution and epidemiology in India. Indian J Gastroenterol 2012; 31:3-12. [PMID: 22311296 DOI: 10.1007/s12664-012-0161-9] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/09/2011] [Accepted: 01/07/2012] [Indexed: 02/04/2023]
Abstract
Giardiasis is a significant cause of diarrheal disease and associated morbidity in children and adults worldwide. In addition to diarrhea, it can also lead to malnutrition and cognitive deficits in children from developing countries. Giardia duodenalis is considered to be a species complex of several assemblages, of which assemblage A and B are predominantly associated with human infections. Assemblage type has been associated with risk of occurrence of symptoms and duration of illness. Hence genotyping of giardial isolates may help understand better the epidemiology and transmission ecology of the disease in a particular setting or area. In India, prevalence rates of Giardia infection in patients with diarrhea range from 0.4% to 70%, and asymptomatic cyst passage has been found to be as high as 50% in rural southern India. In this review, the global distribution of giardial assemblage, zoonotic transmission and the association of assemblage with disease have been discussed, followed by epidemiology of giardiasis in India.
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115
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Abstract
Parasitic diseases cause important losses in public and veterinary health worldwide. Novel drugs, more reliable diagnostic techniques and vaccine candidates are urgently needed. Due to the complexity of parasites and the intricate relationship with their hosts, development of successful tools to fight parasites has been very limited to date. The growing information on individual parasite genomes is now allowing the use of a broader range of potential strategies to gain deeper insights into the host-parasite relationship and has increased the possibilities to develop molecular-based tools in the field of parasitology. Nevertheless, functional studies of respective genes are still scarce. The RNA interference phenomenon resulting in the regulation of protein expression through the specific degradation of defined mRNAs, and more specifically the possibility of artificially induce it, has shown to be a powerful tool for the investigation of proteins function in many organisms. Recent advances in the design and delivery of targeting molecules allow efficient and highly specific gene silencing in different types of parasites, pointing out this technology as a powerful tool for the identification of novel vaccine candidates or drug targets at the high-throughput level in the near future, and could enable researchers to functionally annotate parasite genomes. The aim of this review is to provide a comprehensive overview on the current advances and pitfalls in gene silencing mechanisms, techniques, applications and prospects in animal parasites.
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116
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Collins LJ. Characterizing ncRNAs in Human Pathogenic Protists Using High-Throughput Sequencing Technology. Front Genet 2011; 2:96. [PMID: 22303390 PMCID: PMC3268645 DOI: 10.3389/fgene.2011.00096] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2011] [Accepted: 12/07/2011] [Indexed: 11/16/2022] Open
Abstract
ncRNAs are key genes in many human diseases including cancer and viral infection, as well as providing critical functions in pathogenic organisms such as fungi, bacteria, viruses, and protists. Until now the identification and characterization of ncRNAs associated with disease has been slow or inaccurate requiring many years of testing to understand complicated RNA and protein gene relationships. High-throughput sequencing now offers the opportunity to characterize miRNAs, siRNAs, small nucleolar RNAs (snoRNAs), and long ncRNAs on a genomic scale, making it faster and easier to clarify how these ncRNAs contribute to the disease state. However, this technology is still relatively new, and ncRNA discovery is not an application of high priority for streamlined bioinformatics. Here we summarize background concepts and practical approaches for ncRNA analysis using high-throughput sequencing, and how it relates to understanding human disease. As a case study, we focus on the parasitic protists Giardia lamblia and Trichomonas vaginalis, where large evolutionary distance has meant difficulties in comparing ncRNAs with those from model eukaryotes. A combination of biological, computational, and sequencing approaches has enabled easier classification of ncRNA classes such as snoRNAs, but has also aided the identification of novel classes. It is hoped that a higher level of understanding of ncRNA expression and interaction may aid in the development of less harsh treatment for protist-based diseases.
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Affiliation(s)
- Lesley Joan Collins
- Institute of Fundamental Sciences, Massey University Palmerston North, New Zealand
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117
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Saraiya AA, Li W, Wang CC. A microRNA derived from an apparent canonical biogenesis pathway regulates variant surface protein gene expression in Giardia lamblia. RNA (NEW YORK, N.Y.) 2011; 17:2152-64. [PMID: 22033329 PMCID: PMC3222128 DOI: 10.1261/rna.028118.111] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2011] [Accepted: 09/13/2011] [Indexed: 05/19/2023]
Abstract
We have previously shown that a snoRNA-derived microRNA, miR2, in Giardia lamblia potentially regulates the expression of 22 variant surface protein (VSP) genes. Here, we identified another miRNA, miR4, also capable of regulating the expression of several VSPs but derived from an unannotated open reading frame (ORF) rather than a snoRNA, suggesting a canonical miRNA biogenesis pathway in Giardia. miR4 represses expression of a reporter containing two miR4 antisense sequences at the 3' UTR without causing a corresponding decrease in the mRNA level. This repression requires the presence of the Giardia Argonaute protein (GlAgo) and is reversed by 2' O-methylated antisense oligo to miR4, suggesting an RNA-induced silencing complex (RISC)-mediated mechanism. Furthermore, in vivo and in vitro evidence suggested that the Giardia Dicer protein (GlDcr) is required for miR4 biogenesis. Coimmunoprecipitation of miR4 with GlAgo further verified miR4 as a miRNA. A total of 361 potential target sites for miR4 were bioinformatically identified in Giardia, out of which 69 (32.7%) were associated with VSP genes. miR4 reduces the expression of a reporter containing two copies of the target site from VSP (GL50803_36493) at the 3' UTR. Sixteen of the 69 VSP genes were further found to contain partially overlapping miR2 and miR4 targeting sites. Expression of a reporter carrying the two overlapping sites was inhibited by either miR2 or miR4, but the inhibition was neither synergistic nor additive, suggesting a complex mechanism of miRNA regulation of VSP expression and the presence of a rich miRNAome in Giardia.
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Affiliation(s)
- Ashesh A. Saraiya
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California 94158-2280, USA
| | - Wei Li
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California 94158-2280, USA
| | - Ching C. Wang
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California 94158-2280, USA
- Corresponding author.E-mail .
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118
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Williams CW, Elmendorf HG. Identification and analysis of the RNA degrading complexes and machinery of Giardia lamblia using an in silico approach. BMC Genomics 2011; 12:586. [PMID: 22126454 PMCID: PMC3282835 DOI: 10.1186/1471-2164-12-586] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2011] [Accepted: 11/29/2011] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND RNA degradation is critical to the survival of all cells. With increasing evidence for pervasive transcription in cells, RNA degradation has gained recognition as a means of regulating gene expression. Yet, RNA degradation machinery has been studied extensively in only a few eukaryotic organisms, including Saccharomyces cerevisiae and humans. Giardia lamblia is a parasitic protist with unusual genomic traits: it is binucleated and tetraploid, has a very compact genome, displays a theme of genomic minimalism with cellular machinery commonly comprised of a reduced number of protein components, and has a remarkably large population of long, stable, noncoding, antisense RNAs. RESULTS Here we use in silico approaches to investigate the major RNA degradation machinery in Giardia lamblia and compare it to a broad array of other parasitic protists. We have found key constituents of the deadenylation and decapping machinery and of the 5'-3' RNA degradation pathway. We have similarly found that all of the major 3'-5' RNA degradation pathways are present in Giardia, including both exosome-dependent and exosome-independent machinery. However, we observe significant loss of RNA degradation machinery genes that will result in important differences in the protein composition, and potentially functionality, of the various RNA degradation pathways. This is most apparent in the exosome, the central mediator of 3'-5' degradation, which apparently contains an altered core configuration in both Giardia and Plasmodium, with only four, instead of the canonical six, distinct subunits. Additionally the exosome in Giardia is missing both the Rrp6, Nab3, and Nrd1 proteins, known to be key regulators of noncoding transcript stability in other cells. CONCLUSIONS These findings suggest that although the full complement of the major RNA degradation mechanisms were present - and likely functional - early in eukaryotic evolution, the composition and function of the complexes is more variable than previously appreciated. We suggest that the missing components of the exosome complex provide an explanation for the stable abundance of sterile RNA species in Giardia.
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Affiliation(s)
| | - Heidi G Elmendorf
- Department of Biology, Georgetown University, Washington, DC 20057, USA
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119
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Okamura K. Diversity of animal small RNA pathways and their biological utility. WILEY INTERDISCIPLINARY REVIEWS-RNA 2011; 3:351-68. [PMID: 22086843 DOI: 10.1002/wrna.113] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Higher eukaryotes employ extensive post-transcriptional gene regulation to accomplish fine control of gene expression. The microRNA (miRNA) family plays important roles in the post-transcriptional gene regulation of broad networks of target mRNA expression. Most miRNAs are generated by a conserved mechanism involving two RNase III enzymes Drosha and Dicer. However, work from the past few years has uncovered diverse noncanonical miRNA pathways, which exploit a variety of other RNA processing enzymes. In addition, the discovery of another abundant small RNA family, endogenous short interfering RNAs (endo-siRNAs), has also broadened the catalogs of short regulatory RNAs. This review highlights recent studies that revealed novel small RNA biogenesis pathways, and discusses their relevance to gene regulatory networks.
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Affiliation(s)
- Katsutomo Okamura
- Department of Developmental Biology, Sloan-Kettering Institute, New York, NY, USA.
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120
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Abstract
Giardia lamblia, a parasite of humans, is a major source of waterborne diarrhoeal disease. Giardia is also an excellent system to study basic biochemical processes because it is a single-celled eukaryote with a small genome and its entire life cycle can be replicated in vitro. Giardia trophozoites undergo fundamental changes to survive outside the intestine of their host by differentiating into infective cysts. Encystation entails the synthesis, processing, transport, secretion and extracellular assembly of cyst wall components. To survive within the intestine, Giardia undergoes antigenic variation, a process by which the parasite continuously switches its major surface molecules, allowing the parasite to evade the host's immune response and produce chronic and recurrent infections. The objective of the present chapter is to provide a better understanding of the molecular mechanisms involved in adaptation and differentiation in Giardia, with a particular focus on the process of encystation and antigenic variation of this interesting micro-organism.
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121
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Affiliation(s)
- César G. Prucca
- Laboratory of Biochemistry and Molecular Biology, School of Medicine, Catholic University of Cordoba, CP X5004ASK Cordoba, Argentina;
| | - Fernando D. Rivero
- Laboratory of Biochemistry and Molecular Biology, School of Medicine, Catholic University of Cordoba, CP X5004ASK Cordoba, Argentina;
| | - Hugo D. Luján
- Laboratory of Biochemistry and Molecular Biology, School of Medicine, Catholic University of Cordoba, CP X5004ASK Cordoba, Argentina;
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Jenikova G, Hruz P, Andersson MK, Tejman-Yarden N, Ferreira PCD, Andersen YS, Davids BJ, Gillin FD, Svärd SG, Curtiss R, Eckmann L. Α1-giardin based live heterologous vaccine protects against Giardia lamblia infection in a murine model. Vaccine 2011; 29:9529-37. [PMID: 22001876 DOI: 10.1016/j.vaccine.2011.09.126] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2011] [Revised: 08/15/2011] [Accepted: 09/30/2011] [Indexed: 11/18/2022]
Abstract
Giardia lamblia is a leading protozoan cause of diarrheal disease worldwide, yet preventive medical strategies are not available. A crude veterinary vaccine has been licensed for cats and dogs, but no defined human vaccine is available. We tested the vaccine potential of three conserved antigens previously identified in human and murine giardiasis, α1-giardin, α-enolase, and ornithine carbamoyl transferase, in a murine model of G. lamblia infection. Live recombinant attenuated Salmonella enterica Serovar Typhimurium vaccine strains were constructed that stably expressed each antigen, maintained colonization capacity, and sustained total attenuation in the host. Oral administration of the vaccine strains induced antigen-specific serum IgG, particularly IgG(2A), and mucosal IgA for α1-giardin and α-enolase, but not for ornithine carbamoyl transferase. Immunization with the α1-giardin vaccine induced significant protection against subsequent G. lamblia challenge, which was further enhanced by boosting with cholera toxin or sublingual α1-giardin administration. The α-enolase vaccine afforded no protection. Analysis of α1-giardin from divergent assemblage A and B isolates of G. lamblia revealed >97% amino acid sequence conservation and immunological cross-reactivity, further supporting the potential utility of this antigen in vaccine development. Together. These results indicate that α1-giardin is a suitable candidate antigen for a vaccine against giardiasis.
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Affiliation(s)
- Gabriela Jenikova
- Department of Medicine, University of California, San Diego, La Jolla, CA 92093, United States
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Li W, Saraiya AA, Wang CC. Gene regulation in Giardia lambia involves a putative microRNA derived from a small nucleolar RNA. PLoS Negl Trop Dis 2011; 5:e1338. [PMID: 22028939 PMCID: PMC3196473 DOI: 10.1371/journal.pntd.0001338] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2011] [Accepted: 08/15/2011] [Indexed: 12/21/2022] Open
Abstract
Two core microRNA (miRNA) pathway proteins, Dicer and Argonaute, are found in Giardia lamblia, a deeply branching parasitic protozoan. There are, however, no apparent homologues of Drosha or Exportin5 in the genome. Here, we report a 26 nucleotide (nt) RNA derived from a 106 nt Box C/D snoRNA, GlsR2. This small RNA, designated miR5, localizes to the 3' end of GlsR2 and has a 75 nt hairpin precursor. GlsR2 is processed by the Dicer from Giardia (GlDcr) and generated miR5. Immunoprecipitation of the Argonaute from Giardia (GlAgo) brought down miR5. When a Renilla Luciferase transcript with a 26 nt miR5 antisense sequence at the 3'-untranslated region (3' UTR) was introduced into Giardia trophozoites, Luciferase expression was reduced ∼25% when synthetic miR5 was also introduced. The Luciferase mRNA level remained, however, unchanged, suggesting translation repression by miR5. This inhibition was fully reversed by introducing also a 2'-O-methylated antisense inhibitor of miR5, suggesting that miR5 acts by interacting specifically with the antisense sequence in the mRNA. A partial antisense knock down of GlDcr or GlAgo in Giardia indicated that the former is needed for miR5 biogenesis whereas the latter is required for miR5-mediated translational repression. Potential targets for miR5 with canonical seed sequences were predicted bioinformatically near the stop codon of Giardia mRNAs. Four out of the 21 most likely targets were tested in the Luciferase reporter assay. miR5 was found to inhibit Luciferase expression (∼20%) of transcripts carrying these potential target sites, indicating that snoRNA-derived miRNA can regulate the expression of multiple genes in Giardia.
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Affiliation(s)
- Wei Li
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, United States of America
| | - Ashesh A. Saraiya
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, United States of America
| | - Ching C. Wang
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, United States of America
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124
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RNA interference in protozoan parasites: achievements and challenges. EUKARYOTIC CELL 2011; 10:1156-63. [PMID: 21764910 DOI: 10.1128/ec.05114-11] [Citation(s) in RCA: 102] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Protozoan parasites that profoundly affect mankind represent an exceptionally diverse group of organisms, including Plasmodium, Toxoplasma, Entamoeba, Giardia, trypanosomes, and Leishmania. Despite the overwhelming impact of these parasites, there remain many aspects to be discovered about mechanisms of pathogenesis and how these organisms survive in the host. Combined with the ever-increasing availability of sequenced genomes, RNA interference (RNAi), discovered a mere 13 years ago, has enormously facilitated the analysis of gene function, especially in organisms that are not amenable to classical genetic approaches. Here we review the current status of RNAi in studies of parasitic protozoa, with special emphasis on its use as a postgenomic tool.
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125
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Zhang H, Pompey JM, Singh U. RNA interference in Entamoeba histolytica: implications for parasite biology and gene silencing. Future Microbiol 2011; 6:103-17. [PMID: 21162639 DOI: 10.2217/fmb.10.154] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Entamoeba histolytica is a major health threat to people in developing countries, where it causes invasive diarrhea and liver abscesses. The study of this important human pathogen has been hindered by a lack of tools for genetic manipulation. Recently, a number of genetic approaches based on variations of the RNAi method have been successfully developed and cloning of endogenous small-interfering RNAs from E. histolytica revealed an abundant population of small RNAs with an unusual 5´-polyphosphate structure. However, little is known about the implications of these findings to amebic biology or the mechanisms of gene silencing in this organism. In this article we review the literature relevant to RNAi in E. histolytica, discuss its implications for advances in gene silencing in this organism and outline potential future directions towards understanding the repertoire of RNAi and its impact on the biology of this deep-branching eukaryotic parasite.
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Affiliation(s)
- Hanbang Zhang
- Stanford University School of Medicine, S-143 Grant Building, 300 Pasteur Drive, Stanford, CA 94305, USA
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126
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The emerging world of small silencing RNAs in protozoan parasites. Trends Parasitol 2011; 27:321-7. [PMID: 21497553 DOI: 10.1016/j.pt.2011.03.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2011] [Revised: 03/15/2011] [Accepted: 03/16/2011] [Indexed: 12/14/2022]
Abstract
A new RNA world has emerged in the past 10 years with the discovery of a plethora of 20- to 30-nucleotide long small RNAs that are involved in various gene silencing mechanisms. These small RNAs have considerably changed our view of the regulation of gene expression in eukaryotic organisms, with a major shift towards epigenetic and post-transcriptional mechanisms. In this article, we focus on the striking diversity of small silencing RNAs that have been identified in several protozoan parasites and their potential biological role.
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127
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Batista TM, Marques JT. RNAi pathways in parasitic protists and worms. J Proteomics 2011; 74:1504-14. [PMID: 21385631 DOI: 10.1016/j.jprot.2011.02.032] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2011] [Revised: 02/24/2011] [Accepted: 02/26/2011] [Indexed: 12/15/2022]
Abstract
Tropical diseases caused by parasitic worms and protists are of major public health concern affecting millions of people worldwide. New therapeutic and diagnostic tools would be of great help in dealing with the public health and economic impact of these diseases. RNA interference (RNAi) pathways utilize small non-coding RNAs to regulate gene expression in a sequence-specific manner. In recent years, a wealth of data about the mechanisms and biological functions of RNAi pathways in distinct groups of eukaryotes has been described. Often, RNAi pathways have unique features that are restricted to groups of eukaryotes. The focus of this review will be on RNAi pathways in specific groups of parasitic eukaryotes that include Trypanosoma cruzi, Plasmodium and Schistosoma mansoni. These parasites are the causative agents of Chagas disease, Malaria, and Schistosomiasis, respectively, all of which are tropical diseases that would greatly benefit from the development of new diagnostic and therapeutic tools. In this context, we will describe specific features of RNAi pathways in each of these parasitic eukaryotic groups and discuss how they could be exploited for the treatment of tropical diseases.
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Affiliation(s)
- Thiago Mafra Batista
- Department of Biochemistry and Immunology, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
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128
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Transcriptional changes in Giardia during host–parasite interactions. Int J Parasitol 2011; 41:277-85. [DOI: 10.1016/j.ijpara.2010.09.011] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2010] [Revised: 09/15/2010] [Accepted: 09/16/2010] [Indexed: 11/20/2022]
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Lye LF, Owens K, Shi H, Murta SMF, Vieira AC, Turco SJ, Tschudi C, Ullu E, Beverley SM. Retention and loss of RNA interference pathways in trypanosomatid protozoans. PLoS Pathog 2010; 6:e1001161. [PMID: 21060810 PMCID: PMC2965760 DOI: 10.1371/journal.ppat.1001161] [Citation(s) in RCA: 166] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2010] [Accepted: 09/23/2010] [Indexed: 01/02/2023] Open
Abstract
RNA interference (RNAi) pathways are widespread in metaozoans but the genes required show variable occurrence or activity in eukaryotic microbes, including many pathogens. While some Leishmania lack RNAi activity and Argonaute or Dicer genes, we show that Leishmania braziliensis and other species within the Leishmania subgenus Viannia elaborate active RNAi machinery. Strong attenuation of expression from a variety of reporter and endogenous genes was seen. As expected, RNAi knockdowns of the sole Argonaute gene implicated this protein in RNAi. The potential for functional genetics was established by testing RNAi knockdown lines lacking the paraflagellar rod, a key component of the parasite flagellum. This sets the stage for the systematic manipulation of gene expression through RNAi in these predominantly diploid asexual organisms, and may also allow selective RNAi-based chemotherapy. Functional evolutionary surveys of RNAi genes established that RNAi activity was lost after the separation of the Leishmania subgenus Viannia from the remaining Leishmania species, a divergence associated with profound changes in the parasite infectious cycle and virulence. The genus Leishmania therefore offers an accessible system for testing hypothesis about forces that may select for the loss of RNAi during evolution, such as invasion by viruses, changes in genome plasticity mediated by transposable elements and gene amplification (including those mediating drug resistance), and/or alterations in parasite virulence. RNAi interference pathways play fundamental roles in eukaryotes and provide important methods for the analysis of gene function. Occasionally RNAi has been lost, precluding its use as a tool, as well as raising the question of what forces could lead to loss of such a key pathway. Genomic and functional studies previously showed that within trypanosomatids protozoans RNAi was absent in both Leishmania major and Trypanosoma cruzi. The genome of L. braziliensis, a member of the early diverging Leishmania subgenus Viannia, retained key genes required for RNAi such as an Argonaute. We demonstrated that in fact L. braziliensis shows strong RNAi activity with reporter and endogenous genes affecting flagellar function. These data suggest that RNAi may be productively applied for functional genomic studies in L. braziliensis. We mapped the evolutionary point at which RNAi was lost in lineage leading to Leishmania and Crithidia, and establish that RNAi must have been lost at least twice in the trypanosomatids, once on the lineage leading to T. cruzi and independently following the divergence of the Viannia subgenus from other Leishmania species. Lastly, we discuss hypotheses concerning the forces leading to the loss of RNAi in Leishmania evolution, including viral invasion, increased genome plasticity, and altered virulence.
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Affiliation(s)
- Lon-Fye Lye
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Katherine Owens
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Huafang Shi
- Department of Internal Medicine, Yale University Medical School, New Haven, Connecticut, United States of America
| | - Silvane M. F. Murta
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Ana Carolina Vieira
- Department of Biochemistry, University of Kentucky Medical Center, Lexington, Kentucky, United States of America
| | - Salvatore J. Turco
- Department of Biochemistry, University of Kentucky Medical Center, Lexington, Kentucky, United States of America
| | - Christian Tschudi
- Department of Internal Medicine, Yale University Medical School, New Haven, Connecticut, United States of America
- Department of Epidemiology & Public Health, Yale University Medical School, New Haven, Connecticut, United States of America
| | - Elisabetta Ullu
- Department of Internal Medicine, Yale University Medical School, New Haven, Connecticut, United States of America
- Department of Cell Biology, Yale University Medical School, New Haven, Connecticut, United States of America
| | - Stephen M. Beverley
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, United States of America
- * E-mail:
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130
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Multiplex assay detection of immunoglobulin G antibodies that recognize Giardia intestinalis and Cryptosporidium parvum antigens. CLINICAL AND VACCINE IMMUNOLOGY : CVI 2010; 17:1695-707. [PMID: 20876825 DOI: 10.1128/cvi.00160-10] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Giardiasis and cryptosporidiosis are common enteric parasitic diseases that have similar routes of transmission. In this work, we have identified epitopes within the Giardia variant-specific surface protein (VSP) sequences that are recognized by IgG antibodies from 13 of 14 (93%) sera from patients with stool-confirmed giardiasis. The conserved epitopes are shared among VSPs from both of the assemblages that commonly infect humans, and they are likely to be structural, as both sodium dodecyl sulfate treatment and dithiothreitol reduction decrease antibody recognition. In a multiplex bead assay (MBA), we used three VSP fragments from an assemblage A Giardia strain, three VSP fragments from assemblage B strains, and the α-1 giardin structural antigen to detect IgG antibodies to Giardia and used the recombinant 17- and 27-kDa antigens to simultaneously detect IgG antibodies to Cryptosporidium. The MBA differentiated between sera from Giardia and Cryptosporidium outbreaks and also identified a giardiasis outbreak that may have included cryptosporidiosis cases. Approximately 40% of cryptosporidiosis outbreak samples had high MBA responses for both the 27- and 17-kDa antigens, while <10% of nonoutbreak and giardiasis outbreak samples had high responses. At least 60% of giardiasis outbreak samples were positive for antibodies to multiple Giardia antigens, while ≤12% of nonoutbreak samples and samples from U.S. and British Columbia cryptosporidiosis outbreaks met our definition for Giardia seropositivity. A MBA using multiple parasite antigens may prove useful in the epidemiologic analysis of future waterborne or food-borne outbreaks of diarrheal disease.
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131
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Rivero MR, Kulakova L, Touz MC. Long double-stranded RNA produces specific gene downregulation in Giardia lamblia. J Parasitol 2010; 96:815-9. [PMID: 20476805 DOI: 10.1645/ge-2406.1] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
In many eukaryotes, the introduction of double-stranded RNA (dsRNA) into cells triggers the degradation of mRNAs through a post-transcriptional gene-silencing mechanism called RNA interference or RNAi. In the present study, we found that endogenous long-dsRNA was substantially more effective at producing interference than endogenous, or exogenous, short-dsRNA expression in Giardia lamblia . The effects of this interference were not evident in the highly expressed protein tubulin or the stage-specific cyst wall protein 2. However, long-dsRNA caused potent and specific interference in the medium subunits of adaptins, the RNA-dependent RNA polymerase, and the exogenous green fluorescence protein. Our results suggest that the ability of dsRNA antisense to inhibit the expression of these specific types of proteins is indicative of a gene-specific mechanism.
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Affiliation(s)
- Maria R Rivero
- Instituto de Investigación Médica Mercedes y Martín Ferreyra, INIMEC-CONICET, Friuli 2434, Córdoba, Argentina
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132
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Cui J, Das S, Smith TF, Samuelson J. Trichomonas transmembrane cyclases result from massive gene duplication and concomitant development of pseudogenes. PLoS Negl Trop Dis 2010; 4:e782. [PMID: 20689771 PMCID: PMC2914791 DOI: 10.1371/journal.pntd.0000782] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2009] [Accepted: 07/02/2010] [Indexed: 01/04/2023] Open
Abstract
Background Trichomonas vaginalis has an unusually large genome (∼160 Mb) encoding ∼60,000 proteins. With the goal of beginning to understand why some Trichomonas genes are present in so many copies, we characterized here a family of ∼123 Trichomonas genes that encode transmembrane adenylyl cyclases (TMACs). Methodology/Principal Findings The large family of TMACs genes is the result of recent duplications of a small set of ancestral genes that appear to be unique to trichomonads. Duplicated TMAC genes are not closely associated with repetitive elements, and duplications of flanking sequences are rare. However, there is evidence for TMAC gene replacements by homologous recombination. A high percentage of TMAC genes (∼46%) are pseudogenes, as they contain stop codons and/or frame shifts, or the genes are truncated. Numerous stop codons present in the genome project G3 strain are not present in orthologous genes of two other Trichomonas strains (S1 and B7RC2). Each TMAC is composed of a series of N-terminal transmembrane helices and a single C-terminal cyclase domain that has adenylyl cyclase activity. Multiple TMAC genes are transcribed by Trichomonas cloned by limiting dilution. Conclusions/Significance We conclude that one reason for the unusually large genome of Trichomonas is the presence of unstable families of genes such as those encoding TMACs that are undergoing massive gene duplication and concomitant development of pseudogenes. Trichomonas vaginalis is the only medically important protist (single-cell eukaryote) that is sexually transmitted. The ∼160-Mb Trichomonas genome contains more predicted protein-encoding genes (∼60,000) than the human genome. To begin to understand why there are so many copies of some genes, we chose here to study a large family of genes encoding unique transmembrane cyclases. Our most important results include the following. More than 100 transmembrane cyclase genes do not result from chromosomal duplications, because for the most part only the coding regions of the genes, rather than flanking sequences, are duplicated. Almost half of the transmembrane cyclase genes are pseudogenes, and these pseudogenes are polymorphic among laboratory strains of Trichomonas. Messenger RNAs for numerous transmembrane cyclases are expressed simultaneously, and representative cyclase domains have adenylyl cyclase activity. In summary, the large family of Trichomonas genes encoding transmembrane adenylyl cyclases results from massive gene duplication and concomitant development of pseudogenes.
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Affiliation(s)
- Jike Cui
- Department of Molecular and Cell Biology, Boston University Goldman School of Dental Medicine, Boston, Massachusetts, United States of America
- Graduate Program in Bioinformatics, Boston University, Boston, Massachusetts, United States of America
| | - Suchismita Das
- Department of Molecular and Cell Biology, Boston University Goldman School of Dental Medicine, Boston, Massachusetts, United States of America
| | - Temple F. Smith
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, United States of America
| | - John Samuelson
- Department of Molecular and Cell Biology, Boston University Goldman School of Dental Medicine, Boston, Massachusetts, United States of America
- * E-mail:
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Adam RD, Nigam A, Seshadri V, Martens CA, Farneth GA, Morrison HG, Nash TE, Porcella SF, Patel R. The Giardia lamblia vsp gene repertoire: characteristics, genomic organization, and evolution. BMC Genomics 2010; 11:424. [PMID: 20618957 PMCID: PMC2996952 DOI: 10.1186/1471-2164-11-424] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2010] [Accepted: 07/09/2010] [Indexed: 11/10/2022] Open
Abstract
Background Giardia lamblia trophozoites colonize the intestines of susceptible mammals and cause diarrhea, which can be prolonged despite an intestinal immune response. The variable expression of the variant-specific surface protein (VSP) genes may contribute to this prolonged infection. Only one is expressed at a time, and switching expression from one gene to another occurs by an epigenetic mechanism. Results The WB Giardia isolate has been sequenced at 10× coverage and assembled into 306 contigs as large as 870 kb in size. We have used this assembly to evaluate the genomic organization and evolution of the vsp repertoire. We have identified 228 complete and 75 partial vsp gene sequences for an estimated repertoire of 270 to 303, making up about 4% of the genome. The vsp gene diversity includes 30 genes containing tandem repeats, and 14 vsp pairs of identical genes present in either head to head or tail to tail configurations (designated as inverted pairs), where the two genes are separated by 2 to 4 kb of non-coding DNA. Interestingly, over half the total vsp repertoire is present in the form of linear gene arrays that can contain up to 10 vsp gene members. Lastly, evidence for recombination within and across minor clades of vsp genes is provided. Conclusions The data we present here is the first comprehensive analysis of the vsp gene family from the Genotype A1 WB isolate with an emphasis on vsp characterization, function, evolution and contributions to pathogenesis of this important pathogen.
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Affiliation(s)
- Rodney D Adam
- Departments of Medicine and Immunobiology, University of Arizona College of Medicine, Tucson, AZ, USA.
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134
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Marker S, Le Mouël A, Meyer E, Simon M. Distinct RNA-dependent RNA polymerases are required for RNAi triggered by double-stranded RNA versus truncated transgenes in Paramecium tetraurelia. Nucleic Acids Res 2010; 38:4092-107. [PMID: 20200046 PMCID: PMC2896523 DOI: 10.1093/nar/gkq131] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2010] [Revised: 02/13/2010] [Accepted: 02/15/2010] [Indexed: 12/12/2022] Open
Abstract
In many eukaryotes, RNA-dependent RNA polymerases (RdRPs) play key roles in the RNAi pathway. They have been implicated in the recognition and processing of aberrant transcripts triggering the process, and in amplification of the silencing response. We have tested the functions of RdRP genes from the ciliate Paramecium tetraurelia in experimentally induced and endogenous mechanisms of gene silencing. In this organism, RNAi can be triggered either by high-copy, truncated transgenes or by directly feeding cells with double-stranded RNA (dsRNA). Surprisingly, dsRNA-induced silencing depends on the putatively functional RDR1 and RDR2 genes, which are required for the accumulation of both primary siRNAs and a distinct class of small RNAs suggestive of secondary siRNAs. In contrast, a third gene with a highly divergent catalytic domain, RDR3, is required for siRNA accumulation when RNAi is triggered by truncated transgenes. Our data further implicate RDR3 in the accumulation of previously described endogenous siRNAs and in the regulation of the surface antigen gene family. While only one of these genes is normally expressed in any clonal cell line, the knockdown of RDR3 leads to co-expression of multiple antigens. These results provide evidence for a functional specialization of Paramecium RdRP genes in distinct RNAi pathways operating during vegetative growth.
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Affiliation(s)
- Simone Marker
- Department of Biology, University of Kaiserslautern, Gottlieb-Daimler Street, 67663 Kaiserslautern, Germany, Institut de Biologie de l’Ecole Normale Supérieure, CNRS UMR8197, INSERM U1024, 46 rue d'Ulm, 75005 Paris and UMR7216 Epigénétique et Destin Cellulaire, CNRS, Université Paris-Diderot/Paris 7, 35 rue Hélène Brion, 75013, Paris, France
| | - Anne Le Mouël
- Department of Biology, University of Kaiserslautern, Gottlieb-Daimler Street, 67663 Kaiserslautern, Germany, Institut de Biologie de l’Ecole Normale Supérieure, CNRS UMR8197, INSERM U1024, 46 rue d'Ulm, 75005 Paris and UMR7216 Epigénétique et Destin Cellulaire, CNRS, Université Paris-Diderot/Paris 7, 35 rue Hélène Brion, 75013, Paris, France
| | - Eric Meyer
- Department of Biology, University of Kaiserslautern, Gottlieb-Daimler Street, 67663 Kaiserslautern, Germany, Institut de Biologie de l’Ecole Normale Supérieure, CNRS UMR8197, INSERM U1024, 46 rue d'Ulm, 75005 Paris and UMR7216 Epigénétique et Destin Cellulaire, CNRS, Université Paris-Diderot/Paris 7, 35 rue Hélène Brion, 75013, Paris, France
| | - Martin Simon
- Department of Biology, University of Kaiserslautern, Gottlieb-Daimler Street, 67663 Kaiserslautern, Germany, Institut de Biologie de l’Ecole Normale Supérieure, CNRS UMR8197, INSERM U1024, 46 rue d'Ulm, 75005 Paris and UMR7216 Epigénétique et Destin Cellulaire, CNRS, Université Paris-Diderot/Paris 7, 35 rue Hélène Brion, 75013, Paris, France
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135
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Liu Q, Tuo W, Gao H, Zhu XQ. MicroRNAs of parasites: current status and future perspectives. Parasitol Res 2010; 107:501-7. [DOI: 10.1007/s00436-010-1927-6] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2010] [Accepted: 05/18/2010] [Indexed: 12/26/2022]
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Abstract
microRNAs (miRNAs) in higher multicellular eukaryotes have been extensively studied in recent years. Great progresses have also been achieved for miRNAs in unicellular eukaryotes. All these studies not only enrich our knowledge about the complex expression regulation system in diverse organisms, but also have evolutionary significance for understanding the origin of this system. In this review, Authors summarize the recent advance in the studies of miRNA in unicellular eukaryotes, including that on the most primitive unicellular eukaryote--Giardia. The origin and evolution of miRNA system is also discussed.
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137
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Deitsch K. Calling all antigens. Nat Med 2010; 16:522-3. [DOI: 10.1038/nm0510-522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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138
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Adaptor protein 2 regulates receptor-mediated endocytosis and cyst formation in Giardia lamblia. Biochem J 2010; 428:33-45. [PMID: 20199400 DOI: 10.1042/bj20100096] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The parasite Giardia lamblia possesses PVs (peripheral vacuoles) that function as both endosomes and lysosomes and are implicated in the adaptation, differentiation and survival of the parasite in different environments. The mechanisms by which Giardia traffics essential proteins to these organelles and regulates their secretion have important implications in the control of parasite dissemination. In the present study, we describe the participation of the heterotetrameric clathrin-adaptor protein gAP2 (Giardia adaptor protein 2) complex in lysosomal protein trafficking. A specific monoclonal antibody against the medium subunit (gmu2) of gAP2 showed localization of this complex to the PVs, cytoplasm and plasma membrane in the growing trophozoites. gAP2 also co-localized with clathrin in the PVs, suggesting its involvement in endocytosis. Uptake experiments using standard molecules for the study of endocytosis revealed that gAP2 specifically participated in the endocytosis of LDL (low-density lipoprotein). Targeted down-regulation of the gene encoding gmu2 in growing and encysting trophozoites resulted in a large decrease in the amount of cell growth and cyst wall formation, suggesting a distinct mechanism in which gAP2 is directly involved in both endocytosis and vesicular trafficking.
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139
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Rivero FD, Saura A, Prucca CG, Carranza PG, Torri A, Lujan HD. Disruption of antigenic variation is crucial for effective parasite vaccine. Nat Med 2010; 16:551-7, 1p following 557. [DOI: 10.1038/nm.2141] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2009] [Accepted: 03/18/2010] [Indexed: 12/24/2022]
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Abstract
The eukaryotic intestinal parasite Giardia intestinalis was first described in 1681, when Antonie van Leeuwenhoek undertook a microscopic examination of his own diarrhoeal stool. Nowadays, although G. intestinalis is recognized as a major worldwide contributor to diarrhoeal disease in humans and other mammals, the disease mechanisms are still poorly understood. Owing to its reduced complexity and proposed early evolutionary divergence, G. intestinalis is used as a model eukaryotic system for studying many basic cellular processes. In this Review we discuss recent discoveries in the molecular cell biology and pathogenesis of G. intestinalis.
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141
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Muljo SA, Kanellopoulou C, Aravind L. MicroRNA targeting in mammalian genomes: genes and mechanisms. WILEY INTERDISCIPLINARY REVIEWS. SYSTEMS BIOLOGY AND MEDICINE 2010; 2:148-161. [PMID: 20836019 PMCID: PMC3427708 DOI: 10.1002/wsbm.53] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
We briefly review the history of microRNA (miRNA) research and some of the lessons learnt. To provide some insights as to how and why miRNAs came into existence, we consider the evolution of the RNA interference machinery, miRNA genes, and their targets. We highlight the importance of systems biology approaches to integrate miRNAs as an essential subnetwork for modulating gene expression programs. Building accurate computational models that can simulate highly complex cell-specific gene expression patterns in mammals will lead to a better understanding of miRNAs and their targets in physiological and pathological situations. The impact of miRNAs on medicine, either as potential disease predisposing factors, biomarkers, or therapeutics, is highly anticipated and has started to reveal itself.
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Affiliation(s)
- S A Muljo
- Integrative Immunobiology Unit, Laboratory of Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - C Kanellopoulou
- Dana-Farber Cancer Institute, Department of Cancer Biology, Harvard Medical School, Boston, MA, USA
| | - L Aravind
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
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Sun J, Jiang H, Flores R, Wen J. Gene duplication in the genome of parasitic Giardia lamblia. BMC Evol Biol 2010; 10:49. [PMID: 20163721 PMCID: PMC2829556 DOI: 10.1186/1471-2148-10-49] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2009] [Accepted: 02/17/2010] [Indexed: 11/23/2022] Open
Abstract
Background Giardia are a group of widespread intestinal protozoan parasites in a number of vertebrates. Much evidence from G. lamblia indicated they might be the most primitive extant eukaryotes. When and how such a group of the earliest branching unicellular eukaryotes developed the ability to successfully parasitize the latest branching higher eukaryotes (vertebrates) is an intriguing question. Gene duplication has long been thought to be the most common mechanism in the production of primary resources for the origin of evolutionary novelties. In order to parse the evolutionary trajectory of Giardia parasitic lifestyle, here we carried out a genome-wide analysis about gene duplication patterns in G. lamblia. Results Although genomic comparison showed that in G. lamblia the contents of many fundamental biologic pathways are simplified and the whole genome is very compact, in our study 40% of its genes were identified as duplicated genes. Evolutionary distance analyses of these duplicated genes indicated two rounds of large scale duplication events had occurred in G. lamblia genome. Functional annotation of them further showed that the majority of recent duplicated genes are VSPs (Variant-specific Surface Proteins), which are essential for the successful parasitic life of Giardia in hosts. Based on evolutionary comparison with their hosts, it was found that the rapid expansion of VSPs in G. lamblia is consistent with the evolutionary radiation of placental mammals. Conclusions Based on the genome-wide analysis of duplicated genes in G. lamblia, we found that gene duplication was essential for the origin and evolution of Giardia parasitic lifestyle. The recent expansion of VSPs uniquely occurring in G. lamblia is consistent with the increment of its hosts. Therefore we proposed a hypothesis that the increment of Giradia hosts might be the driving force for the rapid expansion of VSPs.
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Affiliation(s)
- Jun Sun
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, PR China
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143
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Xiao Y, Yin J, Jiang N, Xiang M, Hao L, Lu H, Sang H, Liu X, Xu H, Ankarklev J, Lindh J, Chen Q. Seroepidemiology of human Toxoplasma gondii infection in China. BMC Infect Dis 2010; 10:4. [PMID: 20055991 PMCID: PMC2818656 DOI: 10.1186/1471-2334-10-4] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2009] [Accepted: 01/07/2010] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Toxoplasmosis is an important zoonotic parasitic disease worldwide. In immune competent individuals, Toxoplasma gondii preferentially infects tissues of central nervous systems, which might be an adding factor of certain psychiatric disorders. Congenital transmission of T. gondii during pregnancy has been regarded as a risk factor for the health of newborn infants. While in immune-compromised individuals, the parasite can cause life-threatening infections. This study aims to investigate the prevalence of T. gondii infection among clinically healthy individuals and patients with psychiatric disorders in China and to identify the potential risk factors related to the vulnerability of infection in the population. METHODS Serum samples from 2634 healthy individuals and 547 patients with certain psychiatric disorders in Changchun and Daqing in the northeast, and in Shanghai in the south of China were examined respectively for the levels of anti-T. gondii IgG by indirect ELISA and a direct agglutination assay. Prevalence of T. gondii infection in the Chinese population in respect of gender, age, residence and health status was systematically analyzed. RESULTS The overall anti-T. gondii IgG prevalence in the study population was 12.3%. In the clinically healthy population 12.5% was sero-positive and in the group with psychiatric disorders 11.3% of these patients were positive with anti-T. gondii IgG. A significant difference (P = 0.004) was found between male and female in the healthy population, the seroprevalence was 10.5% in men versus 14.3% in women. Furthermore, the difference of T. gondii infection rate between male and female in the 20-19 year's group was more obvious, with 6.4% in male population and 14.6% in female population. CONCLUSION A significant higher prevalence of T. gondii infection was observed in female in the clinically healthy population. No correlation was found between T. gondii infection and psychiatric disorders in this study. Results suggest that women are more exposed to T. gondii infection than men in China. The data argue for deeper investigations for the potential risk factors that threat the female populations.
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Affiliation(s)
- Yue Xiao
- Key Laboratory of Zoonosis, Ministry of Education, Jilin University, Xi An Da Lu 5333, Changchun 130062, PR China
| | - Jigang Yin
- Key Laboratory of Zoonosis, Ministry of Education, Jilin University, Xi An Da Lu 5333, Changchun 130062, PR China
| | - Ning Jiang
- Key Laboratory of Zoonosis, Ministry of Education, Jilin University, Xi An Da Lu 5333, Changchun 130062, PR China
| | - Mei Xiang
- The Second Hospital of Jilin University, Ziqiang Street 218, Changchun 10041, PR China
| | - Lili Hao
- Institute of Pathogen Biology, Chinese Academy of Medical Sciences, Beijing, Dong Dan San Tiao, Beijing 100730, PR China
| | - Huijun Lu
- Key Laboratory of Zoonosis, Ministry of Education, Jilin University, Xi An Da Lu 5333, Changchun 130062, PR China
| | - Hong Sang
- The Sixth Hospital of Changchun City, North Round Road 4596, Changchun 130040, PR China
| | - Xianying Liu
- The Second Hospital of Jilin University, Ziqiang Street 218, Changchun 10041, PR China
| | - Huiji Xu
- Changzheng Hospital, Shanghai, Fengyang Road 415, Shanghai 200003, PR China
| | - Johan Ankarklev
- Department of Parasitology, Mycology and Environmental Microbiology, Swedish Institute for Infectious Disease Control, Nobels väg 18, 171 82 Solna, Sweden
| | - Johan Lindh
- Department of Parasitology, Mycology and Environmental Microbiology, Swedish Institute for Infectious Disease Control, Nobels väg 18, 171 82 Solna, Sweden
| | - Qijun Chen
- Key Laboratory of Zoonosis, Ministry of Education, Jilin University, Xi An Da Lu 5333, Changchun 130062, PR China
- Institute of Pathogen Biology, Chinese Academy of Medical Sciences, Beijing, Dong Dan San Tiao, Beijing 100730, PR China
- Department of Parasitology, Mycology and Environmental Microbiology, Swedish Institute for Infectious Disease Control, Nobels väg 18, 171 82 Solna, Sweden
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Carranza PG, Lujan HD. New insights regarding the biology of Giardia lamblia. Microbes Infect 2010; 12:71-80. [DOI: 10.1016/j.micinf.2009.09.008] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2009] [Accepted: 09/15/2009] [Indexed: 10/20/2022]
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146
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Raabe CA, Sanchez CP, Randau G, Robeck T, Skryabin BV, Chinni SV, Kube M, Reinhardt R, Ng GH, Manickam R, Kuryshev VY, Lanzer M, Brosius J, Tang TH, Rozhdestvensky TS. A global view of the nonprotein-coding transcriptome in Plasmodium falciparum. Nucleic Acids Res 2009; 38:608-17. [PMID: 19864253 PMCID: PMC2811010 DOI: 10.1093/nar/gkp895] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Nonprotein-coding RNAs (npcRNAs) represent an important class of regulatory molecules that act in many cellular pathways. Here, we describe the experimental identification and validation of the small npcRNA transcriptome of the human malaria parasite Plasmodium falciparum. We identified 630 novel npcRNA candidates. Based on sequence and structural motifs, 43 of them belong to the C/D and H/ACA-box subclasses of small nucleolar RNAs (snoRNAs) and small Cajal body-specific RNAs (scaRNAs). We further observed the exonization of a functional H/ACA snoRNA gene, which might contribute to the regulation of ribosomal protein L7a gene expression. Some of the small npcRNA candidates are from telomeric and subtelomeric repetitive regions, suggesting their potential involvement in maintaining telomeric integrity and subtelomeric gene silencing. We also detected 328 cis-encoded antisense npcRNAs (asRNAs) complementary to P. falciparum protein-coding genes of a wide range of biochemical pathways, including determinants of virulence and pathology. All cis-encoded asRNA genes tested exhibit lifecycle-specific expression profiles. For all but one of the respective sense–antisense pairs, we deduced concordant patterns of expression. Our findings have important implications for a better understanding of gene regulatory mechanisms in P. falciparum, revealing an extended and sophisticated npcRNA network that may control the expression of housekeeping genes and virulence factors.
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Affiliation(s)
- Carsten A Raabe
- Institute of Experimental Pathology, ZMBE, University of Muenster, Von-Esmarch-Str. 56, 48149 Muenster, Germany
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Zhang YQ, Chen DL, Tian HF, Zhang BH, Wen JF. Genome-wide computational identification of microRNAs and their targets in the deep-branching eukaryote Giardia lamblia. Comput Biol Chem 2009; 33:391-6. [DOI: 10.1016/j.compbiolchem.2009.07.013] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2009] [Revised: 07/05/2009] [Accepted: 07/16/2009] [Indexed: 12/29/2022]
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148
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Triggle DJ. The chemist as astronaut: Searching for biologically useful space in the chemical universe. Biochem Pharmacol 2009; 78:217-23. [DOI: 10.1016/j.bcp.2009.02.015] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2009] [Revised: 02/19/2009] [Accepted: 02/19/2009] [Indexed: 12/21/2022]
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149
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Abstract
Eukaryote gene expression is mediated by a cascade of RNA functions that regulate, process, store, transport, and translate RNA transcripts. The RNA network that promotes this cascade depends on a large cohort of proteins that partner RNAs; thus, the modern RNA world of eukaryotes is really a ribonucleoprotein (RNP) world. Features of this "RNP infrastructure" can be related to the high cytosolic density of macromolecules and the large size of eukaryote cells. Because of the densely packed cytosol or nucleoplasm (with its severe restriction on diffusion of macromolecules), partitioning of the eukaryote cell into functionally specialized compartments is essential for efficiency. This necessitates the association of RNA and protein into large RNP complexes including ribosomes and spliceosomes. This is well illustrated by the ubiquitous spliceosome for which most components are conserved throughout eukaryotes and which interacts with other RNP-based machineries. The complexes involved in gene processing in modern eukaryotes have broad phylogenetic distributions suggesting that the common ancestor of extant eukaryotes had a fully evolved RNP network. Thus, the eukaryote genome may be uniquely informative about the transition from an earlier RNA genome world to the modern DNA genome world.
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Affiliation(s)
- Lesley J Collins
- Allan Wilson Center for Molecular Ecology and Evolution, Palmerston North, New Zealand.
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150
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snoRNAs in Giardia lamblia: a novel role in RNA silencing? Trends Parasitol 2009; 25:348-50. [PMID: 19616476 DOI: 10.1016/j.pt.2009.05.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2009] [Revised: 05/05/2009] [Accepted: 05/07/2009] [Indexed: 11/21/2022]
Abstract
In the expanding world of small regulatory RNAs, a recent paper by Saraiya and Wang has reported the identification in the protozoan parasite Giardia lamblia of a novel class of small RNAs, which are derived by Dicer processing of small nucleolar RNAs and have the potential to function as micro RNAs. Interestingly, these RNAs occur not only in this parasite but also in humans.
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