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Sharma M, Zhang H, Ehrenkaufer G, Singh U. Stress Response in Entamoeba histolytica Is Associated with Robust Processing of tRNA to tRNA Halves. mBio 2023; 14:e0345022. [PMID: 36809068 PMCID: PMC10127584 DOI: 10.1128/mbio.03450-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 01/18/2023] [Indexed: 02/23/2023] Open
Abstract
tRNA-derived fragments have been reported in many different organisms and have diverse cellular roles, such as regulating gene expression, inhibiting protein translation, silencing transposable elements, and modulating cell proliferation. In particular, tRNA halves, a class of tRNA fragments produced by the cleavage of tRNAs in the anti-codon loop, have been widely reported to accumulate under stress and regulate translation in cells. Here, we report the presence of tRNA-derived fragments in Entamoeba, with tRNA halves being the most abundant. We further established that tRNA halves accumulate in the parasites upon different stress stimuli such as oxidative stress, heat shock, and serum starvation. We also observed differential expression of tRNA halves during developmental changes of trophozoite-to-cyst conversion, with various tRNA halves accumulating during early encystation. In contrast to other systems, the stress response does not appear to be mediated by a few specific tRNA halves, as multiple tRNAs appear to be processed during the various stresses. Furthermore, we identified some tRNA-derived fragments associated with Entamoeba Argonaute proteins, EhAgo2-2 and EhAgo2-3, which have a preference for different tRNA-derived fragment species. Finally, we show that tRNA halves are packaged inside extracellular vesicles secreted by amoebas. The ubiquitous presence of tRNA-derived fragments, their association with the Argonaute proteins, and the accumulation of tRNA halves during multiple different stresses, including encystation, suggest a nuanced level of gene expression regulation mediated by different tRNA-derived fragments in Entamoeba. IMPORTANCE In the present study, we report for the first time the presence of tRNA-derived fragments in Entamoeba. tRNA-derived fragments were identified by bioinformatics analyses of small-RNA sequencing data sets from the parasites and also confirmed experimentally. We found that tRNA halves accumulated in parasites exposed to environmental stress or during the developmental process of encystation. We also found that shorter tRNA-derived fragments are bound to Entamoeba Argonaute proteins, indicating that they may have a potential role in the Argonaute-mediated RNA-interference pathway, which mediates robust gene silencing in Entamoeba. We noticed that in response to heat shock, the protein translation levels were elevated in the parasites. This effect was reversed in the presence of an analog of leucine, which also reduced the levels of the tRNA halves in the stressed cells. Our results suggest that tRNA-derived fragments in Entamoeba have a possible role in regulating gene expression during environmental stress.
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Affiliation(s)
- Manu Sharma
- Division of Infectious Diseases, Stanford University School of Medicine, Stanford, California, USA
| | - Hanbang Zhang
- Division of Infectious Diseases, Stanford University School of Medicine, Stanford, California, USA
| | - Gretchen Ehrenkaufer
- Division of Infectious Diseases, Stanford University School of Medicine, Stanford, California, USA
| | - Upinder Singh
- Division of Infectious Diseases, Stanford University School of Medicine, Stanford, California, USA
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA
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Singh SS, Mansuri MS, Naiyer S, Kaur D, Agrahari M, Srinivasan S, Jhingan GD, Bhattacharya A, Bhattacharya S. Multi-omics analysis to characterize molecular adaptation of Entamoeba histolytica during serum stress. Proteomics 2022; 22:e2200148. [PMID: 36066285 DOI: 10.1002/pmic.202200148] [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: 04/11/2022] [Revised: 08/07/2022] [Accepted: 08/19/2022] [Indexed: 12/29/2022]
Abstract
Entamoeba histolytica is responsible for dysentery and extraintestinal disease in humans. To establish successful infection, it must generate adaptive response against stress due to host defense mechanisms. We have developed a robust proteomics workflow by combining miniaturized sample preparation, low flow-rate chromatography, and ultra-high sensitivity mass spectrometry, achieving increased proteome coverage, and further integrated proteomics and RNA-seq data to decipher regulation at translational and transcriptional levels. Label-free quantitative proteomics led to identification of 2344 proteins, an improvement over the maximum number identified in E. histolytica proteomic studies. In serum-starved cells, 127 proteins were differentially abundant and were associated with functions including antioxidant activity, cytoskeleton, translation, catalysis, and transport. The virulence factor, Gal/GalNAc-inhibitable lectin subunits, was significantly altered. Integration of transcriptomic and proteomic data revealed that only 30% genes were coordinately regulated at both transcriptional and translational levels. Some highly expressed transcripts did not change in protein abundance. Conversely, genes with no transcriptional change showed enhanced protein abundance, indicating post-transcriptional regulation. This multi-omics approach enables more refined gene expression analysis to understand the adaptive response of E. histolytica during growth stress.
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Affiliation(s)
- Shashi Shekhar Singh
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi, India.,Center for RNA Science and Therapeutics, Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
| | - Mohammad Shahid Mansuri
- Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Sarah Naiyer
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi, India.,Department of Immunology and Microbiology, University of Illinois Chicago, Chicago, Illinois, USA
| | - Devinder Kaur
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi, India.,Central University of Punjab, Bathinda, Punjab, India
| | - Mridula Agrahari
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi, India.,Vproteomics, Valerian Chem Private Limited, New Delhi, India
| | | | | | - Alok Bhattacharya
- Ashoka University, Rajiv Gandhi Education City, Sonipat, Haryana, India
| | - Sudha Bhattacharya
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi, India.,Ashoka University, Rajiv Gandhi Education City, Sonipat, Haryana, India
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RISC in Entamoeba histolytica: Identification of a Protein-Protein Interaction Network for the RNA Interference Pathway in a Deep-Branching Eukaryote. mBio 2021; 12:e0154021. [PMID: 34488447 PMCID: PMC8546589 DOI: 10.1128/mbio.01540-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Entamoeba histolytica is a protozoan parasite that causes amebiasis in humans and is a major health concern in developing countries. Our previous work revealed a functional RNA interference (RNAi) pathway in Entamoeba. Several unusual features encompass the RNAi pathway in the parasite, including small RNAs (sRNAs) with a 5'-polyphosphate structure (identified to date only in Entamoeba and nematodes) and the conspicuous absence of a canonical Dicer enzyme. Currently, little is known about the Entamoeba RNA-induced silencing complex (RISC), which is critical in understanding how RNAi is achieved in the parasite. In this study, we examined the RISC of EhAgo2-2, the most highly expressed Argonaute protein in Entamoeba. We identified 43 protein components of EhAgo2-2 RISC with a broad range of functional activities. Two proteins with nucleosome assembly protein (NAP) domains, not previously observed in other RNAi systems, were identified as novel core members of amebic RISC. We further demonstrated the interaction of these NAPs with Ago using an in vitro recombinant system. Finally, we characterized the interaction network of five RISC components identified in this study to further elucidate the interactions of these RNAi pathway proteins. Our data suggest the presence of closely interacting protein groups within RISC and allowed us to build a map of protein-protein interactions in relation to Ago. Our work is the first to elucidate RISC components in Entamoeba and expands the current knowledge of RISC to a deep-branching single-celled eukaryote. IMPORTANCE Entamoeba histolytica is a leading parasitic cause of death in developing countries, and our efforts are focused on defining the molecular basis of RNA interference (RNAi) gene regulation in this parasite. The Entamoeba RNAi pathway effectively silences a subset of endogenous genes and has also been harnessed as a gene silencing tool to study gene function in this organism. However, little is known about the components of the Entamoeba RNA-induced silencing complex (RISC), which is critical in understanding how gene silencing is achieved in the parasite. This study characterizes, for the first time, the RISC components in Entamoeba and provides new insights in understanding the molecular regulatory mechanisms of RNAi in this parasite, including the demonstration of novel Ago protein-interacting partners. From an evolutionary point of view, our findings expand the current knowledge of RISC to a deep-branching single-celled eukaryote.
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Faridi A, Mansouri M, Macchiaroli N, Afgar A, Mousavi SM, Rosenzvit MC, Harandi MF. MicroRNA profile of the strobilated worms of Echinococcus granulosus derived from in vivo and in vitro systems by using high-throughput approach. Parasitol Res 2021; 120:3203-3214. [PMID: 34351489 DOI: 10.1007/s00436-021-07251-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Accepted: 07/13/2021] [Indexed: 11/26/2022]
Abstract
MicroRNAs are critical gene regulators at the post-transcriptional level and play essential roles in numerous developmental processes in metazoan parasites including the causative agent of cystic echinococcosis, Echinococcus granulosus. The molecular basis of different patterns of E. granulosus development in the canine definitive host and in in vitro culture systems is poorly understood. In the present study, miRNA transcriptomes of the strobilated worms derived from experimental infection in the definitive host were compared with those from diphasic culture system after 60-day protoscoleces cultivation. Total RNA was extracted from in vivo- and in vitro-derived strobilated worms. Small RNA libraries were constructed, and deep sequencing was performed. Subsequently, differential miRNA expressions and target predictions were obtained, and pathway analysis was performed by gene ontology and KEGG. Seven miRNAs were differentially expressed between the in vivo- and in vitro-derived worms. In addition, we reported 13 novel miRNA candidates and 42 conserved miRNAs. Four out of five top miRNAs with the highest read counts were shared between the in vivo and in vitro-derived worms, i.e., egr-miR-10a-5p, egr-let-7-5p, egr-bantam-3p, and egr-miR-71-5p. Target prediction of the differential miRNAs between the two systems showed significant differences in the membrane-enclosed lumen, membrane part, and an intrinsic component of the membrane. Findings of KEGG analysis indicated that differentially expressed miRNAs were involved in hippo, MAPK, and WNT signaling pathways. The study demonstrated a significant difference in miRNA transcriptomes and related signaling pathways between the two systems, suggesting the importance of host-parasite interplay in the fate of protoscoleces development in in vivo and in vitro systems.
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Affiliation(s)
- Ashkan Faridi
- Research Center for Hydatid Disease in Iran, Kerman University of Medical Sciences, Kerman, Iran
| | - Mehdi Mansouri
- Department of Agricultural Biotechnology, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Natalia Macchiaroli
- Laboratorio Biología Molecular de Hidatidosis, Instituto de Microbiología Y Parasitología Médica (IMPaM), Consejo Nacional de Investigaciones Científicas Y Tecnológicas (CONICET), Facultad de Medicina, Universidad de Buenos Aires (UBA), Buenos Aires, Argentina
- Laboratorio de Genómica Y Bioinformática de Patógenos, Instituto de Biociencias, Biotecnología y Biología Traslacional (iB3), Departamento de Fisiología Y Biología Molecular Y Celular, Facultad de Ciencias Exactas Y Naturales, Universidad de Buenos Aires (UBA), Buenos Aires, Argentina
| | - Ali Afgar
- Research Center for Hydatid Disease in Iran, Kerman University of Medical Sciences, Kerman, Iran
| | - Seyed Mohammad Mousavi
- Research Center for Hydatid Disease in Iran, Kerman University of Medical Sciences, Kerman, Iran
| | - Mara C Rosenzvit
- Laboratorio Biología Molecular de Hidatidosis, Instituto de Microbiología Y Parasitología Médica (IMPaM), Consejo Nacional de Investigaciones Científicas Y Tecnológicas (CONICET), Facultad de Medicina, Universidad de Buenos Aires (UBA), Buenos Aires, Argentina
| | - Majid Fasihi Harandi
- Research Center for Hydatid Disease in Iran, Kerman University of Medical Sciences, Kerman, Iran.
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Queuine Is a Nutritional Regulator of Entamoeba histolytica Response to Oxidative Stress and a Virulence Attenuator. mBio 2021; 12:mBio.03549-20. [PMID: 33688012 PMCID: PMC8092309 DOI: 10.1128/mbio.03549-20] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Entamoeba histolytica is a unicellular parasite that causes amebiasis. The parasite resides in the colon and feeds on the colonic microbiota. Queuosine is a naturally occurring modified ribonucleoside found in the first position of the anticodon of the transfer RNAs for Asp, Asn, His, and Tyr. Eukaryotes lack pathways to synthesize queuine, the nucleobase precursor to queuosine, and must obtain it from diet or gut microbiota. Here, we describe the effects of queuine on the physiology of the eukaryotic parasite Entamoeba histolytica, the causative agent of amebic dysentery. Queuine is efficiently incorporated into E. histolytica tRNAs by a tRNA-guanine transglycosylase (EhTGT) and this incorporation stimulates the methylation of C38 in
tRNAGUCAsp. Queuine protects the parasite against oxidative stress (OS) and antagonizes the negative effect that oxidation has on translation by inducing the expression of genes involved in the OS response, such as heat shock protein 70 (Hsp70), antioxidant enzymes, and enzymes involved in DNA repair. On the other hand, queuine impairs E. histolytica virulence by downregulating the expression of genes previously associated with virulence, including cysteine proteases, cytoskeletal proteins, and small GTPases. Silencing of EhTGT prevents incorporation of queuine into tRNAs and strongly impairs methylation of C38 in
tRNAGUCAsp, parasite growth, resistance to OS, and cytopathic activity. Overall, our data reveal that queuine plays a dual role in promoting OS resistance and reducing parasite virulence.
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Santos F, Marcial-Quino J, Gómez-Manzo S, Enríquez-Flores S, Nequiz-Avendaño M, Cortes A, De la Luz León-Avila G, Saavedra E, Pérez-Tamayo R, Olivos-García A. Functional characterization and subcellular distribution of two recombinant cytosolic HSP70 isoforms from Entamoeba histolytica under normal and stress conditions. Parasitol Res 2020; 119:1337-1351. [PMID: 32056023 DOI: 10.1007/s00436-020-06621-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 02/05/2020] [Indexed: 11/26/2022]
Abstract
Amoebiasis is a human intestinal disease caused by the parasite Entamoeba histolytica. It has been previously demonstrated that E. histolytica heat shock protein 70 (EhHSP70) plays an important role in amoebic pathogenicity by protecting the parasite from the dangerous effects of oxidative and nitrosative stresses. Despite its relevance, this protein has not yet been characterized. In this study, the EhHSP70 genes were cloned, and the two recombinant EhHSP70 proteins were expressed, purifying and biochemically characterized. Additionally, after being subjected to some host stressors, the intracellular distribution of the proteins in the parasite was documented. Two amoebic HSP70 isoforms, EhHSP70-A and EhHSP70-B, with 637 and 656 amino acids, respectively, were identified. Kinetic parameters of ATP hydrolysis showed low rates, which were in accordance with those of the HSP70 family members. Circular dichroism analysis showed differences in their secondary structures but similarities in their thermal stability. Immunocytochemistry in trophozoites detected EhHSP70 in the nuclei and cytoplasm as well as a slight overexpression when the parasites were subjected to oxidants and heat. The structural differences of amoebic HSP70s with their human counterparts may be used to design specific inhibitors to treat human amoebiasis.
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Affiliation(s)
- Fabiola Santos
- Unidad de Investigación en Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, 04510, México, Mexico
- Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, 11340, México, Mexico
| | - Jaime Marcial-Quino
- Laboratorio de Bioquímica Genética, Instituto Nacional de Pediatría, Secretaria de Salud, 04530, México, Mexico
| | - Saúl Gómez-Manzo
- Laboratorio de Bioquímica Genética, Instituto Nacional de Pediatría, Secretaria de Salud, 04530, México, Mexico
| | - Sergio Enríquez-Flores
- Grupo de Investigación en Biomoléculas y Salud Infantil, Laboratorio de Errores Innatos del Metabolismo y Tamiz, Instituto Nacional de Pediatría, Secretaria de Salud, 04530, México, Mexico
| | - Mario Nequiz-Avendaño
- Unidad de Investigación en Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, 04510, México, Mexico
| | - Azucena Cortes
- Unidad de Investigación en Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, 04510, México, Mexico
| | - Gloria De la Luz León-Avila
- Departamento de Zoología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, 11340, México, Mexico
| | - Emma Saavedra
- Departamento de Bioquímica, Instituto Nacional de Cardiología Ignacio Chávez, Secretaría de Salud, 14080, México, Mexico
| | - Ruy Pérez-Tamayo
- Unidad de Investigación en Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, 04510, México, Mexico
| | - Alfonso Olivos-García
- Unidad de Investigación en Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, 04510, México, Mexico.
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Naiyer S, Bhattacharya A, Bhattacharya S. Advances in Entamoeba histolytica Biology Through Transcriptomic Analysis. Front Microbiol 2019; 10:1921. [PMID: 31481949 PMCID: PMC6710346 DOI: 10.3389/fmicb.2019.01921] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 08/05/2019] [Indexed: 12/13/2022] Open
Abstract
A large number of transcriptome-level studies in Entamoeba histolytica, the protozoan parasite that causes amoebiasis, have investigated gene expression patterns to help understand the pathology and biology of the organism. They have compared virulent and avirulent strains in lab culture and after tissue invasion, cells grown under different stress conditions, response to anti-amoebic drug treatments, and gene expression changes during the process of encystation. These studies have revealed interesting molecules/pathways that will help increase our mechanistic understanding of differentially expressed genes during growth perturbations and tissue invasion. Some of the important insights obtained from transcriptome studies include the observations that regulation of carbohydrate metabolism may be an important determinant for tissue invasion, while the novel up-regulated genes during encystation include phospholipase D, and meiotic genes, suggesting the possibility of meiosis during the process. Classification of genes according to expression levels showed that amongst the highly transcribed genes in cultured E. histolytica trophozoites were some virulence factors, raising the question of the role of these factors in normal parasite growth. Promoter motifs associated with differential gene expression and regulation were identified. Some of these motifs associated with high gene expression were located downstream of start codon, and were required for efficient transcription. The listing of E. histolytica genes according to transcript expression levels will help us determine the scale of post-transcriptional regulation, and the possible roles of predicted promoter motifs. The small RNA transcriptome is a valuable resource for detailed structural and functional analysis of these molecules and their regulatory roles. These studies provide new drug targets and enhance our understanding of gene regulation in E. histolytica.
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Affiliation(s)
- Sarah Naiyer
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Alok Bhattacharya
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Sudha Bhattacharya
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi, India
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Naiyer S, Kaur D, Ahamad J, Singh SS, Singh YP, Thakur V, Bhattacharya A, Bhattacharya S. Transcriptomic analysis reveals novel downstream regulatory motifs and highly transcribed virulence factor genes of Entamoeba histolytica. BMC Genomics 2019; 20:206. [PMID: 30866809 PMCID: PMC6416950 DOI: 10.1186/s12864-019-5570-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 02/27/2019] [Indexed: 11/16/2022] Open
Abstract
Background Promoter motifs in Entamoeba histolytica were earlier analysed using microarray data with lower dynamic range of gene expression. Additionally, previous transcriptomic studies did not provide information on the nature of highly transcribed genes, and downstream promoter motifs important for gene expression. To address these issues we generated RNA-Seq data and identified the high and low expressing genes, especially with respect to virulence potential. We analysed sequences both upstream and downstream of start site for important motifs. Results We used RNA-Seq data to classify genes according to expression levels, which ranged six orders of magnitude. Data were validated by reporter gene expression. Virulence-related genes (except AIG1) were amongst the highly expressed, while some kinases and BspA family genes were poorly expressed. We looked for conserved motifs in sequences upstream and downstream of the initiation codon. Following enrichment by AME we found seven motifs significantly enriched in high expression- and three in low expression-classes. Two of these motifs (M4 and M6) were located downstream of AUG, were exclusively enriched in high expression class, and were mostly found in ribosomal protein, and translation-related genes. Motif deletion resulted in drastic down regulation of reporter gene expression, showing functional relevance. Distribution of core promoter motifs (TATA, GAAC, and Inr) in all genes revealed that genes with downstream motifs were not preferentially associated with TATA-less promoters. We looked at gene expression changes in cells subjected to growth stress by serum starvation, and experimentally validated the data. Genes showing maximum up regulation belonged to the low or medium expression class, and included genes in signalling pathways, lipid metabolism, DNA repair, Myb transcription factors, BspA, and heat shock. Genes showing maximum down regulation belonged to the high or medium expression class. They included genes for signalling factors, actin, Ariel family, and ribosome biogenesis factors. Conclusion Our analysis has added important new information about the E. histolytica transcriptome. We report for the first time two downstream motifs required for gene expression, which could be used for over expression of E. histolytica genes. Most of the virulence-related genes in this parasite are highly expressed in culture. Electronic supplementary material The online version of this article (10.1186/s12864-019-5570-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sarah Naiyer
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Devinder Kaur
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Jamaluddin Ahamad
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi, India
| | | | | | - Vivek Thakur
- Centre for Systems Biology, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - Alok Bhattacharya
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Sudha Bhattacharya
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi, India.
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Espinosa A, Paz-Y-Miño-C G. Discrimination Experiments in Entamoeba and Evidence from Other Protists Suggest Pathogenic Amebas Cooperate with Kin to Colonize Hosts and Deter Rivals. J Eukaryot Microbiol 2019; 66:354-368. [PMID: 30055104 PMCID: PMC6349510 DOI: 10.1111/jeu.12673] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Revised: 06/27/2018] [Accepted: 07/25/2018] [Indexed: 01/06/2023]
Abstract
Entamoeba histolytica is one of the least understood protists in terms of taxa, clone, and kin discrimination/recognition ability. However, the capacity to tell apart same or self (clone/kin) from different or nonself (nonclone/nonkin) has long been demonstrated in pathogenic eukaryotes like Trypanosoma and Plasmodium, free-living social amebas (Dictyostelium, Polysphondylium), budding yeast (Saccharomyces), and in numerous bacteria and archaea (prokaryotes). Kin discrimination/recognition is explained under inclusive fitness theory; that is, the reproductive advantage that genetically closely related organisms (kin) can gain by cooperating preferably with one another (rather than with distantly related or unrelated individuals), minimizing antagonism and competition with kin, and excluding genetic strangers (or cheaters = noncooperators that benefit from others' investments in altruistic cooperation). In this review, we rely on the outcomes of in vitro pairwise discrimination/recognition encounters between seven Entamoeba lineages to discuss the biological significance of taxa, clone, and kin discrimination/recognition in a range of generalist and specialist species (close or distantly related phylogenetically). We then focus our discussion on the importance of these laboratory observations for E. histolytica's life cycle, host infestation, and implications of these features of the amebas' natural history for human health (including mitigation of amebiasis).
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Affiliation(s)
- Avelina Espinosa
- Department of Biology, Roger Williams University, Bristol, Rhode Island
- New England Center for the Public Understanding of Science, Roger Williams University, Bristol, Rhode Island
| | - Guillermo Paz-Y-Miño-C
- New England Center for the Public Understanding of Science, Roger Williams University, Bristol, Rhode Island
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Rajamanikam A, Hooi HS, Kudva M, Samudi C, Kumar S. Resistance towards metronidazole in Blastocystis sp.: A pathogenic consequence. PLoS One 2019; 14:e0212542. [PMID: 30794628 PMCID: PMC6386359 DOI: 10.1371/journal.pone.0212542] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Accepted: 02/05/2019] [Indexed: 01/13/2023] Open
Abstract
Blastocsytis sp. is a protozoan parasite that has been linked to common gastrointestinal illnesses. Metronidazole, the first line therapy, was reported to show frequent inefficacy. Previously, Blastocystis sp. isolated from different population showed varying metronidazole resistance. However, the effect of metronidazole treatment on pathogenic potentials of Blastocystis sp. isolated from different populations, which is known to have different gut environment, is unclear. This study investigates the in vitro effect of metronidazole on the pathogenic potentials of Blastocystis sp. isolated from urban and orang asli individuals. Blastocystis sp. ST 3 isolated from symptomatic and asymptomatic individuals were treated with a range of metronidazole concentration. The parasites’ growth characteristics, apoptotic rate, specific protease activity and the ability to proliferate cancer cells were analyzed upon treatment with 0.001 mg/l metronidazole. The study demonstrates that Blastocystis sp. isolates showed increase in the parasite numbers especially the amoebic forms (only in urban isolates) after treating with metronidazole at the concentration of 0.001 mg/ml. High number of cells in post-treated isolates coincided with increase of apoptosis. There was a significant increase in cysteine protease of Blastocystis sp. isolates upon treatment despite the initial predominance of serine protease in asymptomatic isolates. Metronidazole resistant Blastocystis sp. also showed significant increase in cancer cell proliferation. Resistance to metronidazole did not show significant different influence on the pathogenicity between Blastocystis sp. isolated from urban and orang asli individual. However, an increase in parasite numbers, higher amoebic forms, cysteine protease and ability to proliferate cancer cells implicates a pathogenic role. The study provides evidence for the first time, the effect of metronidazole towards enhancing pathogenic potentials in Blastocystis sp. when isolated from different gut environment. This necessitates the need for reassessment of metronidazole treatment modalities.
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Affiliation(s)
- Arutchelvan Rajamanikam
- Depatment of Parasitology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Ho Shiaw Hooi
- Department of Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Madhav Kudva
- Gastroenterology and Hepatology Specialist Clinic, Pantai Hospital, Kuala Lumpur, Malaysia
| | - Chandramathi Samudi
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Suresh Kumar
- Depatment of Parasitology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
- * E-mail:
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Avendaño-Borromeo B, Narayanasamy RK, García-Rivera G, Labra-Barrios ML, Lagunes-Guillén AE, Munguía-Chávez B, Castañón-Sánchez CA, Orozco E, Luna-Arias JP. Identification of the gene encoding the TATA box-binding protein-associated factor 1 (TAF1) and its putative role in the heat shock response in the protozoan parasite Entamoeba histolytica. Parasitol Res 2018; 118:517-538. [PMID: 30552577 DOI: 10.1007/s00436-018-6170-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 11/29/2018] [Indexed: 11/26/2022]
Abstract
Transcription factor IID (TFIID) is a cornerstone in the transcription initiation in eukaryotes. It is composed of TBP and approximately 14 different subunits named TBP-associated factors (TAFs). TFIID has a key role in transcription of many genes involved in cell proliferation, cell growth, cell cycle, cell cycle checkpoint, and various other processes as well. Entamoeba histolytica, the protozoan parasite responsible for human amoebiasis, represents a major global health concern. Our research group has previously reported the genes coding the TATA box-binding protein (EhTBP) and TBP-related factor 1 (EhTRF1), which displayed different mRNA levels in trophozoites under different stress conditions. In this work, we identified the TBP-associated factor 1 (Ehtaf1) gene in the E. histolytica genome, which possess a well-conserved DUF domain and a Bromo domain located in the middle and C-terminus of the protein, respectively. The EhTAF1-DUF domain tertiary structure is similar to the corresponding HsTAF1 DUF domain. RT-qPCR experiments with RNA isolated from trophozoites harvested at different time points of the growth curve and under different stress conditions revealed that the Ehtaf1 gene was found slightly upregulated in the death phase of growth curve, but under heat shock stress, it was found upregulated 10 times, suggesting that Ehtaf1 might have an important role in the heat shock stress response. We also found that EhTAF1 is expressed in the nucleus and cytoplasm at 37 °C, but under heat shock stress, it is overexpressed in both the nucleus and cytoplasm, and partially colocalized with EhHSP70 in cytoplasm.
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Affiliation(s)
- Bartolo Avendaño-Borromeo
- Departamento de Biología Celular, Cinvestav-IPN, Av. IPN 2508, Col. San Pedro Zacatenco, 07360, Ciudad de México, Mexico
| | - Ravi Kumar Narayanasamy
- Departamento de Biología Celular, Cinvestav-IPN, Av. IPN 2508, Col. San Pedro Zacatenco, 07360, Ciudad de México, Mexico
| | - Guillermina García-Rivera
- Departamento de Infectómica y Patogénesis Molecular, Cinvestav-IPN, Av. IPN 2508, Col. San Pedro Zacatenco, 07360, Ciudad de México, Mexico
| | - María Luisa Labra-Barrios
- Departamento de Biología Celular, Cinvestav-IPN, Av. IPN 2508, Col. San Pedro Zacatenco, 07360, Ciudad de México, Mexico
| | - Anel E Lagunes-Guillén
- Departamento de Infectómica y Patogénesis Molecular, Cinvestav-IPN, Av. IPN 2508, Col. San Pedro Zacatenco, 07360, Ciudad de México, Mexico
| | - Bibiana Munguía-Chávez
- Departamento de Infectómica y Patogénesis Molecular, Cinvestav-IPN, Av. IPN 2508, Col. San Pedro Zacatenco, 07360, Ciudad de México, Mexico
| | - Carlos Alberto Castañón-Sánchez
- Laboratorio de Investigación Biomédica, Subdirección de Enseñanza e Investigación, Hospital Regional de Alta Especialidad de Oaxaca, Aldama S/N, San Bartolo Coyotepec, 71256, Oaxaca, Mexico
| | - Esther Orozco
- Departamento de Infectómica y Patogénesis Molecular, Cinvestav-IPN, Av. IPN 2508, Col. San Pedro Zacatenco, 07360, Ciudad de México, Mexico
| | - Juan Pedro Luna-Arias
- Departamento de Biología Celular, Cinvestav-IPN, Av. IPN 2508, Col. San Pedro Zacatenco, 07360, Ciudad de México, Mexico.
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12
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Narayanasamy RK, Castañón-Sanchez CA, Luna-Arias JP, García-Rivera G, Avendaño-Borromeo B, Labra-Barrios ML, Valdés J, Herrera-Aguirre ME, Orozco E. The Entamoeba histolytica TBP and TRF1 transcription factors are GAAC-box binding proteins, which display differential gene expression under different stress stimuli and during the interaction with mammalian cells. Parasit Vectors 2018. [PMID: 29514716 PMCID: PMC5842622 DOI: 10.1186/s13071-018-2698-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Entamoeba histolytica is the protozoan parasite responsible for human amebiasis. It causes up to 100,000 deaths worldwide each year. This parasite has two closely related basal transcription factors, the TATA-box binding protein (EhTBP) and the TBP-related factor 1 (EhTRF1). TBP binds to the canonical TATTTAAA-box, as well as to different TATA variants. TRF1 also binds to the TATTTAAA-box. However, their binding capacity to diverse core promoter elements, including the GAAC-element, and their role in gene regulation in this parasite remains unknown. METHODS EMSA experiments were performed to determine the binding capacity of recombinant TBP and TRF1 to TATA variants, GAAC and GAAC-like boxes. For the functional analysis under different stress stimuli (e.g. growth curve, serum depletion, heat-shock, and UV-irradiation) and during the interaction with mammalian cells (erythrocytes, MDCK cell monolayers, and hepatocytes of hamsters), RT-qPCR, and gene knockdown were performed. RESULTS Both transcription factors bound to the different TATA variants tested, as well as to the GAAC-boxes, suggesting that they are GAAC-box-binding proteins. The K D values determined for TBP and TRF1 for the different TATA variants and GAAC-box were in the range of 10-12 M to 10-11 M. During the death phase of growth or in serum depletion, Ehtbp mRNA levels significantly increased, whereas the mRNA level of Ehtrf1 did not change under these conditions. Ehtrf1 gene expression was negatively regulated by UV-irradiation and heat-shock stress, with no changes in Ehtbp gene expression. Moreover, Ehtrf1 gene also showed a negative regulation during erythrophagocytosis, liver abscess formation, and a transient expression level increase at the initial phase of MDCK cell destruction. Finally, the Ehtbp gene knockdown displayed a drastic decrease in the efficiency of erythrophagocytosis in G3 trophozoites. CONCLUSIONS To our knowledge, this study reveals that these basal transcription factors are able to bind multiple core promoter elements. However, their immediate change in gene expression level in response to different stimuli, as well as during the interaction with mammalian cells, and the diminishing of erythrophagocytosis by silencing the Ehtbp gene indicate the different physiological roles of these transcription factors in E. histolytica.
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Affiliation(s)
- Ravi Kumar Narayanasamy
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav-IPN), Av. Instituto Politécnico Nacional 2508, Col. San Pedro Zacatenco, C.P, 07360, Ciudad de México, Mexico
| | - Carlos Alberto Castañón-Sanchez
- Programa de Biomedicina Molecular, Escuela Nacional de Medicina y Homeopatía del Instituto Politécnico Nacional (ENMH-IPN), Guillermo Massieu Helguera 239, Col. La Escalera, C.P, 07320, Ciudad de México, Mexico.,Laboratorio de Investigación Biomédica, Subdirección de Enseñanza e Investigación, Hospital Regional de Alta Especialidad de Oaxaca, Aldama S/N, San Bartolo Coyotepec, C.P, 71256, Oaxaca, Mexico
| | - Juan Pedro Luna-Arias
- Departamento de Biología Celular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav-IPN), Av. Instituto Politécnico Nacional 2508, Col. San Pedro Zacatenco, C.P, 07360, Ciudad de México, Mexico.
| | - Guillermina García-Rivera
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav-IPN), Av. Instituto Politécnico Nacional 2508, Col. San Pedro Zacatenco, C.P, 07360, Ciudad de México, Mexico
| | - Bartolo Avendaño-Borromeo
- Departamento de Biología Celular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav-IPN), Av. Instituto Politécnico Nacional 2508, Col. San Pedro Zacatenco, C.P, 07360, Ciudad de México, Mexico
| | - María Luisa Labra-Barrios
- Departamento de Biología Celular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav-IPN), Av. Instituto Politécnico Nacional 2508, Col. San Pedro Zacatenco, C.P, 07360, Ciudad de México, Mexico
| | - Jesús Valdés
- Departamento de Bioquímica, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav-IPN), Av. Instituto Politécnico Nacional 2508, Col. San Pedro Zacatenco, C.P, 07360, Ciudad de México, Mexico
| | - María Esther Herrera-Aguirre
- Departamento de Biología Celular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav-IPN), Av. Instituto Politécnico Nacional 2508, Col. San Pedro Zacatenco, C.P, 07360, Ciudad de México, Mexico
| | - Esther Orozco
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav-IPN), Av. Instituto Politécnico Nacional 2508, Col. San Pedro Zacatenco, C.P, 07360, Ciudad de México, Mexico
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Nagaraja S, Ankri S. Utilization of Different Omic Approaches to Unravel Stress Response Mechanisms in the Parasite Entamoeba histolytica. Front Cell Infect Microbiol 2018; 8:19. [PMID: 29473019 PMCID: PMC5809450 DOI: 10.3389/fcimb.2018.00019] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 01/16/2018] [Indexed: 12/18/2022] Open
Abstract
During its life cycle, the unicellular parasite Entamoeba histolytica is challenged by a wide variety of environmental stresses, such as fluctuation in glucose concentration, changes in gut microbiota composition, and the release of oxidative and nitrosative species from neutrophils and macrophages. The best mode of survival for this parasite is to continuously adapt itself to the dynamic environment of the host. Our ability to study the stress-induced responses and adaptive mechanisms of this parasite has been transformed through the development of genomics, proteomics or metabolomics (omics sciences). These studies provide insights into different facets of the parasite's behavior in the host. However, there is a dire need for multi-omics data integration to better understand its pathogenic nature, ultimately paving the way to identify new chemotherapeutic targets against amebiasis. This review provides an integration of the most relevant omics information on the mechanisms that are used by E. histolytica to resist environmental stresses.
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Affiliation(s)
- Shruti Nagaraja
- Department of Molecular Microbiology, Ruth and Bruce Rappaport Faculty of Medicine, Technion, Haifa, Israel
| | - Serge Ankri
- Department of Molecular Microbiology, Ruth and Bruce Rappaport Faculty of Medicine, Technion, Haifa, Israel
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Hendrick HM, Welter BH, Hapstack MA, Sykes SE, Sullivan WJ, Temesvari LA. Phosphorylation of Eukaryotic Initiation Factor-2α during Stress and Encystation in Entamoeba Species. PLoS Pathog 2016; 12:e1006085. [PMID: 27930733 PMCID: PMC5179133 DOI: 10.1371/journal.ppat.1006085] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Revised: 12/22/2016] [Accepted: 11/23/2016] [Indexed: 12/21/2022] Open
Abstract
Entamoeba histolytica is an enteric pathogen responsible for amoebic dysentery and liver abscess. It alternates between the host-restricted trophozoite form and the infective environmentally-stable cyst stage. Throughout its lifecycle E. histolytica experiences stress, in part, from host immune pressure. Conversion to cysts is presumed to be a stress-response. In other systems, stress induces phosphorylation of a serine residue on eukaryotic translation initiation factor-2α (eIF2α). This inhibits eIF2α activity resulting in a general decline in protein synthesis. Genomic data reveal that E. histolytica possesses eIF2α (EheIF2α) with a conserved phosphorylatable serine at position 59 (Ser59). Thus, this pathogen may have the machinery for stress-induced translational control. To test this, we exposed cells to different stress conditions and measured the level of total and phospho-EheIF2α. Long-term serum starvation, long-term heat shock, and oxidative stress induced an increase in the level of phospho-EheIF2α, while short-term serum starvation, short-term heat shock, or glucose deprivation did not. Long-term serum starvation also caused a decrease in polyribosome abundance, which is in accordance with the observation that this condition induces phosphorylation of EheIF2α. We generated transgenic cells that overexpress wildtype EheIF2α, a non-phosphorylatable variant of eIF2α in which Ser59 was mutated to alanine (EheIF2α-S59A), or a phosphomimetic variant of eIF2α in which Ser59 was mutated to aspartic acid (EheIF2α-S59D). Consistent with the known functions of eIF2α, cells expressing wildtype or EheIF2α-S59D exhibited increased or decreased translation, respectively. Surprisingly, cells expressing EheIF2α-S59A also exhibited reduced translation. Cells expressing EheIF2α-S59D were more resistant to long-term serum starvation underscoring the significance of EheIF2α phosphorylation in managing stress. Finally, phospho-eIF2α accumulated during encystation in E. invadens, a model encystation system. Together, these data demonstrate that the eIF2α-dependent stress response system is operational in Entamoeba species. Entamoeba histolytica is the causative agent of amoebic dysentery and liver abscess and is prevalent in underdeveloped countries that lack proper sanitation. Infection is acquired by ingestion of the cyst form in contaminated food or water. During infection, the parasite experiences stress including demanding growth conditions and host immune pressure. Conversion to the infective cyst may be induced by such stress. In other organisms, stress causes a decrease in protein biosynthesis by inducing phosphorylation of eIF2α, which participates in translation initiation. We exposed E. histolytica to six different stress conditions and observed that some of these conditions (long-term serum starvation, long-term heat shock, and oxidative stress) induced an increase in the level of phospho-eIF2α. Long-term serum starvation was also accompanied by a decrease in mRNA translation. A cell line expressing a mutant version of eIF2α that behaves as a phosphomimetic exhibited decreased translation and increased survival during long-term serum starvation. Finally, phospho-eIF2α accumulated in cysts of E. invadens, a reptilian pathogen that readily encysts in vitro. Together, these data demonstrate that the eIF2α-dependent stress response system is operational in Entamoeba and may regulate encystation.
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Affiliation(s)
- Holland M. Hendrick
- Department of Biological Sciences, Clemson University Clemson, South Carolina, United States of America
- Eukaryotic Pathogens Innovation Center (EPIC) Clemson University Clemson, South Carolina, United States of America
| | - Brenda H. Welter
- Department of Biological Sciences, Clemson University Clemson, South Carolina, United States of America
- Eukaryotic Pathogens Innovation Center (EPIC) Clemson University Clemson, South Carolina, United States of America
| | - Matthew A. Hapstack
- Department of Biological Sciences, Clemson University Clemson, South Carolina, United States of America
- Eukaryotic Pathogens Innovation Center (EPIC) Clemson University Clemson, South Carolina, United States of America
| | - Steven E. Sykes
- Department of Biological Sciences, Clemson University Clemson, South Carolina, United States of America
- Eukaryotic Pathogens Innovation Center (EPIC) Clemson University Clemson, South Carolina, United States of America
| | - William J. Sullivan
- Department of Pharmacology and Toxicology Indiana University School of Medicine Indianaplois, IN United States of America
- Department of Microbiology and Immunology Indiana University School of Medicine Indianapolis, IN United States of America
| | - Lesly A. Temesvari
- Department of Biological Sciences, Clemson University Clemson, South Carolina, United States of America
- Eukaryotic Pathogens Innovation Center (EPIC) Clemson University Clemson, South Carolina, United States of America
- * E-mail:
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15
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Weber C, Koutero M, Dillies MA, Varet H, Lopez-Camarillo C, Coppée JY, Hon CC, Guillén N. Extensive transcriptome analysis correlates the plasticity of Entamoeba histolytica pathogenesis to rapid phenotype changes depending on the environment. Sci Rep 2016; 6:35852. [PMID: 27767091 PMCID: PMC5073345 DOI: 10.1038/srep35852] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Accepted: 10/06/2016] [Indexed: 01/02/2023] Open
Abstract
Amoebiasis is a human infectious disease due to the amoeba parasite Entamoeba histolytica. The disease appears in only 20% of the infections. Diversity in phenotypes may occur within the same infectious strain in the gut; for instance, parasites can be commensal (in the intestinal lumen) or pathogenic (inside the tissue). The degree of pathogenesis of clinical isolates varies greatly. These findings raise the hypothesis that genetic derivation may account for amoebic diverse phenotypes. The main goal of this study was to analyse gene expression changes of a single virulent amoebic strain in different environmental contexts where it exhibit different degrees of virulence, namely isolated from humans and maintained through animal liver passages, in contact with the human colon and short or prolonged in vitro culture. The study reveals major transcriptome changes in virulent parasites upon contact with human colon explants, including genes related to sugar metabolism, cytoskeleton rearrangement, stress responses and DNA repair. Furthermore, in long-term cultured parasites, drastic changes in gene expression for proteins with functions for proteasome and tRNA activities were found. Globally we conclude that rapid changes in gene expression rather than genetic derivation can sustain the invasive phenotype of a single virulent isolate of E. histolytica.
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Affiliation(s)
- Christian Weber
- Institut Pasteur, Cell Biology of Parasitism Unit, F-75015 Paris, France
- Inserm, U786, F-75015 Paris, France
| | - Mikael Koutero
- Institut Pasteur, Transcriptome and EpiGenome, BioMics, Center for Innovation and Technological Research, F-75015, Paris, France
| | - Marie-Agnes Dillies
- Institut Pasteur, Transcriptome and EpiGenome, BioMics, Center for Innovation and Technological Research, F-75015, Paris, France
- Institut Pasteur, Hub Bioinformatique et Biostatistique – Centre de Bioinformatique, Biostatistique et Biologie Intégrative (C3BI, USR 3756 IP CNRS) – F-75015 Paris, France
| | - Hugo Varet
- Institut Pasteur, Transcriptome and EpiGenome, BioMics, Center for Innovation and Technological Research, F-75015, Paris, France
- Institut Pasteur, Hub Bioinformatique et Biostatistique – Centre de Bioinformatique, Biostatistique et Biologie Intégrative (C3BI, USR 3756 IP CNRS) – F-75015 Paris, France
| | - Cesar Lopez-Camarillo
- Universidad Autonoma de la Ciudad de Mexico, Genomics Sciences Program, Mexico City, Mexico
| | - Jean Yves Coppée
- Institut Pasteur, Transcriptome and EpiGenome, BioMics, Center for Innovation and Technological Research, F-75015, Paris, France
| | - Chung-Chau Hon
- Institut Pasteur, Cell Biology of Parasitism Unit, F-75015 Paris, France
- Inserm, U786, F-75015 Paris, France
| | - Nancy Guillén
- Institut Pasteur, Cell Biology of Parasitism Unit, F-75015 Paris, France
- Inserm, U786, F-75015 Paris, France
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Espinosa A, Paz-Y-Miño-C G, Hackey M, Rutherford S. Entamoeba Clone-Recognition Experiments: Morphometrics, Aggregative Behavior, and Cell-Signaling Characterization. J Eukaryot Microbiol 2016; 63:384-93. [PMID: 26990199 DOI: 10.1111/jeu.12313] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2015] [Revised: 03/09/2016] [Accepted: 03/09/2016] [Indexed: 11/30/2022]
Abstract
Studies on clone- and kin-discrimination in protists have proliferated during the past decade. We report clone-recognition experiments in seven Entamoeba lineages (E. invadens IP-1, E. invadens VK-1:NS, E. terrapinae, E. moshkovskii Laredo, E. moshkovskii Snake, E. histolytica HM-1:IMSS and E. dispar). First, we characterized morphometrically each clone (length, width, and cell-surface area) and documented how they differed statistically from one another (as per single-variable or canonical-discriminant analyses). Second, we demonstrated that amebas themselves could discriminate self (clone) from different (themselves vs. other clones). In mix-cell-line cultures between closely-related (E. invadens IP-1 vs. E. invadens VK-1:NS) or distant-phylogenetic clones (E. terrapinae vs. E. moshkovskii Laredo), amebas consistently aggregated with same-clone members. Third, we identified six putative cell-signals secreted by the amebas (RasGap/Ankyrin, coronin-WD40, actin, protein kinases, heat shock 70, and ubiquitin) and which known functions in Entamoeba spp. included: cell proliferation, cell adhesion, cell movement, and stress-induced encystation. To our knowledge, this is the first multi-clone characterization of Entamoeba spp. morphometrics, aggregative behavior, and cell-signaling secretion in the context of clone-recognition. Protists allow us to study cell-cell recognition from ecological and evolutionary perspectives. Modern protistan lineages can be central to studies about the origins and evolution of multicellularity.
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Affiliation(s)
- Avelina Espinosa
- Department of Biology, Roger Williams University, Bristol, Rhode Island, USA.,New England Center for the Public Understanding of Science, Roger Williams University, Bristol, Rhode Island, USA
| | - Guillermo Paz-Y-Miño-C
- New England Center for the Public Understanding of Science, Roger Williams University, Bristol, Rhode Island, USA
| | - Meagan Hackey
- Department of Biology, Roger Williams University, Bristol, Rhode Island, USA
| | - Scott Rutherford
- Department of Environmental Science, Roger Williams University, Bristol, Rhode Island, USA
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Behera HS, Satpathy G. Characterisation and expression analysis of trophozoite and cyst proteins of Acanthamoeba spp. isolated from Acanthamoeba keratitis (AK) patient. Mol Biochem Parasitol 2016; 205:29-34. [DOI: 10.1016/j.molbiopara.2016.03.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Revised: 02/23/2016] [Accepted: 03/22/2016] [Indexed: 10/22/2022]
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The oxygen reduction pathway and heat shock stress response are both required for Entamoeba histolytica pathogenicity. Curr Genet 2015; 62:295-300. [PMID: 26589893 DOI: 10.1007/s00294-015-0543-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Accepted: 11/11/2015] [Indexed: 10/22/2022]
Abstract
Several species belonging to the genus Entamoeba can colonize the mouth or the human gut; however, only Entamoeba histolytica is pathogenic to the host, causing the disease amoebiasis. This illness is responsible for one hundred thousand human deaths per year worldwide, affecting mainly underdeveloped countries. Throughout its entire life cycle and invasion of human tissues, the parasite is constantly subjected to stress conditions. Under in vitro culture, this microaerophilic parasite can tolerate up to 5 % oxygen concentrations; however, during tissue invasion the parasite has to cope with the higher oxygen content found in well-perfused tissues (4-14 %) and with reactive oxygen and nitrogen species derived from both host and parasite. In this work, the role of the amoebic oxygen reduction pathway (ORP) and heat shock response (HSP) are analyzed in relation to E. histolytica pathogenicity. The data suggest that in contrast with non-pathogenic E. dispar, the higher level of ORP and HSPs displayed by E. histolytica enables its survival in tissues by diminishing and detoxifying intracellular oxidants and repairing damaged proteins to allow metabolic fluxes, replication and immune evasion.
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Ghosh A, Raha S. Molecular and functional characterisation of a stress responsive cysteine protease, EhCP6 from Entamoeba histolytica. Protein Expr Purif 2015; 109:55-61. [DOI: 10.1016/j.pep.2015.02.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Revised: 02/02/2015] [Accepted: 02/03/2015] [Indexed: 11/30/2022]
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20
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Analysis of the isomerase and chaperone-like activities of an amebic PDI (EhPDI). BIOMED RESEARCH INTERNATIONAL 2015; 2015:286972. [PMID: 25695056 PMCID: PMC4324885 DOI: 10.1155/2015/286972] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/10/2014] [Revised: 11/20/2014] [Accepted: 11/24/2014] [Indexed: 12/20/2022]
Abstract
Protein disulfide isomerases (PDI) are eukaryotic oxidoreductases that catalyze the formation and rearrangement of disulfide bonds during folding of substrate proteins. Structurally, PDI enzymes share as a common feature the presence of at least one active thioredoxin-like domain. PDI enzymes are also involved in holding, refolding, and degradation of unfolded or misfolded proteins during stressful conditions. The EhPDI enzyme (a 38 kDa polypeptide with two active thioredoxin-like domains) has been used as a model to gain insights into protein folding and disulfide bond formation in E. histolytica. Here, we performed a functional complementation assay, using a ΔdsbC mutant of E. coli, to test whether EhPDI exhibits isomerase activity in vivo. Our preliminary results showed that EhPDI exhibits isomerase activity; however, further mutagenic analysis revealed significant differences in the functional role of each thioredoxin-like domain. Additional studies confirmed that EhPDI protects heat-labile enzymes against thermal inactivation, extending our knowledge about its chaperone-like activity. The characterization of EhPDI, as an oxidative folding catalyst with chaperone-like function, represents the initial step to dissect the molecular mechanisms involved in protein folding in E. histolytica.
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Bhardwaj AR, Joshi G, Kukreja B, Malik V, Arora P, Pandey R, Shukla RN, Bankar KG, Katiyar-Agarwal S, Goel S, Jagannath A, Kumar A, Agarwal M. Global insights into high temperature and drought stress regulated genes by RNA-Seq in economically important oilseed crop Brassica juncea. BMC PLANT BIOLOGY 2015; 15:9. [PMID: 25604693 PMCID: PMC4310166 DOI: 10.1186/s12870-014-0405-1] [Citation(s) in RCA: 87] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Accepted: 12/22/2014] [Indexed: 05/19/2023]
Abstract
BACKGROUND Brassica juncea var. Varuna is an economically important oilseed crop of family Brassicaceae which is vulnerable to abiotic stresses at specific stages in its life cycle. Till date no attempts have been made to elucidate genome-wide changes in its transcriptome against high temperature or drought stress. To gain global insights into genes, transcription factors and kinases regulated by these stresses and to explore information on coding transcripts that are associated with traits of agronomic importance, we utilized a combinatorial approach of next generation sequencing and de-novo assembly to discover B. juncea transcriptome associated with high temperature and drought stresses. RESULTS We constructed and sequenced three transcriptome libraries namely Brassica control (BC), Brassica high temperature stress (BHS) and Brassica drought stress (BDS). More than 180 million purity filtered reads were generated which were processed through quality parameters and high quality reads were assembled de-novo using SOAPdenovo assembler. A total of 77750 unique transcripts were identified out of which 69,245 (89%) were annotated with high confidence. We established a subset of 19110 transcripts, which were differentially regulated by either high temperature and/or drought stress. Furthermore, 886 and 2834 transcripts that code for transcription factors and kinases, respectively, were also identified. Many of these were responsive to high temperature, drought or both stresses. Maximum number of up-regulated transcription factors in high temperature and drought stress belonged to heat shock factors (HSFs) and dehydration responsive element-binding (DREB) families, respectively. We also identified 239 metabolic pathways, which were perturbed during high temperature and drought treatments. Analysis of gene ontologies associated with differentially regulated genes forecasted their involvement in diverse biological processes. CONCLUSIONS Our study provides first comprehensive discovery of B. juncea transcriptome under high temperature and drought stress conditions. Transcriptome resource generated in this study will enhance our understanding on the molecular mechanisms involved in defining the response of B. juncea against two important abiotic stresses. Furthermore this information would benefit designing of efficient crop improvement strategies for tolerance against conditions of high temperature regimes and water scarcity.
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Affiliation(s)
- Ankur R Bhardwaj
- Department of Botany, University of Delhi Main Campus, Delhi, 110007, India.
| | - Gopal Joshi
- Department of Botany, University of Delhi Main Campus, Delhi, 110007, India.
| | - Bharti Kukreja
- Department of Botany, University of Delhi Main Campus, Delhi, 110007, India.
| | - Vidhi Malik
- Department of Botany, University of Delhi Main Campus, Delhi, 110007, India.
| | - Priyanka Arora
- Department of Botany, University of Delhi Main Campus, Delhi, 110007, India.
| | - Ritu Pandey
- Department of Plant Molecular Biology, University of Delhi South Campus, Delhi, 110021, India.
| | | | | | - Surekha Katiyar-Agarwal
- Department of Plant Molecular Biology, University of Delhi South Campus, Delhi, 110021, India.
| | - Shailendra Goel
- Department of Botany, University of Delhi Main Campus, Delhi, 110007, India.
| | - Arun Jagannath
- Department of Botany, University of Delhi Main Campus, Delhi, 110007, India.
| | - Amar Kumar
- Department of Botany, University of Delhi Main Campus, Delhi, 110007, India.
| | - Manu Agarwal
- Department of Botany, University of Delhi Main Campus, Delhi, 110007, India.
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López-Rosas I, Marchat LA, Olvera BG, Guillen N, Weber C, Hernández de la Cruz O, Ruíz-García E, Astudillo-de la Vega H, López-Camarillo C. Proteomic analysis identifies endoribouclease EhL-PSP and EhRRP41 exosome protein as novel interactors of EhCAF1 deadenylase. J Proteomics 2014; 111:59-73. [PMID: 24998979 DOI: 10.1016/j.jprot.2014.06.019] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2014] [Revised: 05/31/2014] [Accepted: 06/20/2014] [Indexed: 01/17/2023]
Abstract
UNLABELLED In higher eukaryotic cells mRNA degradation initiates by poly(A) tail shortening catalyzed by deadenylases CAF1 and CCR4. In spite of the key role of mRNA turnover in gene expression regulation, the underlying mechanisms remain poorly understood in parasites. Here, we aimed to study the function of EhCAF1 and identify associated proteins in Entamoeba histolytica. By biochemical assays, we evidenced that EhCAF1 has both RNA binding and deadenylase activities in vitro. EhCAF1 was located in cytoplasmic P-bodies that increased in number and size after cellular stress induced by DNA damage, heat shock, and nitric oxide. Using pull-down assays and ESI-MS/MS mass spectrometry, we identified 15 potential EhCAF1-interacting proteins, including the endoribonuclease EhL-PSP. Remarkably, EhCAF1 colocalized with EhL-PSP in cytoplasmic P-bodies in trophozoites. Bioinformatic analysis of EhL-PSP network proteins predicts a potential interaction with EhRRP41 exosome protein. Consistently, we evidenced that EhL-PSP colocalizes and physically interacts with EhRRP41. Strikingly, EhRRP41 did not coimmunoprecipitate EhCAF1, suggesting the existence of two EhL-PSP-containing complexes. In conclusion, our results showed novel interactions between mRNA degradation proteins and evidenced for the first time that EhCAF1 is a functional deadenylase that interacts with EhL-PSP endoribonuclease in P-bodies, while EhL-PSP interacts with EhRRP41 exosome protein in this early-branched eukaryote. BIOLOGICAL SIGNIFICANCE This study provides evidences for the functional deadenylase activity of EhCAF1 and shows a link between different mRNA degradation proteins in E. histolytica. By proteomic tools and pull down assays, we evidenced that EhCAF1 interacts with the putative endoribonuclease EhL-PSP, which in turn interacts with exosome EhRRP41 protein. Our data suggest for the first time the presence of two complexes, one containing the endoribonuclease EhL-PSP and the deadenylase EhCAF1 in P-bodies; and another containing the endoribonuclease EhL-PSP and the exosome EhRRP41 exoribonuclease. Overall, these results provide novel data that may help to understand mRNA decay mechanisms in this parasite.
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Affiliation(s)
- Itzel López-Rosas
- Autonomous University of Mexico City, Genomics Sciences Program, Mexico City, Mexico; Biotechnology Program, National School of Medicine and Homeopathy, National Polytechnic Institute, Mexico City, Mexico
| | - Laurence A Marchat
- Biotechnology Program, National School of Medicine and Homeopathy, National Polytechnic Institute, Mexico City, Mexico; Institutional Program of Molecular Biomedicine, National School of Medicine and Homeopathy, National Polytechnic Institute, Mexico City, Mexico
| | - Beatriz Gallo Olvera
- Biotechnology Program, National School of Medicine and Homeopathy, National Polytechnic Institute, Mexico City, Mexico; Institutional Program of Molecular Biomedicine, National School of Medicine and Homeopathy, National Polytechnic Institute, Mexico City, Mexico
| | - Nancy Guillen
- Unit of Cell Biology for Parasitism, Pasteur Institute, Paris, France; INSERM U786, Paris, France
| | - Christian Weber
- Unit of Cell Biology for Parasitism, Pasteur Institute, Paris, France; INSERM U786, Paris, France
| | | | - Erika Ruíz-García
- Translational Medicine Laboratory, National Institute of Cancerology, Mexico City, Mexico
| | - Horacio Astudillo-de la Vega
- Laboratory of Translational Cancer Research and Cellular Therapy, Oncology Hospital, Medical Center Siglo XXI, Mexico City, Mexico
| | - César López-Camarillo
- Autonomous University of Mexico City, Genomics Sciences Program, Mexico City, Mexico.
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Hernández-Cuevas NA, Weber C, Hon CC, Guillen N. Gene expression profiling in Entamoeba histolytica identifies key components in iron uptake and metabolism. PLoS One 2014; 9:e107102. [PMID: 25210888 PMCID: PMC4161402 DOI: 10.1371/journal.pone.0107102] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Accepted: 08/12/2014] [Indexed: 01/25/2023] Open
Abstract
Entamoeba histolytica is an ameboid parasite that causes colonic dysentery and liver abscesses in humans. The parasite encounters dramatic changes in iron concentration during its invasion of the host, with relatively low levels in the intestinal lumen and then relatively high levels in the blood and liver. The liver notably contains sources of iron; therefore, the parasite's ability to use these sources might be relevant to its survival in the liver and thus the pathogenesis of liver abscesses. The objective of the present study was to identify factors involved in iron uptake, use and storage in E. histolytica. We compared the respective transcriptomes of E. histolytica trophozoites grown in normal medium (containing around 169 µM iron), low-iron medium (around 123 µM iron), iron-deficient medium (around 91 µM iron), and iron-deficient medium replenished with hemoglobin. The differentially expressed genes included those coding for the ATP-binding cassette transporters and major facilitator transporters (which share homology with bacterial siderophores and heme transporters) and genes involved in heme biosynthesis and degradation. Iron deficiency was associated with increased transcription of genes encoding a subset of cell signaling molecules, some of which have previously been linked to adaptation to the intestinal environment and virulence. The present study is the first to have assessed the transcriptome of E. histolytica grown under various iron concentrations. Our results provide insights into the pathways involved in iron uptake and metabolism in this parasite.
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Affiliation(s)
| | - Christian Weber
- Institut Pasteur, Unité Biologie Cellulaire du Parasitisme, Paris, France
- INSERM U786, Paris, France
| | - Chung-Chau Hon
- Institut Pasteur, Unité Biologie Cellulaire du Parasitisme, Paris, France
- INSERM U786, Paris, France
| | - Nancy Guillen
- Institut Pasteur, Unité Biologie Cellulaire du Parasitisme, Paris, France
- INSERM U786, Paris, France
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Crisóstomo-Vázquez MDP, Marevelez-Acosta VA, Flores-Luna A, Jiménez-Cardoso E. The MAK16 gene of Entamoeba histolytica and its identification in isolates from patients. THE KOREAN JOURNAL OF PARASITOLOGY 2014; 52:429-33. [PMID: 25246723 PMCID: PMC4170040 DOI: 10.3347/kjp.2014.52.4.429] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2013] [Revised: 05/28/2014] [Accepted: 06/04/2014] [Indexed: 02/02/2023]
Abstract
To identify sequences of Entamoeba histolytica associated with the development of amebic liver abscess (ALA) in hamsters, subtractive hybridization of cDNA from E. histolytica HM-1:IMSS under 2 growth conditions was performed: 1) cultured in axenic medium and 2) isolated from experimental ALA in hamsters. For this procedure, 6 sequences were obtained. Of these sequences, the mak16 gene was selected for amplification in 29 cultures of E. histolytica isolated from the feces of 10 patients with intestinal symptoms and 19 asymptomatic patients. Only 5 of the 10 isolates obtained from symptomatic patients developed ALA and amplified the mak16 gene, whereas the 19 isolates from asymptomatic patients did not amplify the mak16 gene nor did they develop ALA. Based on the results of Fisher's exact test (P<0.001), an association was inferred between the presence of the mak16 gene of E. histolytica and the ability to develop ALA in hamsters and with the patient's symptoms (P=0.02). The amplification of the mak16 gene suggests that it is an important gene in E. histolytica because it was present in the isolates from hamsters that developed liver damage.
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Affiliation(s)
| | - Víctor Alberto Marevelez-Acosta
- Hospital Infantil de México Federico Gómez, Laboratory of Parasitology Research, Dr. Márquez #162 Col. Doctores, 06720, México, D.F
| | - Andrés Flores-Luna
- Hospital Infantil de México Federico Gómez, Laboratory of Parasitology Research, Dr. Márquez #162 Col. Doctores, 06720, México, D.F
| | - Enedina Jiménez-Cardoso
- Hospital Infantil de México Federico Gómez, Laboratory of Parasitology Research, Dr. Márquez #162 Col. Doctores, 06720, México, D.F
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25
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Entamoeba histolytica adaptation to glucose starvation: a matter of life and death. Curr Opin Microbiol 2014; 20:139-45. [DOI: 10.1016/j.mib.2014.06.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2014] [Revised: 06/11/2014] [Accepted: 06/13/2014] [Indexed: 12/25/2022]
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The Entamoeba histolytica Dnmt2 homolog (Ehmeth) confers resistance to nitrosative stress. EUKARYOTIC CELL 2014; 13:494-503. [PMID: 24562908 DOI: 10.1128/ec.00031-14] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Nitric oxide (NO) has antimicrobial properties against many pathogens due to its reactivity as an S-nitrosylating agent. It inhibits many of the key enzymes that are involved in the metabolism and virulence of the parasite Entamoeba histolytica through S-nitrosylation of essential cysteine residues. Very little information is available on the mechanism of resistance to NO by pathogens in general and by this parasite in particular. Here, we report that exposure of the parasites to S-nitrosoglutathione (GSNO), an NO donor molecule, strongly reduces their viability and protein synthesis. However, the deleterious effects of NO were significantly reduced in trophozoites overexpressing Ehmeth, the cytosine-5 methyltransferase of the Dnmt2 family. Since these trophozoites also exhibited high levels of tRNA(Asp) methylation, the high levels suggested that Ehmeth-mediated tRNA(Asp) methylation is part of the resistance mechanism to NO. We previously reported that enolase, another glycolytic enzyme, binds to Ehmeth and inhibits its activity. We observed that the amount of Ehmeth-enolase complex was significantly reduced in GSNO-treated E. histolytica, which explains the aforementioned increase of tRNA methylation. Specifically, we demonstrated via site-directed mutagenesis that cysteine residues 228 and 229 of Ehmeth are susceptible to S-nitrosylation and are crucial for Ehmeth binding to enolase and for Ehmeth-mediated resistance to NO. These results indicate that Ehmeth has a central role in the response of the parasite to NO, and they contribute to the growing evidence that NO is a regulator of epigenetic mechanisms.
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27
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De Cádiz AE, Jeelani G, Nakada-Tsukui K, Caler E, Nozaki T. Transcriptome analysis of encystation in Entamoeba invadens. PLoS One 2013; 8:e74840. [PMID: 24040350 PMCID: PMC3770568 DOI: 10.1371/journal.pone.0074840] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2012] [Accepted: 08/08/2013] [Indexed: 11/23/2022] Open
Abstract
Encystation is an essential differentiation process for the completion of the life cycle of a group of intestinal protozoa including Entamoeba histolytica, the causative agent of intestinal and extraintestinal amebiasis. However, regulation of gene expression during encystation is poorly understood. To comprehensively understand the process at the molecular level, the transcriptomic profiles of E. invadens, which is a related reptilian species that causes an invasive disease similar to that of E. histolytica, was investigated during encystation. Using a custom-generated Affymetrix platform microarray, we performed time course (0.5, 2, 8, 24, 48, and 120 h) gene expression analysis of encysting E. invadens. ANOVA analysis revealed that a total of 1,528 genes showed ≥3 fold up-regulation at one or more time points, relative to the trophozoite stage. Of these modulated genes, 8% (116 genes) were up-regulated at the early time points (0.5, 2 and 8h), while 63% (962 genes) were up-regulated at the later time points (24, 48, and 120 h). Twenty nine percent (450 genes) are either up-regulated at 2 to 5 time points or constitutively up-regulated in both early and late stages. Among the up-regulated genes are the genes encoding transporters, cytoskeletal proteins, proteins involved in vesicular trafficking (small GTPases), Myb transcription factors, cysteine proteases, components of the proteasome, and enzymes for chitin biosynthesis. This study represents the first kinetic analysis of gene expression during differentiation from the invasive trophozoite to the dormant, infective cyst stage in Entamoeba. Functional analysis on individual genes and their encoded products that are modulated during encystation may lead to the discovery of targets for the development of new chemotherapeutics that interfere with stage conversion of the parasite.
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Affiliation(s)
- Aleyla Escueta De Cádiz
- Department of Parasitology, National Institute of Infectious Diseases, Tokyo, Japan
- Department of Biological Science and Environmental Studies, College of Science and Mathematics, University of the Philippines Mindanao, Davao, Philippines
| | - Ghulam Jeelani
- Department of Parasitology, National Institute of Infectious Diseases, Tokyo, Japan
| | - Kumiko Nakada-Tsukui
- Department of Parasitology, National Institute of Infectious Diseases, Tokyo, Japan
| | - Elisabet Caler
- J. Craig Venter Institute, Rockville, Maryland, United States of America
| | - Tomoyoshi Nozaki
- Department of Parasitology, National Institute of Infectious Diseases, Tokyo, Japan
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
- * E-mail:
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28
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Overexpression of specific cysteine peptidases confers pathogenicity to a nonpathogenic Entamoeba histolytica clone. mBio 2013; 4:mBio.00072-13. [PMID: 23532975 PMCID: PMC3604762 DOI: 10.1128/mbio.00072-13] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Cysteine peptidases (CPs) of Entamoeba histolytica are considered to be important pathogenicity factors. Previous studies have found that under standard axenic culture conditions, only four (ehcp-a1, ehcp-a2, ehcp-a5, and ehcp-a7) out of 35 papain-like ehcp genes present in the E. histolytica genome are expressed at high levels. Little is known about the expression of CPs in E. histolytica during amoebic liver abscess (ALA) formation. In the current study, a quantitative real-time PCR assay was developed to determine the expression of the various ehcp genes during ALA formation in animal models. Increased expression of four ehcp genes (ehcp-a3, -a4, -a10, and -c13) was detected in the gerbil and mouse models. Increased expression of another three ehcp genes (ehcp-a5, -a6, and -a7) was detected in the mouse model only, and two other ehcp genes (ehcp-b8 and -b9) showed increased expression in the gerbil model only. Trophozoites of the nonpathogenic E. histolytica HM-1:IMSS clone A1, which was unable to induce ALAs, were transfected with vectors enabling overexpression of those CPs that are expressed at high levels under culture conditions or during ALA formation. Interestingly, overexpression of ehcp-b8, -b9, and -c13 restored the pathogenic phenotype of the nonpathogenic clone A1 whereas overexpression of various other peptidase genes had no effect on the pathogenicity of this clone.
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29
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López-Rosas I, Orozco E, Marchat LA, García-Rivera G, Guillen N, Weber C, Carrillo-Tapia E, Hernández de la Cruz O, Pérez-Plasencia C, López-Camarillo C. mRNA decay proteins are targeted to poly(A)+ RNA and dsRNA-containing cytoplasmic foci that resemble P-bodies in Entamoeba histolytica. PLoS One 2012; 7:e45966. [PMID: 23029343 PMCID: PMC3454373 DOI: 10.1371/journal.pone.0045966] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2012] [Accepted: 08/23/2012] [Indexed: 01/30/2023] Open
Abstract
In higher eukaryotes, mRNA degradation and RNA-based gene silencing occur in cytoplasmic foci referred to as processing bodies (P-bodies). In protozoan parasites, the presence of P-bodies and their putative role in mRNA decay have yet to be comprehensively addressed. Identification of P-bodies might provide information on how mRNA degradation machineries evolved in lower eukaryotes. Here, we used immunofluorescence and confocal microscopy assays to investigate the cellular localization of mRNA degradation proteins in the human intestinal parasite Entamoeba histolytica and found evidence of the existence of P-bodies. Two mRNA decay factors, namely the EhXRN2 exoribonuclease and the EhDCP2 decapping enzyme, were localized in cytoplasmic foci in a pattern resembling P-body organization. Given that amoebic foci appear to be smaller and less rounded than those described in higher eukaryotes, we have named them "P-body-like structures". These foci contain additional mRNA degradation factors, including the EhCAF1 deadenylase and the EhAGO2-2 protein involved in RNA interference. Biochemical analysis revealed that EhCAF1 co-immunoprecipitated with EhXRN2 but not with EhDCP2 or EhAGO2-2, thus linking deadenylation to 5'-to-3' mRNA decay. The number of EhCAF1-containing foci significantly decreased after inhibition of transcription and translation with actinomycin D and cycloheximide, respectively. Furthermore, results of RNA-FISH assays showed that (i) EhCAF1 colocalized with poly(A)(+) RNA and (ii) during silencing of the Ehpc4 gene by RNA interference, EhAGO2-2 colocalized with small interfering RNAs in cytoplasmic foci. Our observation of decapping, deadenylation and RNA interference proteins within P-body-like foci suggests that these structures have been conserved after originating in the early evolution of eukaryotic lineages. To the best of our knowledge, this is the first study to report on the localization of mRNA decay proteins within P-body-like structures in E. histolytica. Our findings should open up opportunities for deciphering the mechanisms of mRNA degradation and RNA-based gene silencing in this deep-branching eukaryote.
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Affiliation(s)
- Itzel López-Rosas
- Programa en Ciencias Genómicas, Universidad Autónoma de la Ciudad de México, México City, México
| | - Esther Orozco
- Programa en Ciencias Genómicas, Universidad Autónoma de la Ciudad de México, México City, México
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados, Instituto Politécnico Nacional, México City, México
| | - Laurence A. Marchat
- Programa Institucional de Biomedicina Molecular y Red en Biotecnología, Escuela Nacional de Medicina y Homeopatía, Instituto Politécnico Nacional, México City, México
| | - Guillermina García-Rivera
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados, Instituto Politécnico Nacional, México City, México
| | - Nancy Guillen
- Unité Biologie Cellulaire du Parasitisme, Institut Pasteur, Paris, France
- INSERM U786, Paris, France
| | - Christian Weber
- Unité Biologie Cellulaire du Parasitisme, Institut Pasteur, Paris, France
- INSERM U786, Paris, France
| | - Eduardo Carrillo-Tapia
- Programa en Ciencias Genómicas, Universidad Autónoma de la Ciudad de México, México City, México
| | | | - Carlos Pérez-Plasencia
- Unidad de Genómica y Secuenciación Masiva, Instituto Nacional de Cancerología, México City, México
- Unidad de Biomedicina, Facultad de Estudios Superiores-Iztacala, Universidad Nacional Autónoma de México, México City, México
| | - César López-Camarillo
- Programa en Ciencias Genómicas, Universidad Autónoma de la Ciudad de México, México City, México
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30
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A detoxifying oxygen reductase in the anaerobic protozoan Entamoeba histolytica. EUKARYOTIC CELL 2012; 11:1112-8. [PMID: 22798391 DOI: 10.1128/ec.00149-12] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
We report the characterization of a bacterial-type oxygen reductase abundant in the cytoplasm of the anaerobic protozoan parasite Entamoeba histolytica. Upon host infection, E. histolytica is confronted with various oxygen tensions in the host intestine, as well as increased reactive oxygen and nitrogen species at the site of local tissue inflammation. Resistance to oxygen-derived stress thus plays an important role in the pathogenic potential of E. histolytica. The genome of E. histolytica has four genes that encode flavodiiron proteins, which are bacterial-type oxygen or nitric oxide reductases and were likely acquired by lateral gene transfer from prokaryotes. The EhFdp1 gene has higher expression in virulent than in nonvirulent Entamoeba strains and species, hinting that the response to oxidative stress may be one correlate of virulence potential. We demonstrate that EhFdp1 is abundantly expressed in the cytoplasm of E. histolytica and that the protein levels are markedly increased (up to ~5-fold) upon oxygen exposure. Additionally, we produced fully functional recombinant EhFdp1 and demonstrated that this enzyme is a specific and robust oxygen reductase but has poor nitric oxide reductase activity. This observation represents a new mechanism of oxygen resistance in the anaerobic protozoan pathogen E. histolytica.
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Wilson IW, Weedall GD, Hall N. Host-Parasite interactions in Entamoeba histolytica and Entamoeba dispar: what have we learned from their genomes? Parasite Immunol 2012; 34:90-9. [PMID: 21810102 PMCID: PMC3378717 DOI: 10.1111/j.1365-3024.2011.01325.x] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Invasive amoebiasis caused by Entamoeba histolytica is a major global health problem. Virulence is a rare outcome of infection, occurring in fewer than 1 in 10 infections. Not all strains of the parasite are equally virulent, and understanding the mechanisms and causes of virulence is an important goal of Entamoeba research. The sequencing of the genome of E. histolytica and the related avirulent species Entamoeba dispar has allowed whole-genome-scale analyses of genetic divergence and differential gene expression to be undertaken. These studies have helped elucidate mechanisms of virulence and identified genes differentially expressed in virulent and avirulent parasites. Here, we review the current status of the E. histolytica and E. dispar genomes and the findings of a number of genome-scale studies comparing parasites of different virulence.
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Affiliation(s)
- I W Wilson
- Institute of Integrative Biology, University of Liverpool, Liverpool, UK
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32
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Santi-Rocca J, Smith S, Weber C, Pineda E, Hon CC, Saavedra E, Olivos-García A, Rousseau S, Dillies MA, Coppée JY, Guillén N. Endoplasmic reticulum stress-sensing mechanism is activated in Entamoeba histolytica upon treatment with nitric oxide. PLoS One 2012; 7:e31777. [PMID: 22384074 PMCID: PMC3286455 DOI: 10.1371/journal.pone.0031777] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2011] [Accepted: 01/18/2012] [Indexed: 12/14/2022] Open
Abstract
The Endoplasmic Reticulum stores calcium and is a site of protein synthesis and modification. Changes in ER homeostasis lead to stress responses with an activation of the unfolded protein response (UPR). The Entamoeba histolytica endomembrane system is simple compared to those of higher eukaryotes, as a canonical ER is not observed. During amoebiasis, an infection of the human intestine and liver by E. histolytica, nitric oxide (NO) triggers an apoptotic-like event preceded by an impairment of energy production and a loss of important parasite pathogenic features. We address the question of how this ancient eukaryote responds to stress induced by immune components (i.e. NO) and whether stress leads to ER changes and subsequently to an UPR. Gene expression analysis suggested that NO triggers stress responses marked by (i) dramatic up-regulation of hsp genes although a bona fide UPR is absent; (ii) induction of DNA repair and redox gene expression and iii) up-regulation of glycolysis-related gene expression. Enzymology approaches demonstrate that NO directly inhibits glycolysis and enhance cysteine synthase activity. Using live imaging and confocal microscopy we found that NO dramatically provokes extensive ER fragmentation. ER fission in E. histolytica appears as a protective response against stress, as it has been recently proposed for neuron self-defense during neurologic disorders. Chronic ER stress is also involved in metabolic diseases including diabetes, where NO production reduces ER calcium levels and activates cell death. Our data highlighted unique cellular responses of interest to understand the mechanisms of parasite death during amoebiasis.
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Affiliation(s)
- Julien Santi-Rocca
- Institut Pasteur, Unité Biologie Cellulaire du Parasitisme, Paris, France.
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Katz S, Kushnir O, Tovy A, Siman Tov R, Ankri S. The Entamoeba histolytica methylated LINE-binding protein EhMLBP provides protection against heat shock. Cell Microbiol 2011; 14:58-70. [DOI: 10.1111/j.1462-5822.2011.01697.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Tovy A, Hertz R, Siman-Tov R, Syan S, Faust D, Guillen N, Ankri S. Glucose starvation boosts Entamoeba histolytica virulence. PLoS Negl Trop Dis 2011; 5:e1247. [PMID: 21829737 PMCID: PMC3149018 DOI: 10.1371/journal.pntd.0001247] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2010] [Accepted: 06/04/2011] [Indexed: 01/16/2023] Open
Abstract
The unicellular parasite, Entamoeba histolytica, is exposed to numerous adverse conditions, such as nutrient deprivation, during its life cycle stages in the human host. In the present study, we examined whether the parasite virulence could be influenced by glucose starvation (GS). The migratory behaviour of the parasite and its capability to kill mammalian cells and to lyse erythrocytes is strongly enhanced following GS. In order to gain insights into the mechanism underlying the GS boosting effects on virulence, we analyzed differences in protein expression levels in control and glucose-starved trophozoites, by quantitative proteomic analysis. We observed that upstream regulatory element 3-binding protein (URE3-BP), a transcription factor that modulates E.histolytica virulence, and the lysine-rich protein 1 (KRiP1) which is induced during liver abscess development, are upregulated by GS. We also analyzed E. histolytica membrane fractions and noticed that the Gal/GalNAc lectin light subunit LgL1 is up-regulated by GS. Surprisingly, amoebapore A (Ap-A) and cysteine proteinase A5 (CP-A5), two important E. histolytica virulence factors, were strongly down-regulated by GS. While the boosting effect of GS on E. histolytica virulence was conserved in strains silenced for Ap-A and CP-A5, it was lost in LgL1 and in KRiP1 down-regulated strains. These data emphasize the unexpected role of GS in the modulation of E.histolytica virulence and the involvement of KRiP1 and Lgl1 in this phenomenon. During infection, pathogens are exposed to different environmental stresses that are mostly the consequence of the host immune defense. The most studied of these environmental stresses are the response of pathogens to nitric oxide and to hydrogen peroxide, both produced by phagocytes. In contrast, the overall knowledge about the response of pathogens to metabolic stresses is scanty. Amebiasis is caused by the unicellular protozoan parasite Entamoeba histolytica, and has a worldwide distribution with substantial morbidity and mortality. During its journey in the host, the parasite is exposed to the host immune system and to variations in nutrient availability due to the host nutrition status and the competition with the bacterial flora of the large intestine. How E. histolytica responds to glucose starvation (GS) has never been investigated. Here, the authors report that the parasite virulence is boosted by GS. Paradoxically, two well accepted virulence factors, the amoebapore A and the cysteine protease A5 are less abundant in the glucose-starved parasites. This Accordingly, these proteins are not required for the boosting of the E. histolytica virulence, in contrast to KRiP1 and LgL1 that seem to be involved in this phenomenon.
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Affiliation(s)
- Ayala Tovy
- Department of Molecular Microbiology, The Bruce Rappaport Faculty of Medicine, Technion, Israel
| | - Rivka Hertz
- Department of Molecular Microbiology, The Bruce Rappaport Faculty of Medicine, Technion, Israel
| | - Rama Siman-Tov
- Department of Molecular Microbiology, The Bruce Rappaport Faculty of Medicine, Technion, Israel
| | - Sylvie Syan
- Institut Pasteur, Unité Biologie Cellulaire du Parasitisme, Paris, France
- Inserm, U786, Paris, France
| | - Daniela Faust
- Institut Pasteur, Unité Biologie Cellulaire du Parasitisme, Paris, France
- Inserm, U786, Paris, France
| | - Nancy Guillen
- Institut Pasteur, Unité Biologie Cellulaire du Parasitisme, Paris, France
- Inserm, U786, Paris, France
| | - Serge Ankri
- Department of Molecular Microbiology, The Bruce Rappaport Faculty of Medicine, Technion, Israel
- * E-mail:
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Abstract
Normalization has been recognized as a necessary preprocessing step in a variety of high-throughput biotechnologies. A number of normalization methods have been developed specifically for microarrays, some general and others tailored for certain experimental designs. All methods rely on assumptions about data characteristics that are expected to stay constant across samples, although some make it more explicit than others. Most methods make assumptions that certain quantities related to the biological signal of interest stay the same; this is reasonable for many experiments but usually not verifiable. Recently, several platforms have begun to include a large number of negative control probes that nonetheless cover nearly the entire range of the measured signal intensity. Using these probes as a normalization basis makes it possible to normalize without making assumptions about the behavior of the biological signal. We present a subset quantile normalization (SQN) procedure that normalizes based on the distribution of non-specific control features, without restriction on the behavior of specific signals. We illustrate the performance of this method using three different platforms and experimental settings. Compared to two other leading nonlinear normalization procedures, the SQN method preserves more biological variation after normalization while reducing the noise observed on control features. Although the illustration datasets are from microarray experiments, this method is general for all high throughput technologies that include a large set of control features that have constant expectations across samples. It does not require an equal number of features in all samples and tolerates missing data.
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Affiliation(s)
- Zhijin Wu
- Center for Statistical Sciences and Department of Community Health, Brown University, Providence, Rhode Island 02912, USA.
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Regulation of gene expression in protozoa parasites. J Biomed Biotechnol 2010; 2010:726045. [PMID: 20204171 PMCID: PMC2830571 DOI: 10.1155/2010/726045] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2009] [Revised: 11/10/2009] [Accepted: 01/08/2010] [Indexed: 12/25/2022] Open
Abstract
Infections with protozoa parasites are associated with high burdens of morbidity and mortality across the developing world. Despite extensive efforts to control the transmission of these parasites, the spread of populations resistant to drugs and the lack of effective vaccines against them contribute to their persistence as major public health problems. Parasites should perform a strict control on the expression of genes involved in their pathogenicity, differentiation, immune evasion, or drug resistance, and the comprehension of the mechanisms implicated in that control could help to develop novel therapeutic strategies. However, until now these mechanisms are poorly understood in protozoa. Recent investigations into gene expression in protozoa parasites suggest that they possess many of the canonical machineries employed by higher eukaryotes for the control of gene expression at transcriptional, posttranscriptional, and epigenetic levels, but they also contain exclusive mechanisms. Here, we review the current understanding about the regulation of gene expression in Plasmodium sp., Trypanosomatids, Entamoeba histolytica and Trichomonas vaginalis.
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Bansal D, Ave P, Kerneis S, Frileux P, Boché O, Baglin AC, Dubost G, Leguern AS, Prevost MC, Bracha R, Mirelman D, Guillén N, Labruyère E. An ex-vivo human intestinal model to study Entamoeba histolytica pathogenesis. PLoS Negl Trop Dis 2009; 3:e551. [PMID: 19936071 PMCID: PMC2777411 DOI: 10.1371/journal.pntd.0000551] [Citation(s) in RCA: 105] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2009] [Accepted: 10/19/2009] [Indexed: 11/30/2022] Open
Abstract
Amoebiasis (a human intestinal infection affecting 50 million people every year) is caused by the protozoan parasite Entamoeba histolytica. To study the molecular mechanisms underlying human colon invasion by E. histolytica, we have set up an ex vivo human colon model to study the early steps in amoebiasis. Using scanning electron microscopy and histological analyses, we have established that E. histolytica caused the removal of the protective mucus coat during the first two hours of incubation, detached the enterocytes, and then penetrated into the lamina propria by following the crypts of Lieberkühn. Significant cell lysis (determined by the release of lactodehydrogenase) and inflammation (marked by the secretion of pro-inflammatory molecules such as interleukin 1 beta, interferon gamma, interleukin 6, interleukin 8 and tumour necrosis factor) were detected after four hours of incubation. Entamoeba dispar (a closely related non-pathogenic amoeba that also colonizes the human colon) was unable to invade colonic mucosa, lyse cells or induce an inflammatory response. We also examined the behaviour of trophozoites in which genes coding for known virulent factors (such as amoebapores, the Gal/GalNAc lectin and the cysteine protease 5 (CP-A5), which have major roles in cell death, adhesion (to target cells or mucus) and mucus degradation, respectively) were silenced, together with the corresponding tissue responses. Our data revealed that the signalling via the heavy chain Hgl2 or via the light chain Lgl1 of the Gal/GalNAc lectin is not essential to penetrate the human colonic mucosa. In addition, our study demonstrates that E. histolytica silenced for CP-A5 does not penetrate the colonic lamina propria and does not induce the host's pro-inflammatory cytokine secretion. Entamoeba histolytica is the causative agent of amoebiasis, a human disease. Like other enteric infections, the lack of animal models enhances the difficulty of studying the development of amoebiasis. To date, no experimental model has been developed that reproduces the invasive intestinal amoebic lesions seen in human colon. We present the first study that examines, using human colon explants, the early steps of the human colonic barrier invasion by E. histolytica. With this ex vivo integrative model we have investigated both parasite behaviour and the human tissue response. Remarkably, in this model E. histolytica was able to cross and destroy the intestinal barrier evoking a tissue inflammatory response, while E. dispar, a non-pathogenic species, was unable to penetrate nor induce tissue responses. Furthermore, we have explored the role of three virulence factors during the invasive process, using gene-silenced E. histolytica trophozoites, particularly the kinetics of invasion, tissue destruction and induction of an early inflammatory responses. This is, to our knowledge, the first time that their role is highlighted in a complex human system. Our study provides new insights in the molecular mechanisms involved in the early steps of human colon invasion by E. histolytica.
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Affiliation(s)
- Devendra Bansal
- Institut Pasteur, Unité de Biologie Cellulaire du Parasitisme, Paris, France
- INSERM U786, Paris, France
| | - Patrick Ave
- Institut Pasteur, Unité de Recherche et d'Expertise Histotechnologie et Pathologie, Paris, France
| | - Sophie Kerneis
- Institut Pasteur, Imagopole, Plate-forme de Microscopie Ultrastructurale, Paris, France
| | - Pascal Frileux
- Hôpital Foch, Chirurgie générale et digestive, Suresnes, France
| | - Olivier Boché
- Hôpital Foch, Chirurgie générale et digestive, Suresnes, France
| | | | | | | | | | - Rivka Bracha
- Weizmann Institute, Department of Biological Chemistry, Rehovot, Israel
| | - David Mirelman
- Weizmann Institute, Department of Biological Chemistry, Rehovot, Israel
| | - Nancy Guillén
- Institut Pasteur, Unité de Biologie Cellulaire du Parasitisme, Paris, France
- INSERM U786, Paris, France
| | - Elisabeth Labruyère
- Institut Pasteur, Unité de Biologie Cellulaire du Parasitisme, Paris, France
- INSERM U786, Paris, France
- * E-mail:
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Clément-Ziza M, Malabat C, Weber C, Moszer I, Aittokallio T, Letondal C, Rousseau S. Genoscape: a Cytoscape plug-in to automate the retrieval and integration of gene expression data and molecular networks. ACTA ACUST UNITED AC 2009; 25:2617-8. [PMID: 19654116 PMCID: PMC2752617 DOI: 10.1093/bioinformatics/btp464] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Summary: Genoscape is an open-source Cytoscape plug-in that visually integrates gene expression data sets from GenoScript, a transcriptomic database, and KEGG pathways into Cytoscape networks. The generated visualisation highlights gene expression changes and their statistical significance. The plug-in also allows one to browse GenoScript or import transcriptomic data from other sources through tab-separated text files. Genoscape has been successfully used by researchers to investigate the results of gene expression profiling experiments. Availability: Genoscape is an open-source software freely available from the Genoscape webpage (http://www.pasteur.fr/recherche/unites/Gim/genoscape/). Installation instructions and tutorial can also be found at this URL. Contact:Mathieu.clement-ziza@biotec.tu-dresden.de; sandrine.rousseau@pasteur.fr Supplementary information:Supplementary data are available at Bioinformatics online.
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Weber C, Marchat LA, Guillen N, López-Camarillo C. Effects of DNA damage induced by UV irradiation on gene expression in the protozoan parasite Entamoeba histolytica. Mol Biochem Parasitol 2009; 164:165-169. [PMID: 19138709 DOI: 10.1016/j.molbiopara.2008.12.005] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2008] [Revised: 12/03/2008] [Accepted: 12/10/2008] [Indexed: 11/26/2022]
Abstract
Previously, we provided evidence for the role of E. histolytica RAD52 epistasis group genes and the EhRAD51 recombinase in DNA damage response. To identify other genes participating in DNA repair in this protozoan parasite, here we analyzed the transcriptional response to genetic damage induced by ultraviolet light (UV) using cDNA microarrays. We found that 11.6% (350 ORFs) and 17.2% (522 ORFs) of genes were modulated at 5 min and 3h after UV irradiation, respectively. Most genes were less than 2-fold changed evidencing a weak transcriptional activation. The genes encoding so-called "classical" DNA repair proteins were slightly regulated in trophozoites submitted to UV irradiation. We also observed the over-expression of genes encoding for Fe-S clusters-containing proteins, potentially involved in the stress adaptation in response to DNA damage. Several genes encoding cytoskeleton proteins were repressed suggesting that actin dynamics was impaired after UV irradiation. Our analysis highlights novel genes potentially involved in DNA damage response, and these data will contribute to further elucidation of mechanisms regulating genome integrity in this early branch protozoan.
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Affiliation(s)
- Christian Weber
- Institut Pasteur, Unité Biologie Cellulaire du Parasitisme, Paris, France
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40
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Gilchrist CA, Petri WA. Using differential gene expression to study Entamoeba histolytica pathogenesis. Trends Parasitol 2009; 25:124-31. [PMID: 19217826 DOI: 10.1016/j.pt.2008.12.007] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2008] [Revised: 11/26/2008] [Accepted: 12/04/2008] [Indexed: 12/18/2022]
Abstract
The release of the Entamoeba histolytica genome has facilitated the development of techniques to survey rapidly and to relate gene expression with biology. The association and potential contribution of differential gene expression to the life cycle and the virulence of this protozoan parasite of humans are reviewed here.
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Affiliation(s)
- Carol A Gilchrist
- Division of Infectious Diseases and International Health, Departments of Medicine, Microbiology and Pathology, University of Virginia, PO Box 801340, Charlottesville, VA 22908-1340, USA
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Marchat LA, Orozco E, Guillen N, Weber C, López-Camarillo C. Putative DEAD and DExH-box RNA helicases families in Entamoeba histolytica. Gene 2008; 424:1-10. [PMID: 18760338 DOI: 10.1016/j.gene.2008.07.042] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2007] [Revised: 10/23/2007] [Accepted: 07/24/2008] [Indexed: 11/20/2022]
Abstract
RNA helicases catalyze the unwinding of double-stranded RNA structures to perform numerous genetic processes. These enzymes are characterized by the presence of a conserved helicase domain with specific helicases motifs whose amino acid sequence allows the differentiation between DEAD and DExH-box RNA helicase families. Taking advantage of the availability of the complete genome sequence of Entamoeba histolytica, the protozoan responsible for human amoebiasis, we have performed a genomic survey for DEAD and DExH-box RNA helicases encoding genes in this organism. By extensive in silico analysis, we identified 20 EhDEAD and 13 EhDExH-box RNA helicases, which contain almost all the conserved helicase motifs. Additionally, several EhDEAD and EhDExH proteins present specific N- and C-terminal domains that could be related to subcellular localization or function. Phylogenetic studies and sequences analysis suggested that this large EhDEAD/DExH-box RNA helicases family has been generated by gene or internal regions duplication, mutation events, introns formation and motif deletions. Interestingly, EhDexh1 and EhDeaxh10 genes seem to be formed by gene fusion of two ancestral bacterial genes, a mechanism that appears to be evolutionary conserved in the eukaryotic lineage of orthologous proteins. Finally, RT-PCR assays, microarrays and proteomics data analysis showed that several EhDead are differentially expressed in relation to distinct culture conditions. These computational and experimental data provide new information on the evolution of EhDEAD/EhDExH-box RNA helicases and their potential relevance for RNA metabolism in E. histolytica.
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Affiliation(s)
- Laurence A Marchat
- ENMH-IPN, Programa Institucional de Biomedicina Molecular, México DF, Mexico
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42
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Recent insights into Entamoeba development: identification of transcriptional networks associated with stage conversion. Int J Parasitol 2008; 39:41-7. [PMID: 18938171 DOI: 10.1016/j.ijpara.2008.09.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2008] [Accepted: 09/04/2008] [Indexed: 12/11/2022]
Abstract
Entamoeba histolytica is an important human pathogen and a leading parasitic cause of death globally. The parasite life cycle alternates between the trophozoite form, which is motile and causes invasive disease and the cyst stage, which is environmentally resistant and transmits infection. Understanding the triggers that initiate stage conversion is an important yet understudied area of investigation. Recent progress in dissecting the transcriptional networks that regulate E. histolytica development is outlined in this paper.
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43
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Tazreiter M, Leitsch D, Hatzenbichler E, Mair-Scorpio GE, Steinborn R, Schreiber M, Duchêne M. Entamoeba histolytica: response of the parasite to metronidazole challenge on the levels of mRNA and protein expression. Exp Parasitol 2008; 120:403-10. [PMID: 18845147 DOI: 10.1016/j.exppara.2008.09.011] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2008] [Revised: 07/23/2008] [Accepted: 09/18/2008] [Indexed: 10/21/2022]
Abstract
Entamoeba histolytica remains a cause of significant morbidity and mortality in many countries. Although metronidazole has been used for the treatment of amoebiasis for several decades, little is known on how the amoebae react to this challenge on the levels of mRNA and protein expression. In this study, we examined their response using a focused microarray, quantitative RT-PCR, and two-dimensional gel electrophoresis (2DE). The amoebae modestly increased the levels of mRNA coding for superoxide dismutase, peroxiredoxin, ferredoxin, thioredoxin reductase, and the galactose/N-acetylgalactosamine specific lectin light and heavy chains. The mRNAs encoding actin and the 70kDa and 101kDa heat shock proteins were decreased. All the changes occured within 1h of exposition, with very little further changes. In addition, the proteome revealed only very few changes. Taken together, E. histolytica appears to make only modest mRNA and protein expression changes when confronted with an unknown chemical stress.
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Affiliation(s)
- Margit Tazreiter
- Department of Specific Prophylaxis and Tropical Medicine, Center for Physiology, Pathophysiology and Immunology, Medical University of Vienna, Kinderspitalgasse 15, A-1090 Vienna, Austria
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44
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Babosha AV. Inducible lectins and plant resistance to pathogens and abiotic stress. BIOCHEMISTRY (MOSCOW) 2008; 73:812-25. [PMID: 18707590 DOI: 10.1134/s0006297908070109] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Lectin concentration (activity) increases in plant tissues upon infection by pathogens, in response to abiotic stress, as well as during growth and development of tissues. Such a broad range of events accompanied by accumulation of lectins is indicative of their involvement in regulation of integral processes in plant cells. Data concerning the role of lectins in regulation of oxidative stress and stress-induced cytoskeleton rearrangements are presented.
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Affiliation(s)
- A V Babosha
- Tsitsin Main Botanical Garden, Russian Academy of Sciences, Moscow, 127276, Russia.
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45
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Vicente JB, Ehrenkaufer GM, Saraiva LM, Teixeira M, Singh U. Entamoeba histolytica modulates a complex repertoire of novel genes in response to oxidative and nitrosative stresses: implications for amebic pathogenesis. Cell Microbiol 2008; 11:51-69. [PMID: 18778413 DOI: 10.1111/j.1462-5822.2008.01236.x] [Citation(s) in RCA: 86] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Upon host infection, the protozoan parasite Entamoeba histolytica is confronted with reactive oxygen and nitrogen species and must survive these stresses in order to cause invasive disease. We analysed the parasite's response to oxidative and nitrosative stresses, probing the transcriptional changes of trophozoites of a pathogenic strain after a 60 min exposure to H2O2 (1 mM) or a NO donor (dipropylenetriamine-NONOate, 200 microM), using whole-genome DNA microarrays. Genes encoding reactive oxygen and nitrogen species detoxification enzymes had high transcriptional levels under basal conditions and upon exposure to both stresses. On a whole-genome level, there was significant modulation of gene expression by H2O2 (286 genes regulated) and dipropylenetriamine-NONOate (1036 genes regulated) with a significant overlap of genes modulated under both conditions (164 genes). A number of transcriptionally regulated genes were in signalling/regulatory and repair/metabolic pathways. However, the majority of genes with altered transcription encode unknown proteins, suggesting as yet unraveled response pathways in E. histolytica. Trophozoites of a non-pathogenic E. histolytica strain had a significantly muted transcriptional response to H2O2 compared with the pathogenic strain, hinting that differential response to oxidative stress may be one factor that contributes to the pathogenic potential of E. histolytica.
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Affiliation(s)
- João B Vicente
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305-5107, USA
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46
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Sarder P, Nehorai A, Davis PH, Stanley SL. Estimating gene signals from noisy microarray images. IEEE Trans Nanobioscience 2008; 7:142-53. [PMID: 18556262 DOI: 10.1109/tnb.2008.2000745] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
In oligonucleotide microarray experiments, noise is a challenging problem, as biologists now are studying their organisms not in isolation but in the context of a natural environment. In low photomultiplier tube (PMT) voltage images, weak gene signals and their interactions with the background fluorescence noise are most problematic. In addition, nonspecific sequences bind to array spots intermittently causing inaccurate measurements. Conventional techniques cannot precisely separate the foreground and the background signals. In this paper, we propose analytically based estimation technique. We assume a priori spot-shape information using a circular outer periphery with an elliptical center hole. We assume Gaussian statistics for modeling both the foreground and background signals. The mean of the foreground signal quantifies the weak gene signal corresponding to the spot, and the variance gives the measure of the undesired binding that causes fluctuation in the measurement. We propose a foreground-signal and shape-estimation algorithm using the Gibbs sampling method. We compare our developed algorithm with the existing Mann-Whitney (MW)- and expectation maximization (EM)/iterated conditional modes (ICM)-based methods. Our method outperforms the existing methods with considerably smaller mean-square error (MSE) for all signal-to-noise ratios (SNRs) in computer-generated images and gives better qualitative results in low-SNR real-data images. Our method is computationally relatively slow because of its inherent sampling operation and hence only applicable to very noisy-spot images. In a realistic example using our method, we show that the gene-signal fluctuations on the estimated foreground are better observed for the input noisy images with relatively higher undesired bindings.
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Affiliation(s)
- P Sarder
- Department of Electrical and Systems Engineering, Washington University, St. Louis, MO 63130, USA.
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47
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Zamorano A, López-Camarillo C, Orozco E, Weber C, Guillen N, Marchat LA. In silico analysis of EST and genomic sequences allowed the prediction of cis-regulatory elements for Entamoeba histolytica mRNA polyadenylation. Comput Biol Chem 2008; 32:256-263. [PMID: 18514032 DOI: 10.1016/j.compbiolchem.2008.03.019] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2007] [Revised: 03/24/2008] [Accepted: 03/24/2008] [Indexed: 10/22/2022]
Abstract
In most eukaryotic cells, the poly(A) tail at the 3'-end of messenger RNA (mRNA) is essential for nuclear export, translatability, stability and transcription termination. Poly(A) tail formation involves multi-protein complexes that interact with specific sequences in 3'-untranslated region (3'-UTR) of precursor mRNA (pre-mRNA). Here we have performed a computational analysis of a large EST and genomic sequences collection from Entamoeba histolytica, the protozoan parasite responsible for human amoebiasis, to identify conserved elements that could be involved in pre-mRNA polyadenylation. Results evidenced the presence of an AU-rich domain corresponding to the consensus UA(A/U)UU polyadenylation signal or variants, the cleavage and polyadenylation site that is generally denoted by U residue and flanked by two U-rich tracts, and a novel A-rich element. This predicted array was validated through the analysis of genomic sequences and predicted mRNA folding of genes with known polyadenylation site. The molecular organization of pre-mRNA 3'-UTR cis-regulatory elements appears to be roughly conserved through evolutionary scale, whereas the polyadenylation signal seems to be species-specific in protozoan parasites and the novel A-rich element is unique for the primitive eukaryote E. histolytica. To our knowledge, this paper is the first work about the identification of potential pre-mRNA 3'-UTR cis-regulatory sequences through in silico analysis of large sets of cDNA and genomic sequences in a protozoan parasite.
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Affiliation(s)
- Absalom Zamorano
- ENMH-IPN, Programa Institucional de Biomedicina Molecular, Guillermo Massieu Heguera #239, Ticoman, CP 07320, México, D.F., Mexico
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48
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Blazquez S, Guigon G, Weber C, Syan S, Sismeiro O, Coppe JY, Labruyre E, Guilln N. Chemotaxis ofEntamoeba histolyticatowards the pro-inflammatory cytokine TNF is based on PI3K signalling, cytoskeleton reorganization and the GalactoseN-acetylgalactosamine lectin activity. Cell Microbiol 2008; 10:1676-86. [DOI: 10.1111/j.1462-5822.2008.01158.x] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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49
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Characterization of an Entamoeba histolytica high-mobility-group box protein induced during intestinal infection. EUKARYOTIC CELL 2008; 7:1565-72. [PMID: 18658254 DOI: 10.1128/ec.00123-08] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The unicellular eukaryote Entamoeba histolytica is a human parasite that causes amebic dysentery and liver abscess. A genome-wide analysis of gene expression modulated by intestinal colonization and invasion identified an upregulated transcript that encoded a putative high-mobility-group box (HMGB) protein, EhHMGB1. We tested if EhHMGB1 encoded a functional HMGB protein and determined its role in control of parasite gene expression. Recombinant EhHMGB1 was able to bend DNA in vitro, a characteristic of HMGB proteins. Core conserved residues required for DNA bending activity in other HMGB proteins were demonstrated by mutational analysis to be essential for EhHMGB1 activity. EhHMGB1 was also able to enhance the binding of human p53 to its cognate DNA sequence in vitro, which is expected for an HMGB1 protein. Confocal microscopy, using antibodies against the recombinant protein, confirmed its nuclear localization. Overexpression of EhHMGB1 in HM1:IMSS trophozoites led to modulation of 33 transcripts involved in a variety of cellular functions. Of these, 20 were also modulated at either day 1 or day 29 in the mouse model of intestinal amebiasis. Notably, four transcripts with known roles in virulence, including two encoding Gal/GalNAc lectin light chains, were modulated in response to EhHMGB1 overexpression. We concluded that EhHMGB1 was a bona fide HMGB protein with the capacity to recapitulate part of the modulation of parasite gene expression seen during adaptation to the host intestine.
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Clark CG, Alsmark UCM, Tazreiter M, Saito-Nakano Y, Ali V, Marion S, Weber C, Mukherjee C, Bruchhaus I, Tannich E, Leippe M, Sicheritz-Ponten T, Foster PG, Samuelson J, Noël CJ, Hirt RP, Embley TM, Gilchrist CA, Mann BJ, Singh U, Ackers JP, Bhattacharya S, Bhattacharya A, Lohia A, Guillén N, Duchêne M, Nozaki T, Hall N. Structure and content of the Entamoeba histolytica genome. ADVANCES IN PARASITOLOGY 2008; 65:51-190. [PMID: 18063096 DOI: 10.1016/s0065-308x(07)65002-7] [Citation(s) in RCA: 133] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The intestinal parasite Entamoeba histolytica is one of the first protists for which a draft genome sequence has been published. Although the genome is still incomplete, it is unlikely that many genes are missing from the list of those already identified. In this chapter we summarise the features of the genome as they are currently understood and provide previously unpublished analyses of many of the genes.
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Affiliation(s)
- C G Clark
- Department of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK
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