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Komaki-Yasuda K, Kano S. The RNA-binding KH-domain in the unique transcription factor of the malaria parasite is responsible for its transcriptional regulatory activity. PLoS One 2023; 18:e0296165. [PMID: 38128025 PMCID: PMC10734933 DOI: 10.1371/journal.pone.0296165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 12/07/2023] [Indexed: 12/23/2023] Open
Abstract
To date, only a small number of regulatory transcription factors have been predicted from the genome of Plasmodium and Apicomplexan parasites. We previously identified a nuclear factor named Prx regulatory element-binding protein (PREBP) from Plasmodium falciparum. PREBP had been suggested to bind to the cis-element in the promoter of an antioxidant pf1-cys-prx gene, thereby promoting the expression of downstream genes. PREBP has 4 putative K homology (KH) domains, which are known to bind RNA and single-stranded DNA. In this study, to understand the detailed action of PREBP in parasite cells, we first observed that in living parasite cells, PREBP was localized in the nucleus in the trophozoite and schizont stages, in which the expression of the target pf1-cys-prx was enhanced. The interaction of PREBP and the cis-element of pf1-cys-prx in the parasite cells was also confirmed. Further, the activities of PREBP deletion mutants were analyzed, and regions with repeated KH domains in PREBP seemed to be responsible for the recognition of the cis-element. These results led us to hypothesize that Plasmodium and other Apicomplexan parasites might have a transcription factor family with KH domains. Bioinformatic analysis revealed a putative ortholog group including PREBP and several Plasmodium and Apicomplexan factors with KH domains. One of the P. falciparum-derived factors, which were included in the putative ortholog group, was found to be localized at the nucleus in the trophozoite stage, indicating that it might be a novel transcription factor. The discovery of PREBP and putative transcription factors with KH domains suggested that multi-functional proteins with KH domains possibly evolved in the Apicomplexan organisms. They might play key roles in transcriptional regulatory processes that are essential for living organisms and may even represent unique drug targets for malaria therapy.
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Affiliation(s)
- Kanako Komaki-Yasuda
- Research Institute, National Center for Global Health and Medicine, Shinjuku-ku, Tokyo, Japan
| | - Shigeyuki Kano
- Research Institute, National Center for Global Health and Medicine, Shinjuku-ku, Tokyo, Japan
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2
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Shang X, Wang C, Fan Y, Guo G, Wang F, Zhao Y, Sheng F, Tang J, He X, Yu X, Zhang M, Zhu G, Yin S, Mu J, Culleton R, Cao J, Jiang M, Zhang Q. OUP accepted manuscript. Nucleic Acids Res 2022; 50:3413-3431. [PMID: 35288749 PMCID: PMC8989538 DOI: 10.1093/nar/gkac176] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 03/03/2022] [Accepted: 03/05/2022] [Indexed: 11/13/2022] Open
Abstract
Heterochromatin-associated gene silencing controls multiple physiological processes in malaria parasites, however, little is known concerning the regulatory network and cis-acting sequences involved in the organization of heterochromatin and how they modulate heterochromatic gene expression. Based on systematic profiling of genome-wide occupancy of eighteen Apicomplexan AP2 transcription factors by ChIP-seq analysis, we identify and characterize eight heterochromatin-associated factors (PfAP2-HFs), which exhibit preferential enrichment within heterochromatic regions but with differential coverage profiles. Although these ApiAP2s target euchromatic gene loci via specific DNA motifs, they are likely integral components of heterochromatin independent of DNA motif recognition. Systematic knockout screenings of ApiAP2 factors coupled with RNA-seq transcriptomic profiling revealed three activators and three repressors of heterochromatic gene expression including four PfAP2-HFs. Notably, expression of virulence genes is either completely silenced or significantly reduced upon the depletion of PfAP2-HC. Integrated multi-omics analyses reveal autoregulation and feed-forward loops to be common features of the ApiAP2 regulatory network, in addition to the occurrence of dynamic interplay between local chromatin structure and ApiAP2s in transcriptional control. Collectively, this study provides a valuable resource describing the genome-wide landscape of the ApiAP2 family and insights into functional divergence and cooperation within this family during the blood-stage development of malaria parasites.
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Affiliation(s)
| | | | | | | | - Fei Wang
- Laboratory of Molecular Parasitology, Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Tongji Hospital; Clinical Center for Brain and Spinal Cord Research, School of Medicine, Tongji University, Shanghai 200092, China
| | - Yuemeng Zhao
- Laboratory of Molecular Parasitology, Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Tongji Hospital; Clinical Center for Brain and Spinal Cord Research, School of Medicine, Tongji University, Shanghai 200092, China
| | - Fei Sheng
- Laboratory of Molecular Parasitology, Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Tongji Hospital; Clinical Center for Brain and Spinal Cord Research, School of Medicine, Tongji University, Shanghai 200092, China
| | - Jianxia Tang
- National Health Commission Key Laboratory of Parasitic Disease Control and Prevention, Jiangsu Provincial Key Laboratory on Parasite and Vector Control Technology, Jiangsu Institute of Parasitic Diseases, Wuxi, 214064, China
| | - Xiaoqin He
- National Health Commission Key Laboratory of Parasitic Disease Control and Prevention, Jiangsu Provincial Key Laboratory on Parasite and Vector Control Technology, Jiangsu Institute of Parasitic Diseases, Wuxi, 214064, China
| | - Xinyu Yu
- National Health Commission Key Laboratory of Parasitic Disease Control and Prevention, Jiangsu Provincial Key Laboratory on Parasite and Vector Control Technology, Jiangsu Institute of Parasitic Diseases, Wuxi, 214064, China
| | - Meihua Zhang
- National Health Commission Key Laboratory of Parasitic Disease Control and Prevention, Jiangsu Provincial Key Laboratory on Parasite and Vector Control Technology, Jiangsu Institute of Parasitic Diseases, Wuxi, 214064, China
| | - Guoding Zhu
- National Health Commission Key Laboratory of Parasitic Disease Control and Prevention, Jiangsu Provincial Key Laboratory on Parasite and Vector Control Technology, Jiangsu Institute of Parasitic Diseases, Wuxi, 214064, China
| | - Shigang Yin
- Laboratory of Neurological Diseases and Brain Function, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Jianbing Mu
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20892-8132, USA
| | - Richard Culleton
- Division of Molecular Parasitology, Proteo-Science Centre, Ehime University, Matsuyama, Ehime 790-8577, Japan
| | - Jun Cao
- Correspondence may also be addressed to Jun Cao. Tel: +05 10 6878 1007;
| | - Mei Jiang
- Correspondence may also be addressed to Mei Jiang. Tel: +86 21 6598 5138;
| | - Qingfeng Zhang
- To whom correspondence should be addressed. Tel: +86 21 6598 5138;
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3
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Tang J, Chisholm SA, Yeoh LM, Gilson PR, Papenfuss AT, Day KP, Petter M, Duffy MF. Histone modifications associated with gene expression and genome accessibility are dynamically enriched at Plasmodium falciparum regulatory sequences. Epigenetics Chromatin 2020; 13:50. [PMID: 33225957 PMCID: PMC7682024 DOI: 10.1186/s13072-020-00365-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 09/29/2020] [Indexed: 12/15/2022] Open
Abstract
Background The malaria parasite Plasmodium falciparum has an unusually euchromatic genome with poorly conserved positioning of nucleosomes in intergenic sequences and poorly understood mechanisms of gene regulation. Variant histones and histone modifications determine nucleosome stability and recruit trans factors, but their combinatorial contribution to gene regulation is unclear. Results Here, we show that the histone H3 acetylations H3K18ac and H3K27ac and the variant histone Pf H2A.Z are enriched together at regulatory sites upstream of genes. H3K18ac and H3K27ac together dynamically mark regulatory regions of genes expressed during the asexual life cycle. In contrast, H3K4me1 is depleted in intergenic sequence and dynamically depleted upstream of expressed genes. The temporal pattern of H3K27ac and H3K18ac enrichment indicates that they accumulate during S phase and mitosis and are retained at regulatory sequences until at least G1 phase and after cessation of expression of the cognate genes. We integrated our ChIPseq data with existing datasets to show that in schizont stages H3K18ac, H3K27ac and Pf H2A.Z colocalise with the transcription factor PfAP2-I and the bromodomain protein PfBDP1 and are enriched at stably positioned nucleosomes within regions of exposed DNA at active transcriptional start sites. Using transient transfections we showed that sequences enriched with colocalised H3K18ac, H3K27ac and Pf H2A.Z possess promoter activity in schizont stages, but no enhancer-like activity. Conclusions The dynamic H3 acetylations define P. falciparum regulatory sequences and contribute to gene activation. These findings expand the knowledge of the chromatin landscape that regulates gene expression in P. falciparum.
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Affiliation(s)
- Jingyi Tang
- Department of Medicine, The University of Melbourne, Royal Melbourne Hospital, Parkville, VIC, 3050, Australia.,School of Medicine, Faculty of Health, Deakin University, Geelong Waurn Ponds Campus, Waurn Ponds, VIC, 3216, Australia
| | - Scott A Chisholm
- School of BioSciences, The University of Melbourne, Parkville, VIC, 3052, Australia.,Bio21 Institute, Parkville, VIC, 3052, Australia
| | - Lee M Yeoh
- Bio21 Institute, Parkville, VIC, 3052, Australia.,Peter Doherty Institute, Melbourne, VIC, 3000, Australia.,Department of Microbiology and Immunology, The University of Melbourne, Victoria, 3000, Australia
| | - Paul R Gilson
- Macfarlane Burnet Institute for Medical Research and Public Health, Melbourne, VIC, 3004, Australia.,Monash University, Melbourne, VIC, 3800, Australia
| | - Anthony T Papenfuss
- Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.,Department of Mathematics and Statistics, University of Melbourne, Victoria, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia.,Sir Peter MacCallum, Department of Oncology, University of Melbourne, Parkville, VIC, Australia
| | - Karen P Day
- Bio21 Institute, Parkville, VIC, 3052, Australia.,Peter Doherty Institute, Melbourne, VIC, 3000, Australia.,Department of Microbiology and Immunology, The University of Melbourne, Victoria, 3000, Australia
| | - Michaela Petter
- Department of Medicine, The University of Melbourne, Royal Melbourne Hospital, Parkville, VIC, 3050, Australia.,Erlangen University, 91054, Erlangen, Germany
| | - Michael F Duffy
- Department of Medicine, The University of Melbourne, Royal Melbourne Hospital, Parkville, VIC, 3050, Australia. .,Bio21 Institute, Parkville, VIC, 3052, Australia. .,Peter Doherty Institute, Melbourne, VIC, 3000, Australia. .,Department of Microbiology and Immunology, The University of Melbourne, Victoria, 3000, Australia.
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4
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Ubhe S, Rawat M, Verma S, Anamika K, Karmodiya K. Genome-wide identification of novel intergenic enhancer-like elements: implications in the regulation of transcription in Plasmodium falciparum. BMC Genomics 2017; 18:656. [PMID: 28836940 PMCID: PMC5569477 DOI: 10.1186/s12864-017-4052-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Accepted: 08/11/2017] [Indexed: 01/28/2023] Open
Abstract
Background The molecular mechanisms of transcriptional regulation are poorly understood in Plasmodium falciparum. In addition, most of the genes in Plasmodium falciparum are transcriptionally poised and only a handful of cis-regulatory elements are known to operate in transcriptional regulation. Here, we employed an epigenetic signature based approach to identify significance of previously uncharacterised intergenic regions enriched with histone modification marks leading to discovery of enhancer-like elements. Results We found that enhancer-like elements are significantly enriched with H3K4me1, generate unique non-coding bi-directional RNAs and majority of them can function as cis-regulators. Furthermore, functional enhancer reporter assay demonstrates that the enhancer-like elements regulate transcription of target genes in Plasmodium falciparum. Our study also suggests that the Plasmodium genome segregates functionally related genes into discrete housekeeping and pathogenicity/virulence clusters, presumably for robust transcriptional control of virulence/pathogenicity genes. Conclusions This report contributes to the understanding of parasite regulatory genomics by identification of enhancer-like elements, defining their epigenetic and transcriptional features and provides a resource of functional cis-regulatory elements that may give insights into the virulence/pathogenicity of Plasmodium falciparum. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-4052-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Suyog Ubhe
- Department of Biology, Indian Institute of Science Education and Research, Pashan, Pune, 411008, India
| | - Mukul Rawat
- Department of Biology, Indian Institute of Science Education and Research, Pashan, Pune, 411008, India
| | - Srikant Verma
- Labs, Persistent Systems Limited, Pingala - Aryabhata, Erandwane, Pune, 411004, India
| | - Krishanpal Anamika
- Labs, Persistent Systems Limited, Pingala - Aryabhata, Erandwane, Pune, 411004, India
| | - Krishanpal Karmodiya
- Department of Biology, Indian Institute of Science Education and Research, Pashan, Pune, 411008, India.
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5
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Komaki-Yasuda K, Okuwaki M, Nagata K, Kawazu SI, Kano S. Identification of a novel and unique transcription factor in the intraerythrocytic stage of Plasmodium falciparum. PLoS One 2013; 8:e74701. [PMID: 24040327 PMCID: PMC3764013 DOI: 10.1371/journal.pone.0074701] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2013] [Accepted: 08/03/2013] [Indexed: 11/18/2022] Open
Abstract
The mechanisms of stage-specific gene regulation in the malaria parasite Plasmodium falciparum are largely unclear, with only a small number of specific regulatory transcription factors (AP2 family) having been identified. In particular, the transcription factors that function in the intraerythrocytic stage remain to be elucidated. Previously, as a model case for stage-specific transcription in the P. falciparum intraerythrocytic stage, we analyzed the transcriptional regulation of pf1-cys-prx, a trophozoite/schizont-specific gene, and suggested that some nuclear factors bind specifically to the cis-element of pf1-cys-prx and enhance transcription. In the present study, we purified nuclear factors from parasite nuclear extract by 5 steps of chromatography, and identified a factor termed PREBP. PREBP is not included in the AP2 family, and is a novel protein with four K-homology (KH) domains. The KH domain is known to be found in RNA-binding or single-stranded DNA-binding proteins. PREBP is well conserved in Plasmodium species and partially conserved in phylum Apicomplexa. To evaluate the effects of PREBP overexpression, we used a transient overexpression and luciferase assay combined approach. Overexpression of PREBP markedly enhanced luciferase expression under the control of the pf1-cys-prx cis-element. These results provide the first evidence of a novel transcription factor that activates the gene expression in the malaria parasite intraerythrocytic stage. These findings enhance our understanding of the evolution of specific transcription machinery in Plasmodium and other eukaryotes.
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Affiliation(s)
- Kanako Komaki-Yasuda
- Research Institute, National Center for Global Health and Medicine, Shinjuku-ku, Tokyo, Japan
- * E-mail:
| | - Mitsuru Okuwaki
- Graduate School of Comprehensive Human Sciences and Institute of Basic Medical Sciences, University of Tsukuba, Ibaraki, Japan
| | - Kyosuke Nagata
- Graduate School of Comprehensive Human Sciences and Institute of Basic Medical Sciences, University of Tsukuba, Ibaraki, Japan
| | - Shin-ichiro Kawazu
- National Research Center for Protozoan Diseases, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Japan
| | - Shigeyuki Kano
- Research Institute, National Center for Global Health and Medicine, Shinjuku-ku, Tokyo, Japan
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6
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Gretes MC, Poole LB, Karplus PA. Peroxiredoxins in parasites. Antioxid Redox Signal 2012; 17:608-33. [PMID: 22098136 PMCID: PMC3373223 DOI: 10.1089/ars.2011.4404] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/14/2011] [Accepted: 11/18/2011] [Indexed: 12/11/2022]
Abstract
SIGNIFICANCE Parasite survival and virulence relies on effective defenses against reactive oxygen and nitrogen species produced by the host immune system. Peroxiredoxins (Prxs) are ubiquitous enzymes now thought to be central to such defenses and, as such, have potential value as drug targets and vaccine antigens. RECENT ADVANCES Plasmodial and kinetoplastid Prx systems are the most extensively studied, yet remain inadequately understood. For many other parasites our knowledge is even less well developed. Through parasite genome sequencing efforts, however, the key players are being discovered and characterized. Here we describe what is known about the biochemistry, regulation, and cell biology of Prxs in parasitic protozoa, helminths, and fungi. At least one Prx is found in each parasite with a sequenced genome, and a notable theme is the common patterns of expression, localization, and functionality among sequence-similar Prxs in related species. CRITICAL ISSUES The nomenclature of Prxs from parasites is in a state of disarray, causing confusion and making comparative inferences difficult. Here we introduce a systematic Prx naming convention that is consistent between organisms and informative about structural and evolutionary relationships. FUTURE DIRECTIONS The new nomenclature should stimulate the crossfertilization of ideas among parasitologists and with the broader redox research community. The diverse parasite developmental stages and host environments present complex systems in which to explore the variety of roles played by Prxs, with a view toward parlaying what is learned into novel therapies and vaccines that are urgently needed.
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Affiliation(s)
- Michael C. Gretes
- Department of Biochemistry & Biophysics, Oregon State University, Corvallis, Oregon
| | - Leslie B. Poole
- Department of Biochemistry, Wake Forest University School of Medicine, Winston-Salem, North Carolina
| | - P. Andrew Karplus
- Department of Biochemistry & Biophysics, Oregon State University, Corvallis, Oregon
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7
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Wong EH, Hasenkamp S, Horrocks P. Analysis of the molecular mechanisms governing the stage-specific expression of a prototypical housekeeping gene during intraerythrocytic development of P. falciparum. J Mol Biol 2011; 408:205-21. [PMID: 21354176 PMCID: PMC3081073 DOI: 10.1016/j.jmb.2011.02.043] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2010] [Revised: 02/10/2011] [Accepted: 02/17/2011] [Indexed: 01/22/2023]
Abstract
Gene expression during the intraerythrocytic development cycle of the human malarial parasite Plasmodium falciparum is subject to tight temporal control, resulting in a cascade of gene expression to meet the physiological demands of growth, replication, and reinvasion. The roles of the different molecular mechanisms that drive this temporal program of gene expression are poorly understood. Here we report the use of the bxb1 integrase system to reconstitute all aspects of the absolute and temporal control of the prototypical housekeeping gene encoding the proliferating cell nuclear antigen (Pfpcna) around an integrated luciferase reporter cassette. A quantitative analysis of the effect of the serial deletion of 5′ and 3′ genetic elements and sublethal doses of histone deacetylase inhibitors demonstrates that while the absolute control of gene expression could be perturbed, no effect on the temporal control of gene expression was observed. These data provide support for a novel model for the temporal control of potentially hundreds of genes during the intraerythrocytic development of this important human pathogen.
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Affiliation(s)
- Eleanor H. Wong
- Institute for Science and Technology in Medicine, Keele University, Staffordshire ST5 5BG, UK
- School of Medicine, Keele University, Staffordshire ST5 5BG, UK
| | - Sandra Hasenkamp
- Institute for Science and Technology in Medicine, Keele University, Staffordshire ST5 5BG, UK
| | - Paul Horrocks
- Institute for Science and Technology in Medicine, Keele University, Staffordshire ST5 5BG, UK
- School of Medicine, Keele University, Staffordshire ST5 5BG, UK
- Corresponding author. Institute for Science and Technology in Medicine, Keele University, Huxley Building, Staffordshire ST5 5BG, UK.
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8
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Chromatin-mediated epigenetic regulation in the malaria parasite Plasmodium falciparum. EUKARYOTIC CELL 2010; 9:1138-49. [PMID: 20453074 DOI: 10.1128/ec.00036-10] [Citation(s) in RCA: 88] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Malaria is a major public health problem in many developing countries, with the malignant tertian parasite Plasmodium falciparum causing the most malaria-associated mortality. Extensive research, especially with the advancement of genomics and transfection tools, has highlighted the fundamental importance of chromatin-mediated gene regulation in the developmental program of this early-branching eukaryote. The Plasmodium parasite genomes reveal the existence of both canonical and variant histones that make up the nucleosomes, as well as a full collection of conserved enzymes for chromatin remodeling and histone posttranslational modifications (PTMs). Recent studies have identified a wide array of both conserved and novel histone PTMs in P. falciparum, indicating the presence of a complex and divergent "histone code." Genome-wide analysis has begun to decipher the nucleosome landscape and histone modifications associated with the dynamic organization of chromatin structures during the parasite's life cycle. Focused studies on malaria-specific phenomena such as antigenic variation and red cell invasion pathways shed further light on the involvement of epigenetic mechanisms in these processes. Here we review our current understanding of chromatin-mediated gene regulation in malaria parasites, with specific reference to exemplar studies on antigenic variation and host cell invasion.
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9
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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: 1.8] [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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10
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Gopalakrishnan AM, López-Estraño C. Role of cis-regulatory elements on the ring-specific hrp3 promoter in the human parasite Plasmodium falciparum. Parasitol Res 2010; 106:833-45. [PMID: 20127361 DOI: 10.1007/s00436-010-1738-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2009] [Accepted: 01/04/2010] [Indexed: 11/30/2022]
Abstract
Identification of promoter elements responsible for regulation of gene expression has been hampered by the AT richness of P. falciparum intergenic regions. Nested deletions of histidine-rich protein 3 (hrp3) promoter suggested the presence of a multipartite ring-specific element. Linker scanning (LS) of this ring-specific promoter showed that the alteration of several promoter regions decreased the luciferase activity compared to the wild-type configuration, indicating that these regions played a role in gene expression. No homology was observed by comparison of putative regulatory elements of other genes identified by bioinformatic analysis with the hrp3 enhancer, implying a different mechanism of gene regulation by the hrp3 promoter. LS and deletion analysis of the 5' untranslated region (UTR) of the hrp3 suggested that this region contains elements which interact with promoter elements to regulate gene expression. Analysis of the intron in the UTR region suggested that this region does not play a role in stage specificity in the hrp3 promoter. Together, our results indicate the presence of multiple mechanisms of gene regulation in the parasite.
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11
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Horrocks P, Wong E, Russell K, Emes RD. Control of gene expression in Plasmodium falciparum - ten years on. Mol Biochem Parasitol 2008; 164:9-25. [PMID: 19110008 DOI: 10.1016/j.molbiopara.2008.11.010] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2008] [Revised: 11/25/2008] [Accepted: 11/26/2008] [Indexed: 01/24/2023]
Abstract
Ten years ago this journal published a review with an almost identical title detailing how the then recent introduction of transfection technology had advanced our understanding of the molecular control of transcriptional processes in Plasmodium falciparum, particularly in terms of promoter structure and function. In the succeeding years, sequencing of several Plasmodium spp. genomes and application of high throughput global postgenomic technologies have proven as significant, if not more, as has the ability to genetically manipulate these parasites in dissecting the molecular control of gene expression. Here we aim to review our current understanding of the control of gene expression in P. falciparum, including evidence available from other Plasmodium spp. and apicomplexan parasites. Specifically, however, we will address the current polarised debate regarding the level at which control is mediated, and attempt to identify some of the challenges this field faces in the next 10 years.
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Affiliation(s)
- Paul Horrocks
- Institute for Science and Technology in Medicine, Keele University, Staffordshire ST5 5BG, United Kingdom.
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