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Thompson TA, Chahine Z, Le Roch KG. The role of long noncoding RNAs in malaria parasites. Trends Parasitol 2023; 39:517-531. [PMID: 37121862 DOI: 10.1016/j.pt.2023.03.016] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 03/16/2023] [Accepted: 03/18/2023] [Indexed: 05/02/2023]
Abstract
The human malaria parasites, including Plasmodium falciparum, persist as a major cause of global morbidity and mortality. The recent stalling of progress toward malaria elimination substantiates a need for novel interventions. Controlled gene expression is central to the parasite's numerous life cycle transformations and adaptation. With few specific transcription factors (TFs) identified, crucial roles for chromatin states and epigenetics in parasite transcription have become evident. Although many chromatin-modifying enzymes are known, less is known about which factors mediate their impacts on transcriptional variation. Like those of higher eukaryotes, long noncoding RNAs (lncRNAs) have recently been shown to have integral roles in parasite gene regulation. This review aims to summarize recent developments and key findings on the role of lncRNAs in P. falciparum.
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Affiliation(s)
- Trevor A Thompson
- Department of Molecular, Cell and Systems Biology, University of California Riverside, CA, USA
| | - Zeinab Chahine
- Department of Molecular, Cell and Systems Biology, University of California Riverside, CA, USA
| | - Karine G Le Roch
- Department of Molecular, Cell and Systems Biology, University of California Riverside, CA, USA.
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2
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Abstract
In eukaryotic organisms, noncoding RNAs (ncRNAs) have been implicated as important regulators of multifaceted biological processes, including transcriptional, posttranscriptional, and epigenetic regulation of gene expression. In recent years, it is becoming clear that protozoan parasites encode diverse ncRNA transcripts; however, little is known about their cellular functions. Recent advances in high-throughput “omic” studies identified many novel long ncRNAs (lncRNAs) in apicomplexan parasites, some of which undergo splicing, polyadenylation, and encode small proteins. To date, only a few of them are characterized, leaving a big gap in our understanding regarding their origin, mode of action, and functions in parasite biology. In this review, we focus on lncRNAs of the human malaria parasite Plasmodium falciparum and highlight their cellular functions and possible mechanisms of action.
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Affiliation(s)
- Karina Simantov
- Department of Microbiology & Molecular Genetics, The Kuvin Center for the Study of Infectious and Tropical Diseases, IMRIC, The Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Manish Goyal
- Department of Microbiology & Molecular Genetics, The Kuvin Center for the Study of Infectious and Tropical Diseases, IMRIC, The Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Ron Dzikowski
- Department of Microbiology & Molecular Genetics, The Kuvin Center for the Study of Infectious and Tropical Diseases, IMRIC, The Hebrew University-Hadassah Medical School, Jerusalem, Israel
- * E-mail:
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3
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Lodde V, Floris M, Muroni MR, Cucca F, Idda ML. Non-coding RNAs in malaria infection. WILEY INTERDISCIPLINARY REVIEWS. RNA 2022; 13:e1697. [PMID: 34651456 PMCID: PMC9286032 DOI: 10.1002/wrna.1697] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Revised: 09/02/2021] [Accepted: 09/21/2021] [Indexed: 12/31/2022]
Abstract
Malaria is one of the most severe infectious diseases affecting humans and it is caused by protozoan pathogens of the species Plasmodium (spp.). The malaria parasite Plasmodium is characterized by a complex, multistage life cycle that requires tight gene regulation which allows for host invasion and defense against host immune responses. Unfortunately, the mechanisms regulating gene expression during Plasmodium infection remain largely elusive, though several lines of evidence implicate a major involvement of non-coding RNAs (ncRNAs). The ncRNAs have been found to play a key role in regulating transcriptional and post-transcriptional events in a broad range of organisms including Plasmodium. In Plasmodium ncRNAs have been shown to regulate key events in the multistage life cycle and virulence ability. Here we review recent progress involving ncRNAs (microRNAs, long non-coding RNAs, and circular RNAs) and their role as regulators of gene expression during Plasmodium infection in human hosts with focus on the possibility of using these molecules as biomarkers for monitoring disease status. We also discuss the surprising function of ncRNAs in mediating the complex interplay between parasite and human host and future perspectives of the field. This article is categorized under: RNA in Disease and Development > RNA in Disease.
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Affiliation(s)
- Valeria Lodde
- Department of Biomedical SciencesUniversity of SassariSassariItaly
| | - Matteo Floris
- Department of Biomedical SciencesUniversity of SassariSassariItaly
| | - Maria Rosaria Muroni
- Department of Medical, Surgical, and Experimental SciencesUniversity of SassariSassariItaly
| | - Francesco Cucca
- Department of Biomedical SciencesUniversity of SassariSassariItaly
| | - Maria Laura Idda
- Institute for Genetic and Biomedical Research (IRGB), National Research Council (CNR)SassariItaly
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Parreira KS, Scarpelli P, Rezende Lima W, Garcia RS. Contribution of Transcriptome to Elucidate the Biology of Plasmodium spp. Curr Top Med Chem 2022; 22:169-187. [PMID: 35021974 DOI: 10.2174/1568026622666220111140803] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 12/22/2021] [Accepted: 12/26/2021] [Indexed: 11/22/2022]
Abstract
In the present review, we discuss some of the new technologies that have been applied to elucidate how Plasmodium spp escape from the immune system and subvert the host physiology to orchestrate the regulation of its biological pathways. Our manuscript describes how techniques such as microarray approaches, RNA-Seq and single-cell RNA sequencing have contributed to the discovery of transcripts and changed the concept of gene expression regulation in closely related malaria parasite species. Moreover, the text highlights the contributions of high-throughput RNA sequencing for the current knowledge of malaria parasite biology, physiology, vaccine target and the revelation of new players in parasite signaling.
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Affiliation(s)
| | - Pedro Scarpelli
- Departamento de Análises Clínicas e Toxicológicas, Faculdade de Ciências Farmacêuticas, Universidade de São Paulo - USP, São Paulo, Brazil
| | - Wânia Rezende Lima
- Departamento de Medicina, Instituto de Biotecnologia-Universidade Federal de Catalão
| | - R S Garcia
- Departamento de Análises Clínicas e Toxicológicas, Faculdade de Ciências Farmacêuticas, Universidade de São Paulo - USP, São Paulo, Brazil
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5
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Li Y, Baptista RP, Kissinger JC. Noncoding RNAs in Apicomplexan Parasites: An Update. Trends Parasitol 2020; 36:835-849. [DOI: 10.1016/j.pt.2020.07.006] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Revised: 06/26/2020] [Accepted: 07/18/2020] [Indexed: 12/16/2022]
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Plasmodium falciparum specific helicase 2 is a dual, bipolar helicase and is crucial for parasite growth. Sci Rep 2019; 9:1519. [PMID: 30728406 PMCID: PMC6365506 DOI: 10.1038/s41598-018-38032-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 12/19/2018] [Indexed: 12/24/2022] Open
Abstract
Human malaria infection is a major challenge across the globe and is responsible for millions of deaths annually. Rapidly emerging drug resistant strains against the new class of anti-malarial drugs are major threat to control the disease burden worldwide. Helicases are present in every organism and have important role in various nucleic acid metabolic processes. Previously we have reported the presence of three parasite specific helicases (PSH) in Plasmodium falciparum 3D7 strain. Here we present the detailed biochemical characterization of PfPSH2. PfPSH2 is DNA and RNA stimulated ATPase and is able to unwind partially duplex DNA and RNA substrates. It can translocate in both 3' to 5' and 5' to 3' directions. PfPSH2 is expressed in all the stages of intraerythrocytic development and it is localized in cytoplasm in P. falciparum 3D7 strain. The dsRNA mediated inhibition study suggests that PfPSH2 is important for the growth and survival of the parasite. This study presents the detailed characterization of PfPSH2 and lays the foundation for future development of PfPSH2 as drug target.
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Subudhi AK, Boopathi P, Middha S, Acharya J, Rao SN, Mugasimangalam RC, Sirohi P, Kochar SK, Kochar DK, Das A. A cross strain Plasmodium falciparum microarray optimized for the transcriptome analysis of Plasmodium falciparum patient derived isolates. GENOMICS DATA 2016; 9:118-25. [PMID: 27489776 PMCID: PMC4961827 DOI: 10.1016/j.gdata.2016.07.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Revised: 05/10/2016] [Accepted: 07/06/2016] [Indexed: 11/23/2022]
Abstract
Malarial parasite P. falciparum, an apicomplexan protozoan has a 23.3 MB nuclear genome and encodes ~ 5600 transcripts. The genetic diversity of the parasite within and across geographical zones is a challenge to gene expression studies which are essential for understanding of disease process, outcome and developing markers for diagnostics and prognostics. Here, we describe the strategy involved in designing a custom P. falciparum 15K array using the Agilent platform and Genotypic's Right Design methodology to study the transcriptome of Indian field isolates for which genome sequence information is limited. The array contains probes representing genome sequences of two distinct geographical isolates (i.e. 3D7 and HB3) and sub-telomeric var gene sequences of a third isolate (IT4) known to adhere in culture condition. Probes in the array have been selected based on their efficiency to detect transcripts through a 244K array experimentation. Array performance for the 15K array, was evaluated and validated using RNA materials from P. falciparum clinical isolates. A large percentage (91%) of the represented transcripts was detected from Indian P. falciparum patient isolates. Replicated probes and multiple probes representing the same gene showed perfect correlation between them suggesting good probe performance. Additional transcripts could be detected due to inclusion of unique probes representing HB3 strain transcripts. Variant surface antigen (VSA) transcripts were detected by optimized probes representing the VSA genes of three geographically distinct strains. The 15K cross strain P. falciparum array has shown good efficiency in detecting transcripts from P. falciparum parasite samples isolated from patients. The low parasite loads and presence of host RNA makes arrays a preferred platform for gene expression studies over RNA-Seq.
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Affiliation(s)
- Amit Kumar Subudhi
- Department of Biological Sciences, Birla Institute of Technology and Science (BITS), Pilani, Rajasthan, India
| | - P.A. Boopathi
- Department of Biological Sciences, Birla Institute of Technology and Science (BITS), Pilani, Rajasthan, India
| | - Sheetal Middha
- Department of Medicine, S.P. Medical College, Bikaner, Rajasthan, India
| | - Jyoti Acharya
- Department of Medicine, S.P. Medical College, Bikaner, Rajasthan, India
| | | | | | - Paramendra Sirohi
- Department of Medicine, S.P. Medical College, Bikaner, Rajasthan, India
| | - Sanjay K. Kochar
- Department of Medicine, S.P. Medical College, Bikaner, Rajasthan, India
| | | | - Ashis Das
- Department of Biological Sciences, Birla Institute of Technology and Science (BITS), Pilani, Rajasthan, India
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8
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Subudhi AK, Boopathi PA, Pandey I, Kaur R, Middha S, Acharya J, Kochar SK, Kochar DK, Das A. Disease specific modules and hub genes for intervention strategies: A co-expression network based approach for Plasmodium falciparum clinical isolates. INFECTION GENETICS AND EVOLUTION 2015; 35:96-108. [PMID: 26247716 DOI: 10.1016/j.meegid.2015.08.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Revised: 07/29/2015] [Accepted: 08/01/2015] [Indexed: 11/19/2022]
Abstract
Systems biology approaches that are based on gene expression and bioinformatics analysis have been successful in predicting the functions of many genes in Plasmodium falciparum, a protozoan parasite responsible for most of the deaths due to malaria. However, approaches that can provide information about the biological processes that are active in this parasite in vivo during complicated malaria conditions have been scarcely deployed. Here we report the analysis of a weighted gene co-expression based network for P. falciparum, from non-cerebral clinical complications. Gene expression profiles of 20 P. falciparum clinical isolates were utilized to construct the same. A total of 20 highly interacting modules were identified post network creation. In 12 of these modules, at least 10% of the member genes, were found to be differentially regulated in parasites from patient isolates showing complications, when compared with those from patients with uncomplicated disease. Enrichment analysis helped identify biological processes like oxidation-reduction, electron transport chain, protein synthesis, ubiquitin dependent catabolic processes, RNA binding and purine nucleotide metabolic processes as associated with these modules. Additionally, for each module, highly connected hub genes were identified. Detailed functional analysis of many of these, which have known annotated functions underline their importance in parasite development and survival. This suggests, that other hub genes with unknown functions may also be playing crucial roles in parasite biology, and, are potential candidates for intervention strategies.
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Affiliation(s)
- Amit Kumar Subudhi
- Department of Biological Sciences, Birla Institute of Technology and Science (BITS), Pilani, Rajasthan, India.
| | - Pon Arunachalam Boopathi
- Department of Biological Sciences, Birla Institute of Technology and Science (BITS), Pilani, Rajasthan, India.
| | - Isha Pandey
- Department of Biological Sciences, Birla Institute of Technology and Science (BITS), Pilani, Rajasthan, India.
| | - Ramandeep Kaur
- Department of Biological Sciences, Birla Institute of Technology and Science (BITS), Pilani, Rajasthan, India.
| | - Sheetal Middha
- Department of Medicine, S.P. Medical College, Bikaner, Rajasthan, India.
| | - Jyoti Acharya
- Department of Medicine, S.P. Medical College, Bikaner, Rajasthan, India.
| | - Sanjay K Kochar
- Department of Medicine, S.P. Medical College, Bikaner, Rajasthan, India.
| | - Dhanpat K Kochar
- Rajasthan University of Health Sciences, Jaipur, Rajasthan, India.
| | - Ashis Das
- Department of Biological Sciences, Birla Institute of Technology and Science (BITS), Pilani, Rajasthan, India.
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Subudhi AK, Boopathi P, Garg S, Middha S, Acharya J, Pakalapati D, Saxena V, Aiyaz M, Orekondy HB, Mugasimangalam RC, Sirohi P, Kochar SK, Kochar DK, Das A. An in vivo transcriptome data set of natural antisense transcripts from Plasmodium falciparum clinical isolates. GENOMICS DATA 2014; 2:393-5. [PMID: 26484136 PMCID: PMC4536056 DOI: 10.1016/j.gdata.2014.10.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 09/20/2014] [Accepted: 10/01/2014] [Indexed: 11/27/2022]
Abstract
Antisense transcription is pervasive among biological systems and one of the products of antisense transcription is natural antisense transcripts (NATs). Emerging evidences suggest that they are key regulators of gene expression. With the discovery of NATs in Plasmodium falciparum, it has been suggested that these might also be playing regulatory roles in this parasite. However, all the reports describing the diversity of NATs have come from parasites in culture condition except for a recent study published by us. In order to explore the in vivo diversity of NATs in P. falciparum clinical isolates, we performed a whole genome expression profiling using a strand-specific 244 K microarray that contains probes for both sense and antisense transcripts. In this report, we describe the experimental procedure and analysis thereof of the microarray data published recently in Gene Expression Omnibus (GEO) under accession number GSE44921. This published data provide a wealth of information about the prevalence of NATs in P. falciparum clinical isolates from patients with diverse malaria related disease conditions. Supplementary information about the description and interpretation of the data can be found in a recent publication by Subudhi et al. in Experimental Parasitology (2014).
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Affiliation(s)
- Amit Kumar Subudhi
- Department of Biological Sciences, Birla Institute of Technology and Science (BITS), Pilani, Rajasthan, India
| | - P.A. Boopathi
- Department of Biological Sciences, Birla Institute of Technology and Science (BITS), Pilani, Rajasthan, India
| | - Shilpi Garg
- Department of Biological Sciences, Birla Institute of Technology and Science (BITS), Pilani, Rajasthan, India
| | - Sheetal Middha
- Department of Medicine, S.P. Medical College, Bikaner, Rajasthan, India
| | - Jyoti Acharya
- Department of Medicine, S.P. Medical College, Bikaner, Rajasthan, India
| | - Deepak Pakalapati
- Department of Biological Sciences, Birla Institute of Technology and Science (BITS), Pilani, Rajasthan, India
| | - Vishal Saxena
- Department of Biological Sciences, Birla Institute of Technology and Science (BITS), Pilani, Rajasthan, India
| | | | | | | | - Paramendra Sirohi
- Department of Medicine, S.P. Medical College, Bikaner, Rajasthan, India
| | - Sanjay K. Kochar
- Department of Medicine, S.P. Medical College, Bikaner, Rajasthan, India
| | | | - Ashis Das
- Department of Biological Sciences, Birla Institute of Technology and Science (BITS), Pilani, Rajasthan, India
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10
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Boopathi PA, Subudhi AK, Garg S, Middha S, Acharya J, Pakalapati D, Saxena V, Aiyaz M, Chand B, Mugasimangalam RC, Kochar SK, Sirohi P, Kochar DK, Das A. Dataset of natural antisense transcripts in P. vivax clinical isolates derived using custom designed strand-specific microarray. GENOMICS DATA 2014; 2:199-201. [PMID: 26484095 PMCID: PMC4535868 DOI: 10.1016/j.gdata.2014.06.024] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 05/12/2014] [Revised: 06/18/2014] [Accepted: 06/19/2014] [Indexed: 02/01/2023]
Abstract
Natural antisense transcripts (NATs) have been detected in many organisms and shown to regulate gene expression. Similarly, NATs have also been observed in malaria parasites with most studies focused on Plasmodium falciparum. There were no reports on the presence of NATs in Plasmodium vivax, which has also been shown to cause severe malaria like P. falciparum, until a recent study published by us. To identify in vivo prevalence of antisense transcripts in P. vivax clinical isolates, we performed whole genome expression profiling using a custom designed strand-specific microarray that contains probes for both sense and antisense strands. Here we describe the experimental methods and analysis of the microarray data available in Gene Expression Omnibus (GEO) under GSE45165. Our data provides a resource for exploring the presence of antisense transcripts in P. vivax isolated from patients showing varying clinical symptoms. Related information about the description and interpretation of the data can be found in a recent publication by Boopathi and colleagues in Infection, Genetics and Evolution 2013.
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Affiliation(s)
- P A Boopathi
- Department of Biological Sciences, Birla Institute of Technology and Science (BITS), Pilani, Rajasthan, India
| | - Amit Kumar Subudhi
- Department of Biological Sciences, Birla Institute of Technology and Science (BITS), Pilani, Rajasthan, India
| | - Shilpi Garg
- Department of Biological Sciences, Birla Institute of Technology and Science (BITS), Pilani, Rajasthan, India
| | - Sheetal Middha
- Department of Medicine, Sardar Patel Medical College, Bikaner, Rajasthan, India
| | - Jyoti Acharya
- Department of Medicine, Sardar Patel Medical College, Bikaner, Rajasthan, India
| | - Deepak Pakalapati
- Department of Biological Sciences, Birla Institute of Technology and Science (BITS), Pilani, Rajasthan, India
| | - Vishal Saxena
- Department of Biological Sciences, Birla Institute of Technology and Science (BITS), Pilani, Rajasthan, India
| | | | - Bipin Chand
- Genotypic Technology Pvt. Ltd., Bangalore, India
| | | | - Sanjay K Kochar
- Department of Medicine, Sardar Patel Medical College, Bikaner, Rajasthan, India
| | - Parmendra Sirohi
- Department of Medicine, Sardar Patel Medical College, Bikaner, Rajasthan, India
| | - Dhanpat K Kochar
- Rajasthan University of Health Sciences, Jaipur, Rajasthan, India
| | - Ashis Das
- Department of Biological Sciences, Birla Institute of Technology and Science (BITS), Pilani, Rajasthan, India
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