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Bento I, Parrington B, Pascual R, Goldberg AS, Wang E, Liu H, Zelle M, Takahashi JS, Elias JE, Mota MM, Rijo-Ferreira F. Circadian rhythms mediate malaria transmission potential. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.14.594221. [PMID: 38798622 PMCID: PMC11118478 DOI: 10.1101/2024.05.14.594221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Malaria transmission begins when infected female Anopheles mosquitos deposit Plasmodium parasites into the mammalian host's skin during a bloodmeal. The salivary gland-resident sporozoite parasites migrate to the bloodstream, subsequently invading and replicating within hepatocytes. As Anopheles mosquitos are more active at night, with a 24-hour rhythm, we investigated whether their salivary glands are under circadian control, anticipating bloodmeals and modulating sporozoite biology for host encounters. Here we show that approximately half of the mosquito salivary gland transcriptome, particularly genes essential for efficient bloodmeals such as anti-blood clotting factors, exhibits circadian rhythmic expression. Furthermore, we demonstrate that mosquitoes prefer to feed during nighttime, with the amount of blood ingested varying cyclically throughout the day. Notably, we show a substantial subset of the sporozoite transcriptome cycling throughout the day. These include genes involved in parasite motility, potentially modulating the ability to initiate infection at different times of day. Thus, although sporozoites are typically considered quiescent, our results demonstrate their transcriptional activity, revealing robust daily rhythms of gene expression. Our findings suggest a circadian evolutionary relationship between the vector, parasite and mammalian host that together modulate malaria transmission.
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2
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Lee BST, Sinha A, Dedon P, Preiser P. Charting new territory: The Plasmodium falciparum tRNA modification landscape. Biomed J 2024:100745. [PMID: 38734409 DOI: 10.1016/j.bj.2024.100745] [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: 03/26/2024] [Revised: 05/02/2024] [Accepted: 05/05/2024] [Indexed: 05/13/2024] Open
Abstract
Ribonucleoside modifications comprising the epitranscriptome are present in all organisms and all forms of RNA, including mRNA, rRNA and tRNA, the three major RNA components of the translational machinery. Of these, tRNA is the most heavily modified and the tRNA epitranscriptome has the greatest diversity of modifications. In addition to their roles in tRNA biogenesis, quality control, structure, cleavage, and codon recognition, tRNA modifications have been shown to regulate gene expression post-transcriptionally in prokaryotes and eukaryotes, including humans. However, studies investigating the impact of tRNA modifications on gene expression in the malaria parasite Plasmodium falciparum are currently scarce. Current evidence shows that the parasite has a limited capacity for transcriptional control, which points to a heavier reliance on strategies for posttranscriptional regulation such as tRNA epitranscriptome reprogramming. This review addresses the known functions of tRNA modifications in the biology of P. falciparum while highlighting the potential therapeutic opportunities and the value of using P. falciparum as a model organism for addressing several open questions related to the tRNA epitranscriptome.
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Affiliation(s)
- Benjamin Sian Teck Lee
- Antimicrobial Resistance IRG, Singapore MIT Alliance for Research and Technology, Singapore
| | - Ameya Sinha
- Antimicrobial Resistance IRG, Singapore MIT Alliance for Research and Technology, Singapore;; School of Biological Sciences, Nanyang Technological University, Singapore
| | - Peter Dedon
- Antimicrobial Resistance IRG, Singapore MIT Alliance for Research and Technology, Singapore;; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA USA.
| | - Peter Preiser
- Antimicrobial Resistance IRG, Singapore MIT Alliance for Research and Technology, Singapore;; School of Biological Sciences, Nanyang Technological University, Singapore;.
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3
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Pasupureddy R, Verma S, Goyal B, Pant A, Sharma R, Bhatt S, Vashisht K, Singh S, Saxena AK, Dixit R, Chakraborti S, Pandey KC. Understanding the complex formation of falstatin; an endogenous macromolecular inhibitor of falcipains. Int J Biol Macromol 2024; 265:130420. [PMID: 38460641 DOI: 10.1016/j.ijbiomac.2024.130420] [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: 10/31/2023] [Revised: 01/17/2024] [Accepted: 02/22/2024] [Indexed: 03/11/2024]
Abstract
Proteolytic activity constitutes a fundamental process essential for the survival of the malaria parasite and is thus highly regulated. Falstatin, a protease inhibitor of Plasmodium falciparum, tightly regulates the activity of cysteine hemoglobinases, falcipain-2 and 3 (FP2, FP3), by inhibiting FP2 through a single surface exposed loop. However, the multimeric nature of falstatin and its interaction with FP2 remained unexplored. Here we report that the N-terminal falstatin region is highly disordered, and needs chaperone activity (heat-shock protein 70, HSP70) for its folding. Protein-protein interaction assays showed a significant interaction between falstatin and HSP70. Further, characterization of the falstatin multimer through a series of biophysical techniques identified the formation of a falstatin decamer, which was extremely thermostable. Computational analysis of the falstatin decamer showed the presence of five falstatin dimers, with each dimer aligned in a head-to-tail orientation. Further, the falstatin C-terminal region was revealed to be primarily involved in the oligomerization process. Stoichiometric analysis of the FP2-falstatin multimer showed the formation of a heterooligomeric complex in a 1:1 ratio, with the participation of ten subunits of each protein. Taken together, our results report a novel protease-inhibitor complex and strengthens our understanding of the regulatory mechanisms of major plasmodium hemoglobinases.
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Affiliation(s)
- Rahul Pasupureddy
- Parasite-Host Biology Group, ICMR National Institute of Malaria Research, New Delhi, India.
| | - Sonia Verma
- Parasite-Host Biology Group, ICMR National Institute of Malaria Research, New Delhi, India; Department of Biotechnology, Noida Institute of Engineering & Technology, UP, India
| | - Bharti Goyal
- Parasite-Host Biology Group, ICMR National Institute of Malaria Research, New Delhi, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, UP, India
| | - Akansha Pant
- Parasite-Host Biology Group, ICMR National Institute of Malaria Research, New Delhi, India
| | - Ruby Sharma
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Shruti Bhatt
- Department of Biochemistry, University of Delhi South Campus, New Delhi, India.
| | - Kapil Vashisht
- Parasite-Host Biology Group, ICMR National Institute of Malaria Research, New Delhi, India
| | - Shailja Singh
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India.
| | - Ajay K Saxena
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India.
| | - Rajnikant Dixit
- Parasite-Host Biology Group, ICMR National Institute of Malaria Research, New Delhi, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, UP, India.
| | - Soumyananda Chakraborti
- Parasite-Host Biology Group, ICMR National Institute of Malaria Research, New Delhi, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, UP, India.
| | - Kailash C Pandey
- Parasite-Host Biology Group, ICMR National Institute of Malaria Research, New Delhi, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, UP, India.
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4
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Dembele L, Dara A, Maiga M, Maiga FO, Cissoko D, Djimde AA. Imidazolopiperazine (IPZ)-Induced Differential Transcriptomic Responses on Plasmodium falciparum Wild-Type and IPZ-Resistant Mutant Parasites. Genes (Basel) 2023; 14:2124. [PMID: 38136946 PMCID: PMC10743112 DOI: 10.3390/genes14122124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 11/09/2023] [Accepted: 11/16/2023] [Indexed: 12/24/2023] Open
Abstract
Imidazolopiperazine (IPZ), KAF156, a close analogue of GNF179, is a promising antimalarial candidate. IPZ is effective against Plasmodium falciparum and Plasmodium vivax clinical malaria in human with transmission blocking property in animal models and effective against liver stage parasites. Despite these excellent drug efficacy properties, in vitro parasites have shown resistance to IPZ. However, the mechanism of action and resistance of IPZ remained not fully understood. Here, we used transcriptomic analysis to elucidate mode of action of IPZs. We report, in wild-type parasites GNF179 treatment down regulated lipase enzymes, two metabolic pathways: the hydrolysis of Phosphoinositol 4,5-bipohosphate (PIP2) that produce diacyglycerol (DAG) and the cytosolic calcium Ca2+ homeostasis which are known to be essential for P. falciparum survival and proliferation, as well for membrane permeability and protein trafficking. Furthermore, in wild-type parasites, GNF179 repressed expression of Acyl CoA Synthetase, export lipase 1 and esterase enzymes. Thus, in wild-type parasites only, GNF179 treatment affected enzymes leading lipid metabolism, transport, and synthesis. Lastly, our data revealed that IPZs did not perturb known IPZ resistance genes markers pfcarl, pfact, and pfugt regulations, which are all instead possibly involved in the drug resistance that disturb membrane transport targeted by IPZ.
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Affiliation(s)
- Laurent Dembele
- Malaria Research and Training Center, Faculty of Pharmacy, Université des Sciences, des Techniques et des Technologies de Bamako (USTTB), DEAP Point G, Bamako P.O. Box 1805, Mali; (A.D.); (M.M.); (F.O.M.); (D.C.); (A.A.D.)
- African Center of Excellence in Bioinformatics (ACE), Bamako P.O. Box 1805, Mali
- Novartis Institute for Tropical Diseases, 10 Biopolis Road, #05-01 Chromos, Singapore 138670, Singapore
| | - Antoine Dara
- Malaria Research and Training Center, Faculty of Pharmacy, Université des Sciences, des Techniques et des Technologies de Bamako (USTTB), DEAP Point G, Bamako P.O. Box 1805, Mali; (A.D.); (M.M.); (F.O.M.); (D.C.); (A.A.D.)
| | - Mohamed Maiga
- Malaria Research and Training Center, Faculty of Pharmacy, Université des Sciences, des Techniques et des Technologies de Bamako (USTTB), DEAP Point G, Bamako P.O. Box 1805, Mali; (A.D.); (M.M.); (F.O.M.); (D.C.); (A.A.D.)
- African Center of Excellence in Bioinformatics (ACE), Bamako P.O. Box 1805, Mali
| | - Fatoumata O. Maiga
- Malaria Research and Training Center, Faculty of Pharmacy, Université des Sciences, des Techniques et des Technologies de Bamako (USTTB), DEAP Point G, Bamako P.O. Box 1805, Mali; (A.D.); (M.M.); (F.O.M.); (D.C.); (A.A.D.)
- African Center of Excellence in Bioinformatics (ACE), Bamako P.O. Box 1805, Mali
| | - Djeneba Cissoko
- Malaria Research and Training Center, Faculty of Pharmacy, Université des Sciences, des Techniques et des Technologies de Bamako (USTTB), DEAP Point G, Bamako P.O. Box 1805, Mali; (A.D.); (M.M.); (F.O.M.); (D.C.); (A.A.D.)
- African Center of Excellence in Bioinformatics (ACE), Bamako P.O. Box 1805, Mali
| | - Abdoulaye A. Djimde
- Malaria Research and Training Center, Faculty of Pharmacy, Université des Sciences, des Techniques et des Technologies de Bamako (USTTB), DEAP Point G, Bamako P.O. Box 1805, Mali; (A.D.); (M.M.); (F.O.M.); (D.C.); (A.A.D.)
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5
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Borba JB, de Azevedo BR, Ferreira LA, Rimoldi A, Salazar Alvarez LC, Calit J, Bargieri DY, Costa FTM, Andrade CH. Transcriptomics-Guided In Silico Drug Repurposing: Identifying New Candidates with Dual-Stage Antiplasmodial Activity. ACS OMEGA 2023; 8:34084-34090. [PMID: 37744849 PMCID: PMC10515587 DOI: 10.1021/acsomega.3c05138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 08/18/2023] [Indexed: 09/26/2023]
Abstract
In tropical and subtropical areas, malaria stands as a profound public health challenge, causing an estimated 247 million cases worldwide annually. Given the absence of a viable vaccine, the timely and effective treatment of malaria remains a critical priority. However, the growing resistance of parasites to currently utilized drugs underscores the critical need for the identification of new antimalarial therapies. Here, we aimed to identify potential new drug candidates against Plasmodium falciparum, the main causative agent of malaria, by analyzing the transcriptomes of different life stages of the parasite and identifying highly expressed genes. We searched for genes that were expressed in all stages of the parasite's life cycle, including the asexual blood stage, gametocyte stage, liver stage, and sexual stages in the insect vector, using transcriptomics data from publicly available databases. From this analysis, we found 674 overlapping genes, including 409 essential ones. By searching through drug target databases, we discovered 70 potential drug targets and 75 associated bioactive compounds. We sought to expand this analysis to similar compounds to known drugs. So, we found a list of 1557 similar compounds, which we predicted as actives and inactives using previously developed machine learning models against five life stages of Plasmodium spp. From this analysis, two compounds were selected, and the reactions were experimentally evaluated. The compounds HSP-990 and silvestrol aglycone showed potent inhibitory activity at nanomolar concentrations against the P. falciparum 3D7 strain asexual blood stage. Moreover, silvestrol aglycone exhibited low cytotoxicity in mammalian cells, transmission-blocking potential, and inhibitory activity comparable to those of established antimalarials. These findings warrant further investigation of silvestrol aglycone as a potential dual-acting antimalarial and transmission-blocking candidate for malaria control.
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Affiliation(s)
- Joyce
V. B. Borba
- Laboratory
for Molecular Modeling and Drug Design (LabMol), Faculdade de Farmacia, Universidade Federal de Goias, 74605-170 Goiânia, Goiás, Brazil
- Laboratory
of Tropical Diseases—Prof. Dr. Luiz Jacintho da Silva, Department
of Genetics Evolution, Microbiology and Immunology, University of Campinas, 13083-970 Campinas, São
Paulo, Brazil
| | - Beatriz Rosa de Azevedo
- Laboratory
for Molecular Modeling and Drug Design (LabMol), Faculdade de Farmacia, Universidade Federal de Goias, 74605-170 Goiânia, Goiás, Brazil
| | - Larissa A. Ferreira
- Laboratory
of Tropical Diseases—Prof. Dr. Luiz Jacintho da Silva, Department
of Genetics Evolution, Microbiology and Immunology, University of Campinas, 13083-970 Campinas, São
Paulo, Brazil
| | - Aline Rimoldi
- Laboratory
of Tropical Diseases—Prof. Dr. Luiz Jacintho da Silva, Department
of Genetics Evolution, Microbiology and Immunology, University of Campinas, 13083-970 Campinas, São
Paulo, Brazil
| | - Luís C. Salazar Alvarez
- Laboratory
of Tropical Diseases—Prof. Dr. Luiz Jacintho da Silva, Department
of Genetics Evolution, Microbiology and Immunology, University of Campinas, 13083-970 Campinas, São
Paulo, Brazil
| | - Juliana Calit
- Department
of Parasitology, Institute of Biomedical Sciences, University of São Paulo, 05508-000 São Paulo, São Paulo, Brazil
| | - Daniel Y. Bargieri
- Department
of Parasitology, Institute of Biomedical Sciences, University of São Paulo, 05508-000 São Paulo, São Paulo, Brazil
| | - Fabio T. M. Costa
- Laboratory
of Tropical Diseases—Prof. Dr. Luiz Jacintho da Silva, Department
of Genetics Evolution, Microbiology and Immunology, University of Campinas, 13083-970 Campinas, São
Paulo, Brazil
| | - Carolina Horta Andrade
- Laboratory
for Molecular Modeling and Drug Design (LabMol), Faculdade de Farmacia, Universidade Federal de Goias, 74605-170 Goiânia, Goiás, Brazil
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6
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Reers AB, Bautista R, McLellan J, Morales B, Garza R, Bol S, Hanson KK, Bunnik EM. Histone modification analysis reveals common regulators of gene expression in liver and blood stage merozoites of Plasmodium parasites. Epigenetics Chromatin 2023; 16:25. [PMID: 37322481 PMCID: PMC10268464 DOI: 10.1186/s13072-023-00500-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 06/06/2023] [Indexed: 06/17/2023] Open
Abstract
Gene expression in malaria parasites is subject to various layers of regulation, including histone post-translational modifications (PTMs). Gene regulatory mechanisms have been extensively studied during the main developmental stages of Plasmodium parasites inside erythrocytes, from the ring stage following invasion to the schizont stage leading up to egress. However, gene regulation in merozoites that mediate the transition from one host cell to the next is an understudied area of parasite biology. Here, we sought to characterize gene expression and the corresponding histone PTM landscape during this stage of the parasite lifecycle through RNA-seq and ChIP-seq on P. falciparum blood stage schizonts, merozoites, and rings, as well as P. berghei liver stage merozoites. In both hepatic and erythrocytic merozoites, we identified a subset of genes with a unique histone PTM profile characterized by a region of H3K4me3 depletion in their promoter. These genes were upregulated in hepatic and erythrocytic merozoites and rings, had roles in protein export, translation, and host cell remodeling, and shared a DNA motif. These results indicate that similar regulatory mechanisms may underlie merozoite formation in the liver and blood stages. We also observed that H3K4me2 was deposited in gene bodies of gene families encoding variant surface antigens in erythrocytic merozoites, which may facilitate switching of gene expression between different members of these families. Finally, H3K18me and H2K27me were uncoupled from gene expression and were enriched around the centromeres in erythrocytic schizonts and merozoites, suggesting potential roles in the maintenance of chromosomal organization during schizogony. Together, our results demonstrate that extensive changes in gene expression and histone landscape occur during the schizont-to-ring transition to facilitate productive erythrocyte infection. The dynamic remodeling of the transcriptional program in hepatic and erythrocytic merozoites makes this stage attractive as a target for novel anti-malarial drugs that may have activity against both the liver and blood stages.
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Affiliation(s)
- Ashley B Reers
- Department of Microbiology, Immunology, and Molecular Genetics, Long School of Medicine, University of Texas Health Science Center, San Antonio, TX, USA
| | - Rodriel Bautista
- Department of Microbiology, Immunology, and Molecular Genetics, Long School of Medicine, University of Texas Health Science Center, San Antonio, TX, USA
| | - James McLellan
- Department of Molecular Microbiology and Immunology and South Texas Center for Emerging Infectious Diseases, University of Texas San Antonio, San Antonio, TX, USA
| | - Beatriz Morales
- Department of Molecular Microbiology and Immunology and South Texas Center for Emerging Infectious Diseases, University of Texas San Antonio, San Antonio, TX, USA
| | - Rolando Garza
- Department of Microbiology, Immunology, and Molecular Genetics, Long School of Medicine, University of Texas Health Science Center, San Antonio, TX, USA
| | - Sebastiaan Bol
- Department of Microbiology, Immunology, and Molecular Genetics, Long School of Medicine, University of Texas Health Science Center, San Antonio, TX, USA
| | - Kirsten K Hanson
- Department of Molecular Microbiology and Immunology and South Texas Center for Emerging Infectious Diseases, University of Texas San Antonio, San Antonio, TX, USA
| | - Evelien M Bunnik
- Department of Microbiology, Immunology, and Molecular Genetics, Long School of Medicine, University of Texas Health Science Center, San Antonio, TX, USA.
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7
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Guo Y, Chen Y, Wang Y, Wu X, Zhang X, Mao W, Yu H, Guo K, Xu J, Ma L, Guo W, Hu Z, Xin M, Yao Y, Ni Z, Sun Q, Peng H. The translational landscape of bread wheat during grain development. THE PLANT CELL 2023; 35:1848-1867. [PMID: 36905284 PMCID: PMC10226598 DOI: 10.1093/plcell/koad075] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 02/09/2023] [Accepted: 02/19/2023] [Indexed: 05/30/2023]
Abstract
The dynamics of gene expression in crop grains has typically been investigated at the transcriptional level. However, this approach neglects translational regulation, a widespread mechanism that rapidly modulates gene expression to increase the plasticity of organisms. Here, we performed ribosome profiling and polysome profiling to obtain a comprehensive translatome data set of developing bread wheat (Triticum aestivum) grains. We further investigated the genome-wide translational dynamics during grain development, revealing that the translation of many functional genes is modulated in a stage-specific manner. The unbalanced translation between subgenomes is pervasive, which increases the expression flexibility of allohexaploid wheat. In addition, we uncovered widespread previously unannotated translation events, including upstream open reading frames (uORFs), downstream open reading frames (dORFs), and open reading frames (ORFs) in long noncoding RNAs, and characterized the temporal expression dynamics of small ORFs. We demonstrated that uORFs act as cis-regulatory elements that can repress or even enhance the translation of mRNAs. Gene translation may be combinatorially modulated by uORFs, dORFs, and microRNAs. In summary, our study presents a translatomic resource that provides a comprehensive and detailed overview of the translational regulation in developing bread wheat grains. This resource will facilitate future crop improvements for optimal yield and quality.
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Affiliation(s)
- Yiwen Guo
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Yongming Chen
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Yongfa Wang
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Xiaojia Wu
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Xiaoyu Zhang
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Weiwei Mao
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Hongjian Yu
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Kai Guo
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Jin Xu
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Liang Ma
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Weilong Guo
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Zhaorong Hu
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Mingming Xin
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Yingyin Yao
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Zhongfu Ni
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Qixin Sun
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Huiru Peng
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
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8
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Manjunath LE, Singh A, Som S, Eswarappa SM. Mammalian proteome expansion by stop codon readthrough. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1739. [PMID: 35570338 DOI: 10.1002/wrna.1739] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 04/11/2022] [Accepted: 04/16/2022] [Indexed: 12/20/2022]
Abstract
Recognition of a stop codon by translation machinery as a sense codon results in translational readthrough instead of termination. This recoding process, termed stop codon readthrough (SCR) or translational readthrough, is found in all domains of life including mammals. The context of the stop codon, local mRNA topology, and molecules that interact with the mRNA region downstream of the stop codon determine SCR. The products of SCR can have localization, stability, and function different from those of the canonical isoforms. In this review, we discuss how recent technological and computational advances have increased our understanding of the SCR process in the mammalian system. Based on the known molecular events that occur during SCR of multiple mRNAs, we propose transient molecular roadblocks on an mRNA downstream of the stop codon as a possible mechanism for the induction of SCR. We argue, with examples, that the insights gained from the natural SCR events can guide us to develop novel strategies for the treatment of diseases caused by premature stop codons. This article is categorized under: Translation > Regulation.
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Affiliation(s)
- Lekha E Manjunath
- Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka, India
| | - Anumeha Singh
- Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka, India
| | - Saubhik Som
- Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka, India
| | - Sandeep M Eswarappa
- Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka, India
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9
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Siddiqui G, De Paoli A, MacRaild CA, Sexton AE, Boulet C, Shah AD, Batty MB, Schittenhelm RB, Carvalho TG, Creek DJ. A new mass spectral library for high-coverage and reproducible analysis of the Plasmodium falciparum-infected red blood cell proteome. Gigascience 2022; 11:6543637. [PMID: 35254426 PMCID: PMC8900498 DOI: 10.1093/gigascience/giac008] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 11/24/2021] [Accepted: 01/28/2022] [Indexed: 12/03/2022] Open
Abstract
Background Plasmodium falciparum causes the majority of malaria mortality worldwide, and the disease occurs during the asexual red blood cell (RBC) stage of infection. In the absence of an effective and available vaccine, and with increasing drug resistance, asexual RBC stage parasites are an important research focus. In recent years, mass spectrometry–based proteomics using data-dependent acquisition has been extensively used to understand the biochemical processes within the parasite. However, data-dependent acquisition is problematic for the detection of low-abundance proteins and proteome coverage and has poor run-to-run reproducibility. Results Here, we present a comprehensive P. falciparum–infected RBC (iRBC) spectral library to measure the abundance of 44,449 peptides from 3,113 P. falciparum and 1,617 RBC proteins using a data-independent acquisition mass spectrometric approach. The spectral library includes proteins expressed in the 3 morphologically distinct RBC stages (ring, trophozoite, schizont), the RBC compartment of trophozoite-iRBCs, and the cytosolic fraction from uninfected RBCs. This spectral library contains 87% of all P. falciparum proteins that have previously been reported with protein-level evidence in blood stages, as well as 692 previously unidentified proteins. The P. falciparum spectral library was successfully applied to generate semi-quantitative proteomics datasets that characterize the 3 distinct asexual parasite stages in RBCs, and compared artemisinin-resistant (Cam3.IIR539T) and artemisinin-sensitive (Cam3.IIrev) parasites. Conclusion A reproducible, high-coverage proteomics spectral library and analysis method has been generated for investigating sets of proteins expressed in the iRBC stage of P. falciparum malaria. This will provide a foundation for an improved understanding of parasite biology, pathogenesis, drug mechanisms, and vaccine candidate discovery for malaria.
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Affiliation(s)
- Ghizal Siddiqui
- Drug Delivery Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia
| | - Amanda De Paoli
- Drug Delivery Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia
| | - Christopher A MacRaild
- Drug Delivery Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia
| | - Anna E Sexton
- Drug Delivery Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia
| | - Coralie Boulet
- Department of Physiology, Anatomy and Microbiology, La Trobe University, Bundoora, VIC 3086, Australia
| | - Anup D Shah
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia.,Monash Bioinformatics Platform, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Mitchell B Batty
- Drug Delivery Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia
| | - Ralf B Schittenhelm
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Teresa G Carvalho
- Department of Physiology, Anatomy and Microbiology, La Trobe University, Bundoora, VIC 3086, Australia
| | - Darren J Creek
- Drug Delivery Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia
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10
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Qi Y, Zhang Y, Mu Q, Zheng G, Zhang M, Chen B, Huang J, Ma C, Wang X. RNA Secondary Structurome Revealed Distinct Thermoregulation in Plasmodium falciparum. Front Cell Dev Biol 2022; 9:766532. [PMID: 35059397 PMCID: PMC8763798 DOI: 10.3389/fcell.2021.766532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Accepted: 11/19/2021] [Indexed: 11/13/2022] Open
Abstract
The development of Plasmodium parasites, a causative agent of malaria, requests two hosts and the completion of 11 different parasite stages during development. Therefore, an efficient and fast response of parasites to various complex environmental changes, such as ambient temperature, pH, ions, and nutrients, is essential for parasite development and survival. Among many of these environmental changes, temperature is a decisive factor for parasite development and pathogenesis, including the thermoregulation of rRNA expression, gametogenesis, and parasite sequestration in cerebral malaria. However, the exact mechanism of how Plasmodium parasites rapidly respond and adapt to temperature change remains elusive. As a fundamental and pervasive regulator of gene expression, RNA structure can be a specific mechanism for fine tuning various biological processes. For example, dynamic and temperature-dependent changes in RNA secondary structures can control the expression of different gene programs, as shown by RNA thermometers. In this study, we applied the in vitro and in vivo transcriptomic-wide secondary structurome approach icSHAPE to measure parasite RNA structure changes with temperature alteration at single-nucleotide resolution for ring and trophozoite stage parasites. Among 3,000 probed structures at different temperatures, our data showed structural changes in the global transcriptome, such as S-type rRNA, HRPII gene, and the erythrocyte membrane protein family. When the temperature drops from 37°C to 26°C, most of the genes in the trophozoite stage cause significantly more changes to the RNA structure than the genes in the ring stage. A multi-omics analysis of transcriptome data from RNA-seq and RNA structure data from icSHAPE reveals that the specific RNA secondary structure plays a significant role in the regulation of transcript expression for parasites in response to temperature changes. In addition, we identified several RNA thermometers (RNATs) that responded quickly to temperature changes. The possible thermo-responsive RNAs in Plasmodium falciparum were further mapped. To this end, we identified dynamic and temperature-dependent RNA structural changes in the P. falciparum transcriptome and performed a comprehensive characterization of RNA secondary structures over the course of temperature stress in blood stage development. These findings not only contribute to a better understanding of the function of the RNA secondary structure but may also provide novel targets for efficient vaccines or drugs.
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Affiliation(s)
- Yanwei Qi
- Department of Pathogenic Biology and Immunology, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, China
| | - Yuhong Zhang
- Department of Pathogenic Biology and Immunology, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, China
| | - Quankai Mu
- Department of Immunogenetics, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, Japan
| | - Guixing Zheng
- Department of Blood Transfusion, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, China
| | - Mengxin Zhang
- The Third Clinical School, Guangzhou Medical University, Guangzhou, China
| | - Bingxia Chen
- The Third Clinical School, Guangzhou Medical University, Guangzhou, China
| | - Jun Huang
- Department of Pathogenic Biology and Immunology, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, China
| | - Changling Ma
- Department of Pathogenic Biology and Immunology, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, China
| | - Xinhua Wang
- The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, China
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11
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Chahine Z, Le Roch KG. Decrypting the complexity of the human malaria parasite biology through systems biology approaches. FRONTIERS IN SYSTEMS BIOLOGY 2022; 2:940321. [PMID: 37200864 PMCID: PMC10191146 DOI: 10.3389/fsysb.2022.940321] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The human malaria parasite, Plasmodium falciparum, is a unicellular protozoan responsible for over half a million deaths annually. With a complex life cycle alternating between human and invertebrate hosts, this apicomplexan is notoriously adept at evading host immune responses and developing resistance to all clinically administered treatments. Advances in omics-based technologies, increased sensitivity of sequencing platforms and enhanced CRISPR based gene editing tools, have given researchers access to more in-depth and untapped information about this enigmatic micro-organism, a feat thought to be infeasible in the past decade. Here we discuss some of the most important scientific achievements made over the past few years with a focus on novel technologies and platforms that set the stage for subsequent discoveries. We also describe some of the systems-based methods applied to uncover gaps of knowledge left through single-omics applications with the hope that we will soon be able to overcome the spread of this life-threatening disease.
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12
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Li J, Guo Y, Roellig DM, Li N, Feng Y, Xiao L. Cryptosporidium felis differs from other Cryptosporidium spp. in codon usage. Microb Genom 2021; 7. [PMID: 34907893 PMCID: PMC8767354 DOI: 10.1099/mgen.0.000711] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
Cryptosporidium spp. are important enteric pathogens in a wide range of vertebrates including humans. Previous comparative analysis revealed conservation in genome composition, gene content, and gene organization among Cryptosporidium spp., with a progressive reductive evolution in metabolic pathways and invasion-related proteins. In this study, we sequenced the genome of zoonotic pathogen Cryptosporidium felis and conducted a comparative genomic analysis. While most intestinal Cryptosporidium species have similar genomic characteristics and almost complete genome synteny, fewer protein-coding genes and some sequence inversions and translocations were found in the C. felis genome. The C. felis genome exhibits much higher GC content (39.6 %) than other Cryptosporidium species (24.3–32.9 %), especially at the third codon position (GC3) of protein-coding genes. Thus, C. felis has a different codon usage, which increases the use of less energy costly amino acids (Gly and Ala) encoded by GC-rich codons. While the tRNA usage is conserved among Cryptosporidium species, consistent with its higher GC content, C. felis uses a unique tRNA for GTG for valine instead of GTA in other Cryptosporidium species. Both mutational pressures and natural selection are associated with the evolution of the codon usage in Cryptosporidium spp., while natural selection seems to drive the codon usage in C. felis. Other unique features of the C. felis genome include the loss of the entire traditional and alternative electron transport systems and several invasion-related proteins. Thus, the preference for the use of some less energy costly amino acids in C. felis may lead to a more harmonious parasite–host interaction, and the strengthened host-adaptation is reflected by the further reductive evolution of metabolism and host invasion-related proteins.
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Affiliation(s)
- Jiayu Li
- Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, PR China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, PR China
| | - Yaqiong Guo
- Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, PR China
| | - Dawn M. Roellig
- Division of Foodborne, Waterborne and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Na Li
- Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, PR China
| | - Yaoyu Feng
- Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, PR China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, PR China
- *Correspondence: Yaoyu Feng,
| | - Lihua Xiao
- Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, PR China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, PR China
- *Correspondence: Lihua Xiao,
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13
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Dumetz F, Chow EYC, Harris LM, Liew SW, Jensen A, Umar MI, Chung B, Chan TF, Merrick CJ, Kwok CK. G-quadruplex RNA motifs influence gene expression in the malaria parasite Plasmodium falciparum. Nucleic Acids Res 2021; 49:12486-12501. [PMID: 34792144 PMCID: PMC8643661 DOI: 10.1093/nar/gkab1095] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 10/15/2021] [Accepted: 10/21/2021] [Indexed: 11/12/2022] Open
Abstract
G-quadruplexes are non-helical secondary structures that can fold in vivo in both DNA and RNA. In human cells, they can influence replication, transcription and telomere maintenance in DNA, or translation, transcript processing and stability of RNA. We have previously showed that G-quadruplexes are detectable in the DNA of the malaria parasite Plasmodium falciparum, despite a very highly A/T-biased genome with unusually few guanine-rich sequences. Here, we show that RNA G-quadruplexes can also form in P. falciparum RNA, using rG4-seq for transcriptome-wide structure-specific RNA probing. Many of the motifs, detected here via the rG4seeker pipeline, have non-canonical forms and would not be predicted by standard in silico algorithms. However, in vitro biophysical assays verified formation of non-canonical motifs. The G-quadruplexes in the P. falciparum transcriptome are frequently clustered in certain genes and associated with regions encoding low-complexity peptide repeats. They are overrepresented in particular classes of genes, notably those that encode PfEMP1 virulence factors, stress response genes and DNA binding proteins. In vitro translation experiments and in vivo measures of translation efficiency showed that G-quadruplexes can influence the translation of P. falciparum mRNAs. Thus, the G-quadruplex is a novel player in post-transcriptional regulation of gene expression in this major human pathogen.
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Affiliation(s)
- Franck Dumetz
- Department of Pathology, Cambridge University, Tennis Court Road, Cambridge CB2 1QP, UK
| | - Eugene Yui-Ching Chow
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, Chinese University of Hong Kong, Shatin, NT, Hong Kong
| | - Lynne M Harris
- Centre for Applied Entomology and Parasitology, Faculty of Natural Sciences, Keele University, Keele, Staffordshire, ST5 5BG, UK
| | - Shiau Wei Liew
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China
| | - Anders Jensen
- Department of Pathology, Cambridge University, Tennis Court Road, Cambridge CB2 1QP, UK
| | - Mubarak I Umar
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China
| | - Betty Chung
- Department of Pathology, Cambridge University, Tennis Court Road, Cambridge CB2 1QP, UK
| | - Ting Fung Chan
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, Chinese University of Hong Kong, Shatin, NT, Hong Kong
| | - Catherine J Merrick
- Department of Pathology, Cambridge University, Tennis Court Road, Cambridge CB2 1QP, UK
| | - Chun Kit Kwok
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China.,Shenzhen Research Institute of City University of Hong Kong, Shenzhen, China
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14
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Shirokikh NE. Translation complex stabilization on messenger RNA and footprint profiling to study the RNA responses and dynamics of protein biosynthesis in the cells. Crit Rev Biochem Mol Biol 2021; 57:261-304. [PMID: 34852690 DOI: 10.1080/10409238.2021.2006599] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
During protein biosynthesis, ribosomes bind to messenger (m)RNA, locate its protein-coding information, and translate the nucleotide triplets sequentially as codons into the corresponding sequence of amino acids, forming proteins. Non-coding mRNA features, such as 5' and 3' untranslated regions (UTRs), start sites or stop codons of different efficiency, stretches of slower or faster code and nascent polypeptide interactions can alter the translation rates transcript-wise. Most of the homeostatic and signal response pathways of the cells converge on individual mRNA control, as well as alter the global translation output. Among the multitude of approaches to study translational control, one of the most powerful is to infer the locations of translational complexes on mRNA based on the mRNA fragments protected by these complexes from endonucleolytic hydrolysis, or footprints. Translation complex profiling by high-throughput sequencing of the footprints allows to quantify the transcript-wise, as well as global, alterations of translation, and uncover the underlying control mechanisms by attributing footprint locations and sizes to different configurations of the translational complexes. The accuracy of all footprint profiling approaches critically depends on the fidelity of footprint generation and many methods have emerged to preserve certain or multiple configurations of the translational complexes, often in challenging biological material. In this review, a systematic summary of approaches to stabilize translational complexes on mRNA for footprinting is presented and major findings are discussed. Future directions of translation footprint profiling are outlined, focusing on the fidelity and accuracy of inference of the native in vivo translation complex distribution on mRNA.
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Affiliation(s)
- Nikolay E Shirokikh
- Division of Genome Sciences and Cancer, The John Curtin School of Medical Research, The Australian National University, Canberra, Australia
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15
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Shaw PJ, Piriyapongsa J, Kaewprommal P, Wongsombat C, Chaosrikul C, Teeravajanadet K, Boonbangyang M, Uthaipibull C, Kamchonwongpaisan S, Tongsima S. Identifying transcript 5' capped ends in Plasmodium falciparum. PeerJ 2021; 9:e11983. [PMID: 34527439 PMCID: PMC8401752 DOI: 10.7717/peerj.11983] [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] [Received: 01/29/2021] [Accepted: 07/26/2021] [Indexed: 12/15/2022] Open
Abstract
Background The genome of the human malaria parasite Plasmodium falciparum is poorly annotated, in particular, the 5' capped ends of its mRNA transcripts. New approaches are needed to fully catalog P. falciparum transcripts for understanding gene function and regulation in this organism. Methods We developed a transcriptomic method based on next-generation sequencing of complementary DNA (cDNA) enriched for full-length fragments using eIF4E, a 5' cap-binding protein, and an unenriched control. DNA sequencing adapter was added after enrichment of full-length cDNA using two different ligation protocols. From the mapped sequence reads, enrichment scores were calculated for all transcribed nucleotides and used to calculate P-values of 5' capped nucleotide enrichment. Sensitivity and accuracy were increased by combining P-values from replicate experiments. Data were obtained for P. falciparum ring, trophozoite and schizont stages of intra-erythrocytic development. Results 5' capped nucleotide signals were mapped to 17,961 non-overlapping P. falciparum genomic intervals. Analysis of the dominant 5' capped nucleotide in these genomic intervals revealed the presence of two groups with distinctive epigenetic features and sequence patterns. A total of 4,512 transcripts were annotated as 5' capped based on the correspondence of 5' end with 5' capped nucleotide annotated from full-length cDNA data. Discussion The presence of two groups of 5' capped nucleotides suggests that alternative mechanisms may exist for producing 5' capped transcript ends in P. falciparum. The 5' capped transcripts that are antisense, outside of, or partially overlapping coding regions may be important regulators of gene function in P. falciparum.
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Affiliation(s)
- Philip J Shaw
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Jittima Piriyapongsa
- National Biobank of Thailand (NBT), National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Pavita Kaewprommal
- National Biobank of Thailand (NBT), National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Chayaphat Wongsombat
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Chadapohn Chaosrikul
- National Biobank of Thailand (NBT), National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Krirkwit Teeravajanadet
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Manon Boonbangyang
- National Biobank of Thailand (NBT), National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Chairat Uthaipibull
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Sumalee Kamchonwongpaisan
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Sissades Tongsima
- National Biobank of Thailand (NBT), National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
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16
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Michelow IC, Park S, Tsai SW, Rayta B, Pasaje CFA, Nelson S, Early AM, Frosch AP, Ayodo G, Raj DK, Nixon CE, Nixon CP, Pond-Tor S, Friedman JF, Fried M, Duffy PE, Le Roch KG, Niles JC, Kurtis JD. A newly characterized malaria antigen on erythrocyte and merozoite surfaces induces parasite inhibitory antibodies. J Exp Med 2021; 218:e20200170. [PMID: 34342640 PMCID: PMC8340565 DOI: 10.1084/jem.20200170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 05/11/2021] [Accepted: 06/24/2021] [Indexed: 11/13/2022] Open
Abstract
We previously identified a Plasmodium falciparum (Pf) protein of unknown function encoded by a single-copy gene, PF3D7_1134300, as a target of antibodies in plasma of Tanzanian children in a whole-proteome differential screen. Here we characterize this protein as a blood-stage antigen that localizes to the surface membranes of both parasitized erythrocytes and merozoites, hence its designation as Pf erythrocyte membrane and merozoite antigen 1 (PfEMMA1). Mouse anti-PfEMMA1 antisera and affinity-purified human anti-PfEMMA1 antibodies inhibited growth of P. falciparum strains by up to 68% in growth inhibition assays. Following challenge with uniformly fatal Plasmodium berghei (Pb) ANKA, up to 40% of mice immunized with recombinant PbEMMA1 self-cured, and median survival of lethally infected mice was up to 2.6-fold longer than controls (21 vs. 8 d, P = 0.005). Furthermore, high levels of naturally acquired human anti-PfEMMA1 antibodies were associated with a 46% decrease in parasitemia over 2.5 yr of follow-up of Tanzanian children. Together, these findings suggest that antibodies to PfEMMA1 mediate protection against malaria.
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MESH Headings
- Animals
- Antibodies, Protozoan/immunology
- Antigens, Protozoan/genetics
- Antigens, Protozoan/immunology
- Antigens, Protozoan/metabolism
- Child, Preschool
- Erythrocyte Membrane/parasitology
- Female
- Host-Parasite Interactions/physiology
- Humans
- Infant
- Malaria Vaccines/genetics
- Malaria Vaccines/immunology
- Malaria, Falciparum/immunology
- Malaria, Falciparum/mortality
- Malaria, Falciparum/parasitology
- Merozoites/immunology
- Merozoites/metabolism
- Mice, Inbred BALB C
- Plasmodium falciparum/immunology
- Plasmodium falciparum/pathogenicity
- Plasmodium falciparum/physiology
- Polymorphism, Single Nucleotide
- Protozoan Proteins/chemistry
- Protozoan Proteins/genetics
- Protozoan Proteins/immunology
- Protozoan Proteins/metabolism
- Recombinant Proteins/genetics
- Recombinant Proteins/immunology
- Recombinant Proteins/metabolism
- Tanzania
- Mice
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Affiliation(s)
- Ian C. Michelow
- Department of Pediatrics, Division of Infectious Diseases, The Warren Alpert Medical School of Brown University, Providence, RI
- Center for International Health Research, Rhode Island Hospital, Providence, RI
| | - Sangshin Park
- Center for International Health Research, Rhode Island Hospital, Providence, RI
- Graduate School of Urban Public Health & Department of Urban Big Data Convergence, University of Seoul, Seoul, Republic of Korea
| | - Shu-Whei Tsai
- Department of Pediatrics, Division of Infectious Diseases, The Warren Alpert Medical School of Brown University, Providence, RI
- Center for International Health Research, Rhode Island Hospital, Providence, RI
| | - Bonnie Rayta
- Department of Pediatrics, Division of Infectious Diseases, The Warren Alpert Medical School of Brown University, Providence, RI
- Center for International Health Research, Rhode Island Hospital, Providence, RI
| | | | - Sara Nelson
- Department of Pediatrics, Division of Infectious Diseases, The Warren Alpert Medical School of Brown University, Providence, RI
- Center for International Health Research, Rhode Island Hospital, Providence, RI
| | - Angela M. Early
- Infectious Disease and Microbiome Program, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA
| | - Anne P. Frosch
- Department of Medicine, Hennepin Healthcare Research Institute, University of Minnesota, Minneapolis, MN
| | - George Ayodo
- Kenya Medical Research Institute, Centre of Global Health Research, Kisumu, Kenya
- Jaramogi Oginga Odinga University of Science and Technology, Bondo, Kenya
| | - Dipak K. Raj
- Center for International Health Research, Rhode Island Hospital, Providence, RI
- Department of Pathology and Laboratory Medicine, The Warren Alpert Medical School of Brown University, Providence, RI
| | - Christina E. Nixon
- Center for International Health Research, Rhode Island Hospital, Providence, RI
- Department of Pathology and Laboratory Medicine, The Warren Alpert Medical School of Brown University, Providence, RI
| | - Christian P. Nixon
- Center for International Health Research, Rhode Island Hospital, Providence, RI
- Department of Pathology and Laboratory Medicine, The Warren Alpert Medical School of Brown University, Providence, RI
| | - Sunthorn Pond-Tor
- Center for International Health Research, Rhode Island Hospital, Providence, RI
- Department of Pathology and Laboratory Medicine, The Warren Alpert Medical School of Brown University, Providence, RI
| | - Jennifer F. Friedman
- Center for International Health Research, Rhode Island Hospital, Providence, RI
- Department of Pediatrics, The Warren Alpert Medical School of Brown University, Providence, RI
| | - Michal Fried
- Laboratory of Malaria Immunology and Vaccinology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD
| | - Patrick E. Duffy
- Laboratory of Malaria Immunology and Vaccinology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD
| | - Karine G. Le Roch
- Department of Molecular, Cell and Systems Biology, Center for Infectious Disease and Vector Research, University of California, Riverside, Riverside, CA
| | - Jacquin C. Niles
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA
| | - Jonathan D. Kurtis
- Center for International Health Research, Rhode Island Hospital, Providence, RI
- Department of Pathology and Laboratory Medicine, The Warren Alpert Medical School of Brown University, Providence, RI
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17
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Alvarez DR, Ospina A, Barwell T, Zheng B, Dey A, Li C, Basu S, Shi X, Kadri S, Chakrabarti K. The RNA structurome in the asexual blood stages of malaria pathogen plasmodium falciparum. RNA Biol 2021; 18:2480-2497. [PMID: 33960872 DOI: 10.1080/15476286.2021.1926747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
Plasmodium falciparum is a deadly human pathogen responsible for the devastating disease called malaria. In this study, we measured the differential accumulation of RNA secondary structures in coding and non-coding transcripts from the asexual developmental cycle in P. falciparum in human red blood cells. Our comprehensive analysis that combined high-throughput nuclease mapping of RNA structures by duplex RNA-seq, SHAPE-directed RNA structure validation, immunoaffinity purification and characterization of antisense RNAs collectively measured differentially base-paired RNA regions throughout the parasite's asexual RBC cycle. Our mapping data not only aligned to a diverse pool of RNAs with known structures but also enabled us to identify new structural RNA regions in the malaria genome. On average, approximately 71% of the genes with secondary structures are found to be protein coding mRNAs. The mapping pattern of these base-paired RNAs corresponded to all regions of mRNAs, including the 5' UTR, CDS and 3' UTR as well as the start and stop codons. Histone family genes which are known to form secondary structures in their mRNAs and transcripts from genes which are important for transcriptional and post-transcriptional control, such as the unique plant-like transcription factor family, ApiAP2, DNA-/RNA-binding protein, Alba3 and proteins important for RBC invasion and malaria cytoadherence also showed strong accumulation of duplex RNA reads in various asexual stages in P. falciparum. Intriguingly, our study determined stage-specific, dynamic relationships between mRNA structural contents and translation efficiency in P. falciparum asexual blood stages, suggesting an essential role of RNA structural changes in malaria gene expression programs.
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Affiliation(s)
- Diana Renteria Alvarez
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, North Carolina, USA
| | - Alejandra Ospina
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, North Carolina, USA
| | - Tiffany Barwell
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, North Carolina, USA
| | - Bo Zheng
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, North Carolina, USA
| | - Abhishek Dey
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, North Carolina, USA
| | - Chong Li
- Temple University, Philadelphia, PA, USA
| | - Shrabani Basu
- Division of Medical Genetics, Children's Hospital of Pittsburgh of UPMC, Pittsburgh, PA, USA
| | | | - Sabah Kadri
- Division of Health and Biomedical Informatics, Northwestern University Feinberg School of Medicine and Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL, USA
| | - Kausik Chakrabarti
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, North Carolina, USA
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18
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Cortés GT, Beltran MMG, Gómez-Alegría CJ, Wiser MF. Identification of a protein unique to the genus Plasmodium that contains a WD40 repeat domain and extensive low-complexity sequence. Parasitol Res 2021; 120:2617-2629. [PMID: 34142223 DOI: 10.1007/s00436-021-07190-z] [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: 03/01/2021] [Accepted: 05/11/2021] [Indexed: 11/27/2022]
Abstract
Proteins containing WD40 domains play important roles in the formation of multiprotein complexes. Little is known about WD40 proteins in the malaria parasite. This report contains the initial description of a WD40 protein that is unique to the genus Plasmodium and possibly closely related genera. The N-terminal portion of this protein consists of seven WD40 repeats that are highly conserved in all Plasmodium species. Following the N-terminal region is a central region that is conserved within the major Plasmodium clades, such as parasites of great apes, monkeys, rodents, and birds, but partially conserved across all Plasmodium species. This central region contains extensive low-complexity sequence and is predicted to have a disordered structure. Proteins with disordered structure generally function in molecular interactions. The C-terminal region is semi-conserved across all Plasmodium species and has no notable features. This WD40 repeat protein likely functions in some aspect of parasite biology that is unique to Plasmodium and this uniqueness makes the protein a possible target for therapeutic intervention.
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Affiliation(s)
- Gladys T Cortés
- Departamento de Salud Pública, Facultad de Medicina, Grupo Biologia Celular, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Martha Margarita Gonzalez Beltran
- Ex alumna de la Maestría en Ciencias-Bioquímica, Departamento de Química, Facultad de Ciencias, Universidad Nacional de Colombia, Grupo UNIMOL, Bogotá, Colombia
| | - Claudio J Gómez-Alegría
- Departamento de Farmacia, Facultad de Ciencias, Universidad Nacional de Colombia, Grupo UNIMOL, Bogotá, Colombia
| | - Mark F Wiser
- Department of Tropical Medicine, Tulane University School of Public Health and Tropical Medicine, 1440 Canal Street, Suite 2301, New Orleans, LA, 70112-2824, USA.
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19
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The role of upstream open reading frames in translation regulation in the apicomplexan parasites Plasmodium falciparum and Toxoplasma gondii. Parasitology 2021; 148:1277-1287. [PMID: 34099078 PMCID: PMC8383288 DOI: 10.1017/s0031182021000937] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
During their complex life cycles, the Apicomplexan parasites Plasmodium falciparum and Toxoplasma gondii employ several layers of regulation of their gene expression. One such layer is mediated at the level of translation through upstream open reading frames (uORFs). As uORFs are found in the upstream regions of a majority of transcripts in both the parasites, it is essential that their roles in translational regulation be appreciated to a greater extent. This review provides a comprehensive summary of studies that show uORF-mediated gene regulation in these parasites and highlights examples of clinically and physiologically relevant genes, including var2csa in P. falciparum, and ApiAT1 in T. gondii, that exhibit uORF-mediated regulation. In addition to these examples, several studies that use bioinformatics, transcriptomics, proteomics and ribosome profiling also indicate the possibility of widespread translational regulation by uORFs. Further analysis of these genome-wide datasets, taking into account uORFs associated with each gene, will reveal novel genes involved in key biological pathways such as cell-cycle progression, stress-response and pathogenicity. The cumulative evidence from studies presented in this review suggests that uORFs will play crucial roles in regulating gene expression during clinical disease caused by these important human pathogens.
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20
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Behari J, Borkar P, Vindu A, Dandewad V, Upadrasta S, Shanmugam D, Seshadri V. Conserved RNA Binding Activity of Phosphatidyl Inositol 5-Phosphate 4-Kinase (PIP4K2A). Front Mol Biosci 2021; 8:631281. [PMID: 34124142 PMCID: PMC8194828 DOI: 10.3389/fmolb.2021.631281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 04/28/2021] [Indexed: 12/04/2022] Open
Abstract
Plasmodium falciparum is a causative agent for malaria and has a complex life cycle in human and mosquito hosts. During its life cycle, the malarial parasite Plasmodium goes through different asexual and sexual stages, in humans and mosquitoes. Expression of stage-specific proteins is important for successful completion of its life cycle and requires tight gene regulation. In the case of Plasmodium, due to relative paucity of the transcription factors, it is postulated that posttranscriptional regulation plays an important role in stage-specific gene expression. Translation repression of specific set of mRNA has been reported in gametocyte stages of the parasite. A conserved element present in the 3′UTR of some of these transcripts was identified. Phosphatidylinositol 5-phosphate 4-kinase (PIP4K2A) was identified as the protein that associates with these RNA. We now show that the RNA binding activity of PIP4K2A is independent of its kinase activity. We also observe that PIP4K2A is imported into the parasite from the host on Plasmodium berghei and Toxoplasma gondii. The RNA binding activity of PIP4K2A seems to be conserved across species from Drosophila and C. elegans to humans, suggesting that the RNA binding activity of PIP4K may be important, and there may be host transcripts that may be regulated by PIP4K2A. These results identify a novel RNA binding role for PIP4K2A that may not only play a role in Plasmodium propagation but may also function in regulating gene expression in multicellular organisms.
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Affiliation(s)
- Jatin Behari
- National Centre for Cell Science, Pune, India.,Department of Biotechnology, SPPU, Pune, India
| | - Pranita Borkar
- National Centre for Cell Science, Pune, India.,Department of Biotechnology, SPPU, Pune, India
| | - Arya Vindu
- National Centre for Cell Science, Pune, India.,Department of Biotechnology, SPPU, Pune, India
| | - Vishal Dandewad
- National Centre for Cell Science, Pune, India.,Department of Biotechnology, SPPU, Pune, India
| | - Sindhuri Upadrasta
- CSIR-National Chemical Laboratory, Pune, India.,Academy of Scientific and Innovative Research, Ghaziabad, India
| | - Dhanasekaran Shanmugam
- CSIR-National Chemical Laboratory, Pune, India.,Academy of Scientific and Innovative Research, Ghaziabad, India
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21
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Soni K, Kempf G, Manalastas-Cantos K, Hendricks A, Flemming D, Guizetti J, Simon B, Frischknecht F, Svergun DI, Wild K, Sinning I. Structural analysis of the SRP Alu domain from Plasmodium falciparum reveals a non-canonical open conformation. Commun Biol 2021; 4:600. [PMID: 34017052 PMCID: PMC8137916 DOI: 10.1038/s42003-021-02132-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 04/22/2021] [Indexed: 12/25/2022] Open
Abstract
The eukaryotic signal recognition particle (SRP) contains an Alu domain, which docks into the factor binding site of translating ribosomes and confers translation retardation. The canonical Alu domain consists of the SRP9/14 protein heterodimer and a tRNA-like folded Alu RNA that adopts a strictly 'closed' conformation involving a loop-loop pseudoknot. Here, we study the structure of the Alu domain from Plasmodium falciparum (PfAlu), a divergent apicomplexan protozoan that causes human malaria. Using NMR, SAXS and cryo-EM analyses, we show that, in contrast to its prokaryotic and eukaryotic counterparts, the PfAlu domain adopts an 'open' Y-shaped conformation. We show that cytoplasmic P. falciparum ribosomes are non-discriminative and recognize both the open PfAlu and closed human Alu domains with nanomolar affinity. In contrast, human ribosomes do not provide high affinity binding sites for either of the Alu domains. Our analyses extend the structural database of Alu domains to the protozoan species and reveal species-specific differences in the recognition of SRP Alu domains by ribosomes.
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Affiliation(s)
- Komal Soni
- Heidelberg University Biochemistry Center (BZH), Heidelberg, Germany
| | - Georg Kempf
- Heidelberg University Biochemistry Center (BZH), Heidelberg, Germany
| | | | - Astrid Hendricks
- Heidelberg University Biochemistry Center (BZH), Heidelberg, Germany
| | - Dirk Flemming
- Heidelberg University Biochemistry Center (BZH), Heidelberg, Germany
| | - Julien Guizetti
- Integrative Parasitology, Center for Infectious Diseases, Heidelberg University Hospital, Heidelberg, Germany
| | - Bernd Simon
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Friedrich Frischknecht
- Integrative Parasitology, Center for Infectious Diseases, Heidelberg University Hospital, Heidelberg, Germany
| | | | - Klemens Wild
- Heidelberg University Biochemistry Center (BZH), Heidelberg, Germany
| | - Irmgard Sinning
- Heidelberg University Biochemistry Center (BZH), Heidelberg, Germany.
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22
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Kamaliddin C, Guillochon E, Salnot V, Rombaut D, Huguet S, Guillonneau F, Houzé S, Cot M, Deloron P, Argy N, Bertin GI. Comprehensive Analysis of Transcript and Protein Relative Abundance During Blood Stages of Plasmodium falciparum Infection. J Proteome Res 2021; 20:1206-1216. [PMID: 33475364 DOI: 10.1021/acs.jproteome.0c00496] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Plasmodium falciparum is the main causative agent of human malaria. During the intraerythrocytic development cycle, the P. falciparum morphology changes dramatically from circulating young rings to sequestered mature trophozoites and schizonts. Sequestered forms contribute to the pathophysiology of severe malaria as the infected erythrocytes obstruct the microvascular flow in deep organs and induce local inflammation. However, the sequestration mechanism limits the access to the corresponding parasitic form in the clinical samples from patients infected with P. falciparum. To complement this deficiency, we aimed to evaluate the relevance of mRNA study as a proxy of protein expression in sequestered parasites. To do so, we conducted a proteotranscriptomic analysis using five independent P. falciparum laboratory strain samples. RNA sequencing was performed, and the mRNA expression level was assessed on circulating ring-stage parasites. The level of protein expression were measured by LC-MS/MS on the corresponding sequestered mature forms after 18-24 h of maturation. Overall, our results showed a strong transcriptome/transcriptome and a very strong proteome/proteome correlation between samples. Moreover, positive correlations of mRNA and protein expression levels were found between ring-stage transcriptomes and mature form proteomes. However, twice more transcripts were identified at the ring stage than proteins at the mature trophozoite stage. A high level of transcript expression did not guarantee the detection of the corresponding protein. Finally, we pointed out discrepancies at the individual gene level. Taken together, our results show that transcript and protein expressions are overall correlated. However, mRNA abundance is not a perfect proxy of protein expression at the individual level. Importantly, our study shows limitations of the "blind" use of RNA-seq and the importance of multiomics approaches for P. falciparum blood stage study in clinical samples.
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Affiliation(s)
- Claire Kamaliddin
- Université de Paris UMR261-MERIT Faculté de Pharmacie, 4 Ave. de l'observatoire, Île-de-France, FR 75006 Paris, France
| | - Emilie Guillochon
- Université de Paris UMR261-MERIT Faculté de Pharmacie, 4 Ave. de l'observatoire, Île-de-France, FR 75006 Paris, France
| | - Virginie Salnot
- Université de Paris, 3p5-Proteom'IC Platform Institut Cochin, INSERM, U1016, CNRS, UMR8104, Île-de-France, FR 75006 Paris, France
| | - David Rombaut
- Université de Paris, 3p5-Proteom'IC Platform Institut Cochin, INSERM, U1016, CNRS, UMR8104, Île-de-France, FR 75006 Paris, France
| | - Stéphanie Huguet
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91405 Orsay, France.,Université de Paris, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), 91405 Orsay, France
| | - François Guillonneau
- Université de Paris, 3p5-Proteom'IC Platform Institut Cochin, INSERM, U1016, CNRS, UMR8104, Île-de-France, FR 75006 Paris, France
| | - Sandrine Houzé
- Université de Paris UMR261-MERIT Faculté de Pharmacie, 4 Ave. de l'observatoire, Île-de-France, FR 75006 Paris, France.,Centre National de Référence pour le Paludisme, Bichat-Claude Bernard Hospital, 75018 Paris, France.,Parasitology Laboratory, Bichat-Claude Bernard Hospital, 75018 Paris, France
| | - Michel Cot
- Université de Paris UMR261-MERIT Faculté de Pharmacie, 4 Ave. de l'observatoire, Île-de-France, FR 75006 Paris, France
| | - Philippe Deloron
- Université de Paris UMR261-MERIT Faculté de Pharmacie, 4 Ave. de l'observatoire, Île-de-France, FR 75006 Paris, France
| | - Nicolas Argy
- Université de Paris UMR261-MERIT Faculté de Pharmacie, 4 Ave. de l'observatoire, Île-de-France, FR 75006 Paris, France.,Centre National de Référence pour le Paludisme, Bichat-Claude Bernard Hospital, 75018 Paris, France.,Parasitology Laboratory, Bichat-Claude Bernard Hospital, 75018 Paris, France
| | - Gwladys I Bertin
- Université de Paris UMR261-MERIT Faculté de Pharmacie, 4 Ave. de l'observatoire, Île-de-France, FR 75006 Paris, France
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23
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Nasamu AS, Falla A, Pasaje CFA, Wall BA, Wagner JC, Ganesan SM, Goldfless SJ, Niles JC. An integrated platform for genome engineering and gene expression perturbation in Plasmodium falciparum. Sci Rep 2021; 11:342. [PMID: 33431920 PMCID: PMC7801740 DOI: 10.1038/s41598-020-77644-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 11/13/2020] [Indexed: 11/24/2022] Open
Abstract
Establishing robust genome engineering methods in the malarial parasite, Plasmodium falciparum, has the potential to substantially improve the efficiency with which we gain understanding of this pathogen's biology to propel treatment and elimination efforts. Methods for manipulating gene expression and engineering the P. falciparum genome have been validated. However, a significant barrier to fully leveraging these advances is the difficulty associated with assembling the extremely high AT content DNA constructs required for modifying the P. falciparum genome. These are frequently unstable in commonly-used circular plasmids. We address this bottleneck by devising a DNA assembly framework leveraging the improved reliability with which large AT-rich regions can be efficiently manipulated in linear plasmids. This framework integrates several key functional genetics outcomes via CRISPR/Cas9 and other methods from a common, validated framework. Overall, this molecular toolkit enables P. falciparum genetics broadly and facilitates deeper interrogation of parasite genes involved in diverse biological processes.
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Affiliation(s)
- Armiyaw S Nasamu
- Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Room 56-341B, Cambridge, MA, 02139, USA
| | - Alejandra Falla
- Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Room 56-341B, Cambridge, MA, 02139, USA
| | - Charisse Flerida A Pasaje
- Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Room 56-341B, Cambridge, MA, 02139, USA
| | - Bridget A Wall
- Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Room 56-341B, Cambridge, MA, 02139, USA
| | - Jeffrey C Wagner
- Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Room 56-341B, Cambridge, MA, 02139, USA
| | - Suresh M Ganesan
- Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Room 56-341B, Cambridge, MA, 02139, USA
| | - Stephen J Goldfless
- Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Room 56-341B, Cambridge, MA, 02139, USA
| | - Jacquin C Niles
- Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Room 56-341B, Cambridge, MA, 02139, USA.
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24
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Manjunath LE, Singh A, Sahoo S, Mishra A, Padmarajan J, Basavaraju CG, Eswarappa SM. Stop codon read-through of mammalian MTCH2 leading to an unstable isoform regulates mitochondrial membrane potential. J Biol Chem 2020; 295:17009-17026. [PMID: 33028634 PMCID: PMC7863902 DOI: 10.1074/jbc.ra120.014253] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 10/02/2020] [Indexed: 12/13/2022] Open
Abstract
Stop codon read-through (SCR) is a process of continuation of translation beyond a stop codon. This phenomenon, which occurs only in certain mRNAs under specific conditions, leads to a longer isoform with properties different from that of the canonical isoform. MTCH2, which encodes a mitochondrial protein that regulates mitochondrial metabolism, was selected as a potential read-through candidate based on evolutionary conservation observed in the proximal region of its 3' UTR. Here, we demonstrate translational read-through across two evolutionarily conserved, in-frame stop codons of MTCH2 using luminescence- and fluorescence-based assays, and by analyzing ribosome-profiling and mass spectrometry (MS) data. This phenomenon generates two isoforms, MTCH2x and MTCH2xx (single- and double-SCR products, respectively), in addition to the canonical isoform MTCH2, from the same mRNA. Our experiments revealed that a cis-acting 12-nucleotide sequence in the proximal 3' UTR of MTCH2 is the necessary signal for SCR. Functional characterization showed that MTCH2 and MTCH2x were localized to mitochondria with a long t1/2 (>36 h). However, MTCH2xx was found predominantly in the cytoplasm. This mislocalization and its unique C terminus led to increased degradation, as shown by greatly reduced t1/2 (<1 h). MTCH2 read-through-deficient cells, generated using CRISPR-Cas9, showed increased MTCH2 expression and, consistent with this, decreased mitochondrial membrane potential. Thus, double-SCR of MTCH2 regulates its own expression levels contributing toward the maintenance of normal mitochondrial membrane potential.
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Affiliation(s)
- Lekha E Manjunath
- Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka, India
| | - Anumeha Singh
- Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka, India
| | - Sarthak Sahoo
- Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka, India
| | - Ashutosh Mishra
- Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka, India
| | - Jinsha Padmarajan
- Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka, India
| | | | - Sandeep M Eswarappa
- Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka, India.
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25
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Pavlovic Djuranovic S, Erath J, Andrews RJ, Bayguinov PO, Chung JJ, Chalker DL, Fitzpatrick JAJ, Moss WN, Szczesny P, Djuranovic S. Plasmodium falciparum translational machinery condones polyadenosine repeats. eLife 2020; 9:e57799. [PMID: 32469313 PMCID: PMC7295572 DOI: 10.7554/elife.57799] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 05/28/2020] [Indexed: 01/04/2023] Open
Abstract
Plasmodium falciparum is a causative agent of human malaria. Sixty percent of mRNAs from its extremely AT-rich (81%) genome harbor long polyadenosine (polyA) runs within their ORFs, distinguishing the parasite from its hosts and other sequenced organisms. Recent studies indicate polyA runs cause ribosome stalling and frameshifting, triggering mRNA surveillance pathways and attenuating protein synthesis. Here, we show that P. falciparum is an exception to this rule. We demonstrate that both endogenous genes and reporter sequences containing long polyA runs are efficiently and accurately translated in P. falciparum cells. We show that polyA runs do not elicit any response from No Go Decay (NGD) or result in the production of frameshifted proteins. This is in stark contrast to what we observe in human cells or T. thermophila, an organism with similar AT-content. Finally, using stalling reporters we show that Plasmodium cells evolved not to have a fully functional NGD pathway.
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Affiliation(s)
| | - Jessey Erath
- Department of Cell Biology and Physiology, Washington University School of MedicineSt. LouisUnited States
| | - Ryan J Andrews
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State UniversityAmesUnited States
| | - Peter O Bayguinov
- Washington University Center for Cellular Imaging, Washington University School of MedicineSt. LouisUnited States
| | - Joyce J Chung
- Department of Biology, Washington UniversitySt LouisUnited States
| | | | - James AJ Fitzpatrick
- Department of Cell Biology and Physiology, Washington University School of MedicineSt. LouisUnited States
- Washington University Center for Cellular Imaging, Washington University School of MedicineSt. LouisUnited States
- Department of Neuroscience, Washington University School of MedicineSt. LouisUnited States
- Department of Biomedical Engineering, Washington UniversitySt LouisUnited States
| | - Walter N Moss
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State UniversityAmesUnited States
| | - Pawel Szczesny
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, Department of BioinformaticsWarsawPoland
| | - Sergej Djuranovic
- Department of Cell Biology and Physiology, Washington University School of MedicineSt. LouisUnited States
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26
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Messenger RNAs with large numbers of upstream open reading frames are translated via leaky scanning and reinitiation in the asexual stages of Plasmodium falciparum. Parasitology 2020; 147:1100-1113. [DOI: 10.1017/s0031182020000840] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
AbstractThe genome of Plasmodium falciparum has one of the most skewed base-pair compositions of any eukaryote, with an AT content of 80–90%. As start and stop codons are AT-rich, the probability of finding upstream open reading frames (uORFs) in messenger RNAs (mRNAs) is high and parasite mRNAs have an average of 11 uORFs in their leader sequences. Similar to other eukaryotes, uORFs repress the translation of the downstream open reading frame (dORF) in P. falciparum, yet the parasite translation machinery is able to bypass these uORFs and reach the dORF to initiate translation. This can happen by leaky scanning and/or reinitiation.In this report, we assessed leaky scanning and reinitiation by studying the effect of uORFs on the translation of a dORF, in this case, the luciferase reporter gene, and showed that both mechanisms are employed in the asexual blood stages of P. falciparum. Furthermore, in addition to the codon usage of the uORF, translation of the dORF is governed by the Kozak sequence and length of the uORF, and inter-cistronic distance between the uORF and dORF. Based on these features whole-genome data was analysed to uncover classes of genes that might be regulated by uORFs. This study indicates that leaky scanning and reinitiation appear to be widespread in asexual stages of P. falciparum, which may require modifications of existing factors that are involved in translation initiation in addition to novel, parasite-specific proteins.
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27
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LaMonte GM, Rocamora F, Marapana DS, Gnädig NF, Ottilie S, Luth MR, Worgall TS, Goldgof GM, Mohunlal R, Santha Kumar TR, Thompson JK, Vigil E, Yang J, Hutson D, Johnson T, Huang J, Williams RM, Zou BY, Cheung AL, Kumar P, Egan TJ, Lee MCS, Siegel D, Cowman AF, Fidock DA, Winzeler EA. Pan-active imidazolopiperazine antimalarials target the Plasmodium falciparum intracellular secretory pathway. Nat Commun 2020; 11:1780. [PMID: 32286267 PMCID: PMC7156427 DOI: 10.1038/s41467-020-15440-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 03/01/2020] [Indexed: 12/12/2022] Open
Abstract
A promising new compound class for treating human malaria is the imidazolopiperazines (IZP) class. IZP compounds KAF156 (Ganaplacide) and GNF179 are effective against Plasmodium symptomatic asexual blood-stage infections, and are able to prevent transmission and block infection in animal models. But despite the identification of resistance mechanisms in P. falciparum, the mode of action of IZPs remains unknown. To investigate, we here combine in vitro evolution and genome analysis in Saccharomyces cerevisiae with molecular, metabolomic, and chemogenomic methods in P. falciparum. Our findings reveal that IZP-resistant S. cerevisiae clones carry mutations in genes involved in Endoplasmic Reticulum (ER)-based lipid homeostasis and autophagy. In Plasmodium, IZPs inhibit protein trafficking, block the establishment of new permeation pathways, and cause ER expansion. Our data highlight a mechanism for blocking parasite development that is distinct from those of standard compounds used to treat malaria, and demonstrate the potential of IZPs for studying ER-dependent protein processing.
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Affiliation(s)
- Gregory M LaMonte
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Frances Rocamora
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Danushka S Marapana
- Division of Infection and Immunity, Walter and Eliza Hall Institute for Medical Research, Parkville, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Nina F Gnädig
- Department of Microbiology & Immunology, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Sabine Ottilie
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Madeline R Luth
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Tilla S Worgall
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Gregory M Goldgof
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
- Department of Laboratory Medicine, University of California, San Francisco, CA, 94143, USA
| | - Roxanne Mohunlal
- Department of Microbiology & Immunology, Columbia University Irving Medical Center, New York, NY, 10032, USA
- Department of Chemistry, University of Cape Town, Rondebosch, 7700, South Africa
| | - T R Santha Kumar
- Department of Microbiology & Immunology, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Jennifer K Thompson
- Division of Infection and Immunity, Walter and Eliza Hall Institute for Medical Research, Parkville, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Edgar Vigil
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Jennifer Yang
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Dylan Hutson
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Trevor Johnson
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Jianbo Huang
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Roy M Williams
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Bing Yu Zou
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Andrea L Cheung
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Prianka Kumar
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Timothy J Egan
- Department of Chemistry, University of Cape Town, Rondebosch, 7700, South Africa
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Rondebosch, 7700, South Africa
| | - Marcus C S Lee
- Parasites and Microbes Programme, Wellcome Sanger Institute, Hinxton, CB10 1SA, UK
| | - Dionicio Siegel
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Alan F Cowman
- Division of Infection and Immunity, Walter and Eliza Hall Institute for Medical Research, Parkville, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, 3010, Australia
| | - David A Fidock
- Department of Microbiology & Immunology, Columbia University Irving Medical Center, New York, NY, 10032, USA
- Division of Infectious Diseases, Department of Medicine, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Elizabeth A Winzeler
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA.
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28
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Kaushik M, Nehra A, Gill SS, Gill R. Unraveling CAF-1 family in Plasmodium falciparum: comparative genome-wide identification and phylogenetic analysis among eukaryotes, expression profiling and protein-protein interaction studies. 3 Biotech 2020; 10:143. [PMID: 32206492 DOI: 10.1007/s13205-020-2096-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 01/24/2020] [Indexed: 11/29/2022] Open
Abstract
The present research reports a detailed in silico analysis of chromatin assembly factor-1 (CAF-1) family in human malaria parasite Plasmodium falciparum. Our analysis revealed five chromatin assembly factor-1 genes in P. falciparum (PfCAF-1) and the PfCAF-1 family was divided into two classes where, Class A belongs to the CAF-1 complex and others are kept in Class B. For comparative studies, orthologs of PfCAF-1 family were identified across 53 eukaryotic species and evolutionary relationships were drawn for different CAF-1 subfamilies. The phylogenetic analysis revealed grouping of evolutionary-related species together, although, divergence was observed in branching pattern. A detailed analysis of domain composition highlighted species-specific features viz. species-specific KDDS repeats of 84 amino acids were identified in PfCAF-1A whereas, members of CAF-1C/RbAp48 and RbAp46 subfamily exhibited least variation in size and domain composition. The qRT-PCR analysis revealed upregulation of PfCAF-1 members in trophozoite or schizont stage. Furthermore, a comparative expression analysis of the available transcriptome and proteome data along with qRT-PCR analysis revealed mixed expression patterns (coordination as well as non-coordination between different studies). Protein-protein interaction network analyses of PfCAF-1 family were carried out highlighting important complexes based on interologs. The PfRbAp48 was found to be highly connected with a total of 108 PPIs followed by PfRbAp46. The results unravel insights into the PfCAF-1 family and identify unique features, thus opening new perspectives for further targeted developments to understand and combat malaria menace.
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Affiliation(s)
- Manjeri Kaushik
- Centre for Biotechnology, Maharshi Dayanand University, Rohtak, Haryana 124 001 India
| | - Ashima Nehra
- Centre for Biotechnology, Maharshi Dayanand University, Rohtak, Haryana 124 001 India
| | - Sarvajeet Singh Gill
- Centre for Biotechnology, Maharshi Dayanand University, Rohtak, Haryana 124 001 India
| | - Ritu Gill
- Centre for Biotechnology, Maharshi Dayanand University, Rohtak, Haryana 124 001 India
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Identifying the Translatome of Mouse NEBD-Stage Oocytes via SSP-Profiling; A Novel Polysome Fractionation Method. Int J Mol Sci 2020; 21:ijms21041254. [PMID: 32070012 PMCID: PMC7072993 DOI: 10.3390/ijms21041254] [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: 01/07/2020] [Revised: 02/03/2020] [Accepted: 02/10/2020] [Indexed: 12/13/2022] Open
Abstract
Meiotic maturation of oocyte relies on pre-synthesised maternal mRNA, the translation of which is highly coordinated in space and time. Here, we provide a detailed polysome profiling protocol that demonstrates a combination of the sucrose gradient ultracentrifugation in small SW55Ti tubes with the qRT-PCR-based quantification of 18S and 28S rRNAs in fractionated polysome profile. This newly optimised method, named Scarce Sample Polysome Profiling (SSP-profiling), is suitable for both scarce and conventional sample sizes and is compatible with downstream RNA-seq to identify polysome associated transcripts. Utilising SSP-profiling we have assayed the translatome of mouse oocytes at the onset of nuclear envelope breakdown (NEBD)—a developmental point, the study of which is important for furthering our understanding of the molecular mechanisms leading to oocyte aneuploidy. Our analyses identified 1847 transcripts with moderate to strong polysome occupancy, including abundantly represented mRNAs encoding mitochondrial and ribosomal proteins, proteasomal components, glycolytic and amino acids synthetic enzymes, proteins involved in cytoskeleton organization plus RNA-binding and translation initiation factors. In addition to transcripts encoding known players of meiotic progression, we also identified several mRNAs encoding proteins of unknown function. Polysome profiles generated using SSP-profiling were more than comparable to those developed using existing conventional approaches, being demonstrably superior in their resolution, reproducibility, versatility, speed of derivation and downstream protocol applicability.
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Batugedara G, Lu XM, Saraf A, Sardiu ME, Cort A, Abel S, Prudhomme J, Washburn MP, Florens L, Bunnik EM, Le Roch KG. The chromatin bound proteome of the human malaria parasite. Microb Genom 2020; 6:e000327. [PMID: 32017676 PMCID: PMC7067212 DOI: 10.1099/mgen.0.000327] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 12/20/2019] [Indexed: 12/15/2022] Open
Abstract
Proteins interacting with DNA are fundamental for mediating processes such as gene expression, DNA replication and maintenance of genome integrity. Accumulating evidence suggests that the chromatin of apicomplexan parasites, such as Plasmodium falciparum, is highly organized, and this structure provides an epigenetic mechanism for transcriptional regulation. To investigate how parasite chromatin structure is being regulated, we undertook comparative genomics analysis using 12 distinct eukaryotic genomes. We identified conserved and parasite-specific chromatin-associated domains (CADs) and proteins (CAPs). We then used the chromatin enrichment for proteomics (ChEP) approach to experimentally capture CAPs in P. falciparum. A topological scoring analysis of the proteomics dataset revealed stage-specific enrichments of CADs and CAPs. Finally, we characterized, two candidate CAPs: a conserved homologue of the structural maintenance of chromosome 3 protein and a homologue of the crowded-like nuclei protein, a plant-like protein functionally analogous to animal nuclear lamina proteins. Collectively, our results provide a comprehensive overview of CAPs in apicomplexans, and contribute to our understanding of the complex molecular components regulating chromatin structure and genome architecture in these deadly parasites.
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Affiliation(s)
- Gayani Batugedara
- Department of Molecular, Cell and Systems Biology, University of California Riverside, Riverside, CA 92521, USA
| | - Xueqing M. Lu
- Department of Molecular, Cell and Systems Biology, University of California Riverside, Riverside, CA 92521, USA
| | - Anita Saraf
- Stowers Institute for Medical Research, 1000 E. 50th Street, Kansas City, MO 64110, USA
| | - Mihaela E. Sardiu
- Stowers Institute for Medical Research, 1000 E. 50th Street, Kansas City, MO 64110, USA
| | - Anthony Cort
- Department of Molecular, Cell and Systems Biology, University of California Riverside, Riverside, CA 92521, USA
| | - Steven Abel
- Department of Molecular, Cell and Systems Biology, University of California Riverside, Riverside, CA 92521, USA
| | - Jacques Prudhomme
- Department of Molecular, Cell and Systems Biology, University of California Riverside, Riverside, CA 92521, USA
| | - Michael P. Washburn
- Stowers Institute for Medical Research, 1000 E. 50th Street, Kansas City, MO 64110, USA
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Laurence Florens
- Stowers Institute for Medical Research, 1000 E. 50th Street, Kansas City, MO 64110, USA
| | - Evelien M. Bunnik
- Department of Microbiology, Immunology and Molecular Genetics, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Karine G. Le Roch
- Department of Molecular, Cell and Systems Biology, University of California Riverside, Riverside, CA 92521, USA
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Affiliation(s)
- Kelly T. Rios
- Department of Biochemistry and Molecular Biology, The Huck Center for Malaria Research, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Scott E. Lindner
- Department of Biochemistry and Molecular Biology, The Huck Center for Malaria Research, Pennsylvania State University, University Park, Pennsylvania, United States of America
- * E-mail:
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Erath J, Djuranovic S, Djuranovic SP. Adaptation of Translational Machinery in Malaria Parasites to Accommodate Translation of Poly-Adenosine Stretches Throughout Its Life Cycle. Front Microbiol 2019; 10:2823. [PMID: 31866984 PMCID: PMC6908487 DOI: 10.3389/fmicb.2019.02823] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 11/21/2019] [Indexed: 11/13/2022] Open
Abstract
Malaria is caused by unicellular apicomplexan parasites of the genus Plasmodium, which includes the major human parasite Plasmodium falciparum. The complex cycle of the malaria parasite in both mosquito and human hosts has been studied extensively. There is tight control of gene expression in each developmental stage, and at every level of gene synthesis: from RNA transcription, to its subsequent translation, and finally post-translational modifications of the resulting protein. Whole-genome sequencing of P. falciparum has laid the foundation for significant biological advances by revealing surprising genomic information. The P. falciparum genome is extremely AT-rich (∼80%), with a substantial portion of genes encoding intragenic polyadenosine (polyA) tracks being expressed throughout the entire parasite life cycle. In most eukaryotes, intragenic polyA runs act as negative regulators of gene expression. Recent studies have shown that translation of mRNAs containing 12 or more consecutive adenosines results in ribosomal stalling and frameshifting; activating mRNA surveillance mechanisms. In contrast, P. falciparum translational machinery can efficiently and accurately translate polyA tracks without activating mRNA surveillance pathways. This unique feature of P. falciparum raises interesting questions: (1) How is P. falciparum able to efficiently and correctly translate polyA track transcripts, and (2) What are the specifics of the translational machinery and mRNA surveillance mechanisms that separate P. falciparum from other organisms? In this review, we analyze possible evolutionary shifts in P. falciparum protein synthesis machinery that allow efficient translation of an AU rich-transcriptome. We focus on physiological and structural differences of P. falciparum stage specific ribosomes, ribosome-associated proteins, and changes in mRNA surveillance mechanisms throughout the complete parasite life cycle, with an emphasis on the mosquito and liver stages.
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Affiliation(s)
| | - Sergej Djuranovic
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO, United States
| | - Slavica Pavlovic Djuranovic
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO, United States
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Bennink S, Pradel G. The molecular machinery of translational control in malaria parasites. Mol Microbiol 2019; 112:1658-1673. [PMID: 31531994 DOI: 10.1111/mmi.14388] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/14/2019] [Indexed: 12/30/2022]
Abstract
Translational control regulates the levels of protein synthesized from its transcript and is key for the rapid adjustment of gene expression in response to environmental stimuli. The regulation of translation is of special importance for malaria parasites, which pass through a complex life cycle that includes various replication phases in the different organs of the human and mosquito hosts and a sexual reproduction phase in the mosquito midgut. In particular, the quiescent transmission stages rely on translational control to rapidly adapt to the new environment, once they switch over from the human to the mosquito and vice versa. Three control mechanisms are currently proposed in Plasmodium, (1) global regulation that acts on the translation initiation complex; (2) mRNA-specific regulation, involving cis control elements, mRNA-binding proteins and translational repressors; and (3) induced mRNA decay by the Ccr4-Not and the RNA exosome complex. The main molecules controlling translation are highly conserved in malaria parasites and an increasing number of studies shed light on the interwoven pathways leading to the up or downregulation of protein synthesis in the diverse plasmodial stages. We here highlight recent findings on translational control during life cycle progression of Plasmodium and discuss the molecules involved in regulating protein synthesis.
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Affiliation(s)
- Sandra Bennink
- Division of Cellular and Applied Infection Biology, Institute of Zoology, RWTH Aachen University, Worringerweg 1, 52074, Aachen, Germany
| | - Gabriele Pradel
- Division of Cellular and Applied Infection Biology, Institute of Zoology, RWTH Aachen University, Worringerweg 1, 52074, Aachen, Germany
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Caldelari R, Dogga S, Schmid MW, Franke-Fayard B, Janse CJ, Soldati-Favre D, Heussler V. Transcriptome analysis of Plasmodium berghei during exo-erythrocytic development. Malar J 2019; 18:330. [PMID: 31551073 PMCID: PMC6760107 DOI: 10.1186/s12936-019-2968-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 09/17/2019] [Indexed: 12/18/2022] Open
Abstract
Background The complex life cycle of malaria parasites requires well-orchestrated stage specific gene expression. In the vertebrate host the parasites grow and multiply by schizogony in two different environments: within erythrocytes and within hepatocytes. Whereas erythrocytic parasites are well-studied in this respect, relatively little is known about the exo-erythrocytic stages. Methods In an attempt to fill this gap, genome wide RNA-seq analyses of various exo-erythrocytic stages of Plasmodium berghei including sporozoites, samples from a time-course of liver stage development and detached cells were performed. These latter contain infectious merozoites and represent the final step in exo-erythrocytic development. Results The analysis represents the complete transcriptome of the entire life cycle of P. berghei parasites with temporal detailed analysis of the liver stage allowing comparison of gene expression across the progression of the life cycle. These RNA-seq data from different developmental stages were used to cluster genes with similar expression profiles, in order to infer their functions. A comparison with published data from other parasite stages confirmed stage-specific gene expression and revealed numerous genes that are expressed differentially in blood and exo-erythrocytic stages. One of the most exo-erythrocytic stage-specific genes was PBANKA_1003900, which has previously been annotated as a “gametocyte specific protein”. The promoter of this gene drove high GFP expression in exo-erythrocytic stages, confirming its expression profile seen by RNA-seq. Conclusions The comparative analysis of the genome wide mRNA expression profiles of erythrocytic and different exo-erythrocytic stages could be used to improve the understanding of gene regulation in Plasmodium parasites and can be used to model exo-erythrocytic stage metabolic networks toward the identification of differences in metabolic processes during schizogony in erythrocytes and hepatocytes.
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Affiliation(s)
- Reto Caldelari
- Institute of Cell Biology, University of Bern, Bern, Switzerland.
| | - Sunil Dogga
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva CMU, Geneva, Switzerland
| | | | - Blandine Franke-Fayard
- Leiden Malaria Research Group, Department of Parasitology, Leiden University Medical Center, Leiden, The Netherlands
| | - Chris J Janse
- Leiden Malaria Research Group, Department of Parasitology, Leiden University Medical Center, Leiden, The Netherlands
| | - Dominique Soldati-Favre
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva CMU, Geneva, Switzerland
| | - Volker Heussler
- Institute of Cell Biology, University of Bern, Bern, Switzerland.
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Wichers JS, Scholz JAM, Strauss J, Witt S, Lill A, Ehnold LI, Neupert N, Liffner B, Lühken R, Petter M, Lorenzen S, Wilson DW, Löw C, Lavazec C, Bruchhaus I, Tannich E, Gilberger TW, Bachmann A. Dissecting the Gene Expression, Localization, Membrane Topology, and Function of the Plasmodium falciparum STEVOR Protein Family. mBio 2019; 10:e01500-19. [PMID: 31363031 PMCID: PMC6667621 DOI: 10.1128/mbio.01500-19] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Accepted: 07/02/2019] [Indexed: 01/22/2023] Open
Abstract
During its intraerythrocytic development, the malaria parasite Plasmodium falciparum exposes variant surface antigens (VSAs) on infected erythrocytes to establish and maintain an infection. One family of small VSAs is the polymorphic STEVOR proteins, which are marked for export to the host cell surface through their PEXEL signal peptide. Interestingly, some STEVORs have also been reported to localize to the parasite plasma membrane and apical organelles, pointing toward a putative function in host cell egress or invasion. Using deep RNA sequencing analysis, we characterized P. falciparumstevor gene expression across the intraerythrocytic development cycle, including free merozoites, in detail and used the resulting stevor expression profiles for hierarchical clustering. We found that most stevor genes show biphasic expression oscillation, with maximum expression during trophozoite stages and a second peak in late schizonts. We selected four STEVOR variants, confirmed the expected export of these proteins to the host cell membrane, and tracked them to a secondary location, either to the parasite plasma membrane or the secretory organelles of merozoites in late schizont stages. We investigated the function of a particular STEVOR that showed rhoptry localization and demonstrated its role at the parasite-host interface during host cell invasion by specific antisera and targeted gene disruption. Experimentally determined membrane topology of this STEVOR revealed a single transmembrane domain exposing the semiconserved as well as variable protein regions to the cell surface.IMPORTANCE Malaria claims about half a million lives each year. Plasmodium falciparum, the causative agent of the most severe form of the disease, uses proteins that are translocated to the surface of infected erythrocytes for immune evasion. To circumvent the detection of these gene products by the immune system, the parasite evolved a complex strategy that includes gene duplications and elaborate sequence polymorphism. STEVORs are one family of these variant surface antigens and are encoded by about 40 genes. Using deep RNA sequencing of blood-stage parasites, including free merozoites, we first established stevor expression of the cultured isolate and compared it with published transcriptomes. We reveal a biphasic expression of most stevor genes and confirm this for individual STEVORs at the protein level. The membrane topology of a rhoptry-associated variant was experimentally elucidated and linked to host cell invasion, underlining the importance of this multifunctional protein family for parasite proliferation.
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Affiliation(s)
- J Stephan Wichers
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
- Centre for Structural Systems Biology, Hamburg, Germany
| | | | - Jan Strauss
- Centre for Structural Systems Biology (CSSB), DESY, and European Molecular Biology Laboratory Hamburg, Hamburg, Germany
| | - Susanne Witt
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Andrés Lill
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
- Centre for Structural Systems Biology, Hamburg, Germany
| | | | | | - Benjamin Liffner
- Research Centre for Infectious Diseases, School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia
| | - Renke Lühken
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Michaela Petter
- Institute of Microbiology, University Hospital Erlangen, Erlangen, Germany
| | - Stephan Lorenzen
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Danny W Wilson
- Research Centre for Infectious Diseases, School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia
- Burnet Institute, Melbourne, Victoria, Australia
| | - Christian Löw
- Centre for Structural Systems Biology (CSSB), DESY, and European Molecular Biology Laboratory Hamburg, Hamburg, Germany
| | | | - Iris Bruchhaus
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Egbert Tannich
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Tim W Gilberger
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
- Centre for Structural Systems Biology, Hamburg, Germany
- Biology Department, University of Hamburg, Hamburg, Germany
| | - Anna Bachmann
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
- Centre for Structural Systems Biology, Hamburg, Germany
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Abstract
Toxoplasma gondii is a single-celled parasite that has infected up to one-third of the world’s population. Significant overhauls in gene expression in both the parasite and the host cell accompany parasite invasion, and a better understanding of these changes may lead to the development of new therapeutic agents. In this study, we employed ribosome profiling to determine the changes that occur at the levels of transcription and translation in both the parasite and the infected host cell at the same time. We discovered features of Toxoplasma mRNAs that suggest a means for controlling parasite gene expression under stressful conditions. We also show that differences in host gene expression occur depending on whether they are confluent or not. Our findings demonstrate the feasibility of using ribosomal profiling to interrogate the host-parasite dynamic under a variety of conditions. Toxoplasma gondii is a ubiquitous obligate intracellular parasite that infects the nucleated cells of warm-blooded animals. From within the parasitophorous vacuole in which they reside, Toxoplasma tachyzoites secrete an arsenal of effector proteins that can reprogram host gene expression to facilitate parasite survival and replication. Gaining a better understanding of how host gene expression is altered upon infection is central for understanding parasite strategies for host invasion and for developing new parasite therapies. Here, we applied ribosome profiling coupled with mRNA measurements to concurrently study gene expression in the parasite and in host human foreskin fibroblasts. By examining the parasite transcriptome and translatome, we identified potential upstream open reading frames that may permit the stress-induced preferential translation of parasite mRNAs. We also determined that tachyzoites reduce host death-associated pathways and increase survival, proliferation, and motility in both quiescent and proliferative host cell models of infection. Additionally, proliferative cells alter their gene expression in ways that are consistent with massive transcriptional rewiring, while quiescent cells were best characterized by reentry into the cell cycle. We also identified a translational control regimen consistent with mechanistic target of rapamycin (mTOR) activation in quiescent cells and, to a lesser degree, in proliferative cells. This study illustrates the utility of the method for dissection of gene expression programs simultaneously in the parasite and host. IMPORTANCEToxoplasma gondii is a single-celled parasite that has infected up to one-third of the world’s population. Significant overhauls in gene expression in both the parasite and the host cell accompany parasite invasion, and a better understanding of these changes may lead to the development of new therapeutic agents. In this study, we employed ribosome profiling to determine the changes that occur at the levels of transcription and translation in both the parasite and the infected host cell at the same time. We discovered features of Toxoplasma mRNAs that suggest a means for controlling parasite gene expression under stressful conditions. We also show that differences in host gene expression occur depending on whether they are confluent or not. Our findings demonstrate the feasibility of using ribosomal profiling to interrogate the host-parasite dynamic under a variety of conditions.
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PfMSA180 is a novel Plasmodium falciparum vaccine antigen that interacts with human erythrocyte integrin associated protein (CD47). Sci Rep 2019; 9:5923. [PMID: 30976034 PMCID: PMC6459815 DOI: 10.1038/s41598-019-42366-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Accepted: 03/28/2019] [Indexed: 12/14/2022] Open
Abstract
Malaria symptoms and pathology are initiated by invasion of host erythrocytes by Plasmodium merozoites in a complex process that involves interactions between parasite and host erythrocyte proteins. Erythrocyte invasion presents attractive targets for malaria vaccine and drug development. Recently it was observed that antibodies against PfMSA180 (PF3D7_1014100) are associated with protection from symptomatic malaria, suggesting that this protein is a target of naturally acquired protective antibodies. Here we characterize PfMSA180, a ~170 kDa merozoite surface antigen that is potentially involved in erythrocyte invasion. PfMSA180 synthesized by the wheat germ cell-free system was used to raise antibodies in rabbits. Growth inhibition assays revealed that parasite invasion is inhibited by antibodies to the PfMSA180 C-terminal region, which contains an erythrocyte-binding domain. Surface plasmon resonance analysis showed that PfMSA180 specifically interacts with human erythrocyte integrin associated protein (CD47), suggesting that PfMSA180 plays a role during merozoite invasion of erythrocytes. Polymorphism analysis revealed that pfmsa180 is highly conserved among field isolates. We show that naturally acquired PfMSA180-specific antibodies responses are associated with protective immunity in a malaria-exposed Thai population. In sum, the data presented here supports further evaluation of the conserved erythrocyte-binding C-terminal region of PfMSA180 as an asexual blood-stage malaria vaccine candidate.
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ApiAP2 Transcription Factors in Apicomplexan Parasites. Pathogens 2019; 8:pathogens8020047. [PMID: 30959972 PMCID: PMC6631176 DOI: 10.3390/pathogens8020047] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 03/26/2019] [Accepted: 03/28/2019] [Indexed: 12/26/2022] Open
Abstract
Apicomplexan parasites are protozoan organisms that are characterised by complex life cycles and they include medically important species, such as the malaria parasite Plasmodium and the causative agents of toxoplasmosis (Toxoplasma gondii) and cryptosporidiosis (Cryptosporidium spp.). Apicomplexan parasites can infect one or more hosts, in which they differentiate into several morphologically and metabolically distinct life cycle stages. These developmental transitions rely on changes in gene expression. In the last few years, the important roles of different members of the ApiAP2 transcription factor family in regulating life cycle transitions and other aspects of parasite biology have become apparent. Here, we review recent progress in our understanding of the different members of the ApiAP2 transcription factor family in apicomplexan parasites.
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Guan L, Ma X, Zhou X, Tan B, Wang ZY. An optimized method to obtain high-quality RNA from cassava storage root. 3 Biotech 2019; 9:118. [PMID: 30854278 PMCID: PMC6399363 DOI: 10.1007/s13205-019-1608-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 02/01/2019] [Indexed: 12/23/2022] Open
Abstract
Extracting RNA with high quality and integrity is crucial for molecular biology studies in eukaryotes. However, RNA isolation from cassava storage root raises a great concern because it contains large amounts of polysaccharides and polyphenol compounds. In the current study, four RNA extraction methods were evaluated for extracting RNA from cassava storage root. We found that the modified TM method (MTM) is timesaving and low-cost extraction method with high quality and quantities of RNA. The effectiveness of the improved method was assessed for qPCR analysis of four selected genes from total RNA of storage root. The improved protocol generated 4.18-5.94 µg RNA/g fresh weight. An A260/280 ratios of RNA samples are ranged from 2.14 to 2.17. The RIN values are ranged from 7.2 to 8.0. Importantly, isolated total RNA by MTM was successfully used for library construction and transcriptome sequencing. Therefore, we provide an efficient and low-cost method, MTM, for extracting high quality and quantities of RNA from cassava storage root.
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Affiliation(s)
- Lulu Guan
- Key Laboratory for Sustainable Utilization of Tropical Bioresource, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, 570228 Hainan China
| | - Xiaowen Ma
- Key Laboratory for Sustainable Utilization of Tropical Bioresource, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, 570228 Hainan China
| | - Xiaoxia Zhou
- Key Laboratory for Sustainable Utilization of Tropical Bioresource, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, 570228 Hainan China
| | - Bowen Tan
- Key Laboratory for Sustainable Utilization of Tropical Bioresource, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, 570228 Hainan China
| | - Zhen-Yu Wang
- Key Laboratory for Sustainable Utilization of Tropical Bioresource, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, 570228 Hainan China
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Abstract
Alternative splicing is a widespread, essential, and complex component of gene regulation. Apicomplexan parasites have long been recognized to produce alternatively spliced transcripts for some genes and can produce multiple protein products that are essential for parasite growth. Alternative splicing is a widespread, essential, and complex component of gene regulation. Apicomplexan parasites have long been recognized to produce alternatively spliced transcripts for some genes and can produce multiple protein products that are essential for parasite growth. Recent approaches are now providing more wide-ranging surveys of the extent of alternative splicing; some indicate that alternative splicing is less widespread than in other model eukaryotes, whereas others suggest levels comparable to those of previously studied groups. In many cases, apicomplexan alternative splicing events appear not to generate multiple alternative proteins but instead produce aberrant or noncoding transcripts. Nonetheless, appropriate regulation of alternative splicing is clearly essential in Plasmodium and Toxoplasma parasites, suggesting a biological role for at least some of the alternative splicing observed. Several studies have now disrupted conserved regulators of alternative splicing and demonstrated lethal effects in apicomplexans. This minireview discusses methods to accurately determine the extent of alternative splicing in Apicomplexa and discuss potential biological roles for this conserved process in a phylum of parasites with compact genomes.
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Ramaprasad A, Subudhi AK, Culleton R, Pain A. A fast and cost-effective microsampling protocol incorporating reduced animal usage for time-series transcriptomics in rodent malaria parasites. Malar J 2019; 18:26. [PMID: 30683099 PMCID: PMC6347755 DOI: 10.1186/s12936-019-2659-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 01/18/2019] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND The transcriptional regulation that occurs in malaria parasites during the erythrocytic stages of infection can be studied in vivo with rodent malaria parasites propagated in mice. Time-series transcriptome profiling commonly involves the euthanasia of groups of mice at specific time points followed by the extraction of parasite RNA from whole blood samples. Current methodologies for parasite RNA extraction involve several steps and when multiple time points are profiled, these protocols are laborious, time-consuming, and require the euthanization of large cohorts of mice. RESULTS A simplified protocol has been designed for parasite RNA extraction from blood volumes as low as 20 μL (microsamples), serially bled from mice via tail snips and directly lysed with TRIzol reagent. Gene expression data derived from microsampling using RNA-seq were closely matched to those derived from larger volumes of leucocyte-depleted and saponin-treated blood obtained from euthanized mice with high reproducibility between biological replicates. Transcriptome profiling of microsamples taken at different time points during the intra-erythrocytic developmental cycle of the rodent malaria parasite Plasmodium vinckei revealed the transcriptional cascade commonly observed in malaria parasites. CONCLUSIONS Microsampling is a quick, robust and cost-efficient approach to sample collection for in vivo time-series transcriptomic studies in rodent malaria parasites.
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Affiliation(s)
- Abhinay Ramaprasad
- Pathogen Genomics Laboratory, Biological and Environmental Sciences and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia. .,Malaria Unit, Department of Pathology, Institute of Tropical Medicine (NEKKEN), Nagasaki University, 1-12-4 Sakamoto, Nagasaki, 852-8523, Japan.
| | - Amit Kumar Subudhi
- Pathogen Genomics Laboratory, Biological and Environmental Sciences and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia
| | - Richard Culleton
- Malaria Unit, Department of Pathology, Institute of Tropical Medicine (NEKKEN), Nagasaki University, 1-12-4 Sakamoto, Nagasaki, 852-8523, Japan
| | - Arnab Pain
- Pathogen Genomics Laboratory, Biological and Environmental Sciences and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia.
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42
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Todorovic M, Simic M. Clustering and pattern recognition in bioengineering and autonomous systems. ACTA ACUST UNITED AC 2019. [DOI: 10.1016/j.procs.2019.09.411] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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43
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Bah SY, Morang'a CM, Kengne-Ouafo JA, Amenga-Etego L, Awandare GA. Highlights on the Application of Genomics and Bioinformatics in the Fight Against Infectious Diseases: Challenges and Opportunities in Africa. Front Genet 2018; 9:575. [PMID: 30538723 PMCID: PMC6277583 DOI: 10.3389/fgene.2018.00575] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 11/08/2018] [Indexed: 01/18/2023] Open
Abstract
Genomics and bioinformatics are increasingly contributing to our understanding of infectious diseases caused by bacterial pathogens such as Mycobacterium tuberculosis and parasites such as Plasmodium falciparum. This ranges from investigations of disease outbreaks and pathogenesis, host and pathogen genomic variation, and host immune evasion mechanisms to identification of potential diagnostic markers and vaccine targets. High throughput genomics data generated from pathogens and animal models can be combined with host genomics and patients’ health records to give advice on treatment options as well as potential drug and vaccine interactions. However, despite accounting for the highest burden of infectious diseases, Africa has the lowest research output on infectious disease genomics. Here we review the contributions of genomics and bioinformatics to the management of infectious diseases of serious public health concern in Africa including tuberculosis (TB), dengue fever, malaria and filariasis. Furthermore, we discuss how genomics and bioinformatics can be applied to identify drug and vaccine targets. We conclude by identifying challenges to genomics research in Africa and highlighting how these can be overcome where possible.
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Affiliation(s)
- Saikou Y Bah
- West African Centre for Cell Biology of Infectious Pathogens, University of Ghana, Accra, Ghana.,Vaccine and Immunity Theme, MRC Unit The Gambia at London School of Hygiene & Tropical Medicine, Banjul, Gambia
| | - Collins Misita Morang'a
- West African Centre for Cell Biology of Infectious Pathogens, University of Ghana, Accra, Ghana
| | - Jonas A Kengne-Ouafo
- West African Centre for Cell Biology of Infectious Pathogens, University of Ghana, Accra, Ghana
| | - Lucas Amenga-Etego
- West African Centre for Cell Biology of Infectious Pathogens, University of Ghana, Accra, Ghana
| | - Gordon A Awandare
- West African Centre for Cell Biology of Infectious Pathogens, University of Ghana, Accra, Ghana
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44
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Ng CS, Sinha A, Aniweh Y, Nah Q, Babu IR, Gu C, Chionh YH, Dedon PC, Preiser PR. tRNA epitranscriptomics and biased codon are linked to proteome expression in Plasmodium falciparum. Mol Syst Biol 2018; 14:e8009. [PMID: 30287681 PMCID: PMC6171970 DOI: 10.15252/msb.20178009] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Revised: 08/09/2018] [Accepted: 09/07/2018] [Indexed: 12/24/2022] Open
Abstract
Among components of the translational machinery, ribonucleoside modifications on tRNAs are emerging as critical regulators of cell physiology and stress response. Here, we demonstrate highly coordinated behavior of the repertoire of tRNA modifications of Plasmodium falciparum throughout the intra-erythrocytic developmental cycle (IDC). We observed both a synchronized increase in 22 of 28 modifications from ring to trophozoite stage, consistent with tRNA maturation during translational up-regulation, and asynchronous changes in six modifications. Quantitative analysis of ~2,100 proteins across the IDC revealed that up- and down-regulated proteins in late but not early stages have a marked codon bias that directly correlates with parallel changes in tRNA modifications and enhanced translational efficiency. We thus propose a model in which tRNA modifications modulate the abundance of stage-specific proteins by enhancing translation efficiency of codon-biased transcripts for critical genes. These findings reveal novel epitranscriptomic and translational control mechanisms in the development and pathogenesis of Plasmodium parasites.
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Affiliation(s)
- Chee Sheng Ng
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore City, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore City, Singapore
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Ameya Sinha
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore City, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore City, Singapore
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Yaw Aniweh
- School of Biological Sciences, Nanyang Technological University, Singapore City, Singapore
| | - Qianhui Nah
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore City, Singapore
| | - Indrakanti Ramesh Babu
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Chen Gu
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Yok Hian Chionh
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore City, Singapore
- Department of Microbiology and Immunology Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore City, Singapore
| | - Peter C Dedon
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore City, Singapore
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Peter R Preiser
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore City, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore City, Singapore
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45
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Armistead JS, Jennison C, O'Neill MT, Lopaticki S, Liehl P, Hanson KK, Annoura T, Rajasekaran P, Erickson SM, Tonkin CJ, Khan SM, Mota MM, Boddey JA. Plasmodium falciparum
subtilisin-like ookinete protein SOPT plays an important and conserved role during ookinete infection of the Anopheles stephensi
midgut. Mol Microbiol 2018; 109:458-473. [DOI: 10.1111/mmi.13993] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/22/2018] [Indexed: 11/27/2022]
Affiliation(s)
- Jennifer S. Armistead
- The Walter and Eliza Hall Institute of Medical Research; Parkville 3052 Australia
- Department of Medical Biology; The University of Melbourne; Parkville 3052 Australia
| | - Charlie Jennison
- The Walter and Eliza Hall Institute of Medical Research; Parkville 3052 Australia
- Department of Medical Biology; The University of Melbourne; Parkville 3052 Australia
| | - Matthew T. O'Neill
- The Walter and Eliza Hall Institute of Medical Research; Parkville 3052 Australia
| | - Sash Lopaticki
- The Walter and Eliza Hall Institute of Medical Research; Parkville 3052 Australia
| | - Peter Liehl
- Instituto de Medicina Molecular, Faculdade de Medicina; Universidade de Lisboa; 1649-028 Lisbon Portugal
| | - Kirsten K. Hanson
- Instituto de Medicina Molecular, Faculdade de Medicina; Universidade de Lisboa; 1649-028 Lisbon Portugal
| | - Takeshi Annoura
- Leiden Malaria Research Group, Parasitology; Leiden University Medical Centre; 2333ZA Leiden the Netherlands
| | - Pravin Rajasekaran
- The Walter and Eliza Hall Institute of Medical Research; Parkville 3052 Australia
- Department of Medical Biology; The University of Melbourne; Parkville 3052 Australia
| | - Sara M. Erickson
- The Walter and Eliza Hall Institute of Medical Research; Parkville 3052 Australia
- Department of Medical Biology; The University of Melbourne; Parkville 3052 Australia
| | - Christopher J. Tonkin
- The Walter and Eliza Hall Institute of Medical Research; Parkville 3052 Australia
- Department of Medical Biology; The University of Melbourne; Parkville 3052 Australia
| | - Shahid M. Khan
- Leiden Malaria Research Group, Parasitology; Leiden University Medical Centre; 2333ZA Leiden the Netherlands
| | - Maria M. Mota
- Instituto de Medicina Molecular, Faculdade de Medicina; Universidade de Lisboa; 1649-028 Lisbon Portugal
| | - Justin A. Boddey
- The Walter and Eliza Hall Institute of Medical Research; Parkville 3052 Australia
- Department of Medical Biology; The University of Melbourne; Parkville 3052 Australia
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46
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Li M, Zhang X, Yang H, Li X, Cui Z. Soil sustainable utilization technology: mechanism of flavonols in resistance process of heavy metal. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2018; 25:26669-26681. [PMID: 30003485 DOI: 10.1007/s11356-018-2485-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 06/04/2018] [Indexed: 06/08/2023]
Abstract
The soil ecosystem is critical for agricultural production, affecting many aspects of human health. Soil has more unknown biodiversity and edaphic parameters than any other ecosystem especially when polluted. Metagenomics and metatranscriptomics were applied to research on toxicological characteristics of Pb and resistance mechanism of flavonols. Rhizosphere microorganisms-plants system, a unified system closely related to soil environment was taken as research object. Results emphasize gene expression changes in different test groups. Gene ontology enrichment and eggNOG showed that Pb has a toxic effect on gene and protein function which concentrated on ATPase and ATP-dependent activity. Differentially expressed genes in the flavonols group indicated that flavonols regulate amino acid transport and other transportation process related to Pb stress. Kegg analysis represents that Pb interferences energy production process via not only the upstream like glycolysis and tricarboxylic acid (TCA) circle but also oxidative phosphorylation process, which can also produce reactive oxygen species and impact the eliminating process. Flavonols have shown the ability in alleviating toxic effect of Pb and improving the resistance of plants. Flavonols can recover the electronic transmission and other process in TCA and oxidative phosphorylation via ascorbic acid-glutathione metabolism. Flavonols activated antioxidative process and non-specific immunity via vitamins B2-B6 metabolism.
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Affiliation(s)
- Min Li
- School of Environmental Science and Engineering, Shandong University, Jinan, 250100, China
| | - Xu Zhang
- School of Environmental Science and Engineering, Shandong University, Jinan, 250100, China.
- Department of Plant and Microbial Biology, University of Zurich, 8008, Zurich, Switzerland.
| | - Huanhuan Yang
- School of Life Science, Shandong University, Jinan, 250100, China
| | - Xinxin Li
- School of Environmental Science and Engineering, Shandong University, Jinan, 250100, China
| | - Zhaojie Cui
- School of Environmental Science and Engineering, Shandong University, Jinan, 250100, China.
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47
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Batugedara G, Le Roch KG. Unraveling the 3D genome of human malaria parasites. Semin Cell Dev Biol 2018; 90:144-153. [PMID: 30009946 DOI: 10.1016/j.semcdb.2018.07.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 07/03/2018] [Indexed: 01/31/2023]
Abstract
The chromosomes within the eukaryotic cell nucleus are highly dynamic and adopt complex hierarchical structures. Understanding how this three-dimensional (3D) nuclear architectureaffects gene regulation, cell cycle progression and disease pathogenesis are important biological questions in development and disease. Recently, many genome-wide technologies including chromosome conformation capture (3C) and 3C-based methodologies (4C, 5C, and Hi-C) have been developed to investigate 3D chromatin structure. In this review, we introduce 3D genome methodologies, with a focus on their application for understanding the nuclear architecture of the human malaria parasite, Plasmodium falciparum. An increasing amount of evidence now suggests that gene regulation in the parasite is largely regulated by epigenetic mechanisms and nuclear reorganization. Here, we explore the 3D genome architecture of P. falciparum, including local and global chromatin structure. In addition, molecular components important for maintaining 3D chromatin organization including architectural proteins and long non-coding RNAs are discussed. Collectively, these studies contribute to our understanding of how the plasticity of 3D genome architecture regulates gene expression and cell cycle progression in this deadly parasite.
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Affiliation(s)
- Gayani Batugedara
- Department of Molecular, Cell and Systems Biology, University of California Riverside, Riverside, CA 92521, USA
| | - Karine G Le Roch
- Department of Molecular, Cell and Systems Biology, University of California Riverside, Riverside, CA 92521, USA.
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48
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Painter HJ, Chung NC, Sebastian A, Albert I, Storey JD, Llinás M. Genome-wide real-time in vivo transcriptional dynamics during Plasmodium falciparum blood-stage development. Nat Commun 2018; 9:2656. [PMID: 29985403 PMCID: PMC6037754 DOI: 10.1038/s41467-018-04966-3] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 05/31/2018] [Indexed: 01/12/2023] Open
Abstract
Genome-wide analysis of transcription in the malaria parasite Plasmodium falciparum has revealed robust variation in steady-state mRNA abundance throughout the 48-h intraerythrocytic developmental cycle (IDC), suggesting that this process is highly dynamic and tightly regulated. Here, we utilize rapid 4-thiouracil (4-TU) incorporation via pyrimidine salvage to specifically label, capture, and quantify newly-synthesized RNA transcripts at every hour throughout the IDC. This high-resolution global analysis of the transcriptome captures the timing and rate of transcription for each newly synthesized mRNA in vivo, revealing active transcription throughout all IDC stages. Using a statistical model to predict the mRNA dynamics contributing to the total mRNA abundance at each timepoint, we find varying degrees of transcription and stabilization for each mRNA corresponding to developmental transitions. Finally, our results provide new insight into co-regulation of mRNAs throughout the IDC through regulatory DNA sequence motifs, thereby expanding our understanding of P. falciparum mRNA dynamics. Transcriptomic analysis often doesn’t differentiate between newly synthesized and stabilized mRNAs. Using rapid 4-thiouracil incorporation, Painter et al. here define genome-wide active transcription throughout Plasmodium blood-stage developmental stages and identify associated regulatory DNA sequence motifs.
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Affiliation(s)
- Heather J Painter
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, 16802, USA.,Huck Center for Malaria Research, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Neo Christopher Chung
- Lewis-Sigler Institute for Integrative Genomics and Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA.,Institute of Informatics, Faculty of Mathematics, Informatics, and Mechanics, University of Warsaw, 02-097 Warsaw, Poland
| | - Aswathy Sebastian
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Istvan Albert
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, 16802, USA
| | - John D Storey
- Lewis-Sigler Institute for Integrative Genomics and Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA.,Center for Statistics and Machine Learning, Princeton University, Princeton, NJ, 08544, USA
| | - Manuel Llinás
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, 16802, USA. .,Huck Center for Malaria Research, The Pennsylvania State University, University Park, PA, 16802, USA. .,Department of Chemistry, The Pennsylvania State University, University Park, PA, 16802, USA.
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49
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Bunnik EM, Cook KB, Varoquaux N, Batugedara G, Prudhomme J, Cort A, Shi L, Andolina C, Ross LS, Brady D, Fidock DA, Nosten F, Tewari R, Sinnis P, Ay F, Vert JP, Noble WS, Le Roch KG. Changes in genome organization of parasite-specific gene families during the Plasmodium transmission stages. Nat Commun 2018; 9:1910. [PMID: 29765020 PMCID: PMC5954139 DOI: 10.1038/s41467-018-04295-5] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 04/18/2018] [Indexed: 12/20/2022] Open
Abstract
The development of malaria parasites throughout their various life cycle stages is coordinated by changes in gene expression. We previously showed that the three-dimensional organization of the Plasmodium falciparum genome is strongly associated with gene expression during its replication cycle inside red blood cells. Here, we analyze genome organization in the P. falciparum and P. vivax transmission stages. Major changes occur in the localization and interactions of genes involved in pathogenesis and immune evasion, host cell invasion, sexual differentiation, and master regulation of gene expression. Furthermore, we observe reorganization of subtelomeric heterochromatin around genes involved in host cell remodeling. Depletion of heterochromatin protein 1 (PfHP1) resulted in loss of interactions between virulence genes, confirming that PfHP1 is essential for maintenance of the repressive center. Our results suggest that the three-dimensional genome structure of human malaria parasites is strongly connected with transcriptional activity of specific gene families throughout the life cycle.
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Affiliation(s)
- Evelien M Bunnik
- Department of Microbiology, Immunology & Molecular Genetics, The University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX, 78229, USA
- Department of Molecular, Cell and Systems Biology, University of California Riverside, 900 University Ave, Riverside, CA, 92521, USA
| | - Kate B Cook
- Department of Genome Sciences, University of Washington, 3720 15th Ave NE, Seattle, WA, 98195, USA
| | - Nelle Varoquaux
- Department of Statistics, University of California, 367 Evans Hall, Berkeley, CA, 94720, USA
- Berkeley Institute for Data Science, 190 Doe Library, Berkeley, CA, 94720, USA
- MINES ParisTech, PSL Research University, CBIO-Centre for Computational Biology, 60 boulevard Saint-Michel, 75006, Paris, France
- Institut Curie, 75248, Paris, France
- U900, INSERM, Paris, 75248, France
| | - Gayani Batugedara
- Department of Molecular, Cell and Systems Biology, University of California Riverside, 900 University Ave, Riverside, CA, 92521, USA
| | - Jacques Prudhomme
- Department of Molecular, Cell and Systems Biology, University of California Riverside, 900 University Ave, Riverside, CA, 92521, USA
| | - Anthony Cort
- Department of Molecular, Cell and Systems Biology, University of California Riverside, 900 University Ave, Riverside, CA, 92521, USA
| | - Lirong Shi
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, 615N. Wolfe Street, E5132, Baltimore, MD, 21205, USA
| | - Chiara Andolina
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine Research building, University of Oxford, Old Road campus, Roosevelt Drive, Headington, Oxford, OX3 7FZ, UK
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Tak, 63110, Thailand
| | - Leila S Ross
- Department of Microbiology and Immunology, Columbia University Medical Center, 701W. 168 St., HHSC 1208, New York, NY, 10032, USA
| | - Declan Brady
- School of Life Sciences, Queens Medical Centre, University of Nottingham, Nottingham, NG7 2UH, UK
| | - David A Fidock
- Department of Microbiology and Immunology, Columbia University Medical Center, 701W. 168 St., HHSC 1208, New York, NY, 10032, USA
- Division of Infectious Diseases, Department of Medicine, Columbia University, New York, NY, 10032, USA
| | - Francois Nosten
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine Research building, University of Oxford, Old Road campus, Roosevelt Drive, Headington, Oxford, OX3 7FZ, UK
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Tak, 63110, Thailand
| | - Rita Tewari
- School of Life Sciences, Queens Medical Centre, University of Nottingham, Nottingham, NG7 2UH, UK
| | - Photini Sinnis
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, 615N. Wolfe Street, E5132, Baltimore, MD, 21205, USA
| | - Ferhat Ay
- La Jolla Institute for Allergy & Immunology, 9420 Athena Cir, La Jolla, CA, 92037, USA
| | - Jean-Philippe Vert
- MINES ParisTech, PSL Research University, CBIO-Centre for Computational Biology, 60 boulevard Saint-Michel, 75006, Paris, France
- Institut Curie, 75248, Paris, France
- U900, INSERM, Paris, 75248, France
- Département de mathématiques et applications, École normale supérieure, CNRS, PSL Research University, Paris, 75005, France
| | - William Stafford Noble
- Department of Genome Sciences, University of Washington, 3720 15th Ave NE, Seattle, WA, 98195, USA.
- Department of Computer Science and Engineering, University of Washington, Seattle, WA, 98195, USA.
| | - Karine G Le Roch
- Department of Molecular, Cell and Systems Biology, University of California Riverside, 900 University Ave, Riverside, CA, 92521, USA.
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50
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Eastman G, Smircich P, Sotelo-Silveira JR. Following Ribosome Footprints to Understand Translation at a Genome Wide Level. Comput Struct Biotechnol J 2018; 16:167-176. [PMID: 30069283 PMCID: PMC6066590 DOI: 10.1016/j.csbj.2018.04.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Revised: 04/06/2018] [Accepted: 04/10/2018] [Indexed: 12/11/2022] Open
Abstract
Protein translation is a key step in gene expression. The development of Ribosome Profiling has allowed the global analysis of this process at sub-codon resolution. In the last years the method has been applied to several models ranging from bacteria to mammalian cells yielding a surprising amount of insight on the mechanism and the regulation of translation. In this review we describe the key aspects of the experimental protocol and comment on the main conclusions raised in different models.
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Affiliation(s)
- Guillermo Eastman
- Department of Genomics, Instituto de Investigaciones Biológicas Clemente Estable, MEC, Av. Italia 3318, Montevideo, CP 11600, Uruguay
| | - Pablo Smircich
- Department of Genomics, Instituto de Investigaciones Biológicas Clemente Estable, MEC, Av. Italia 3318, Montevideo, CP 11600, Uruguay
- Laboratory of Molecular Interactions, Facultad de Ciencias, Universidad de la República, Iguá 4225, Montevideo, CP 11400, Uruguay
| | - José R. Sotelo-Silveira
- Department of Genomics, Instituto de Investigaciones Biológicas Clemente Estable, MEC, Av. Italia 3318, Montevideo, CP 11600, Uruguay
- Department of Cell and Molecular Biology, Facultad de Ciencias, Universidad de la República, Iguá 4225, Montevideo, CP 11400, Uruguay
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